From b551125f936abea78c937a98864ec9873e5b99b4 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Sat, 9 Sep 2017 22:12:15 +0930 Subject: [PATCH 0001/5331] {bio}[dummy]manta-1.1.1 --- easybuild/easyconfigs/m/manta/manta-1.1.1.eb | 40 ++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/manta/manta-1.1.1.eb diff --git a/easybuild/easyconfigs/m/manta/manta-1.1.1.eb b/easybuild/easyconfigs/m/manta/manta-1.1.1.eb new file mode 100644 index 00000000000..ea00b582a8c --- /dev/null +++ b/easybuild/easyconfigs/m/manta/manta-1.1.1.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: MIT +# +# Notes:: This is a binary build and only works on 64-bit linux +## + +easyblock = 'CmdCp' + +name = 'manta' +version = '1.1.1' + +homepage = 'https://github.com/arq5x/lumpy-sv' +description = """A probabilistic framework for structural variant discovery. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/Illumina/manta/releases/download/v%(version)s'] +sources = ['manta-%(version)s.centos5_x86_64.tar.bz2'] +# https://github.com/Illumina/manta/releases/download/v1.1.1/manta-1.1.1.centos5_x86_64.tar.bz2 + +skipsteps = ['build'] + +files_to_copy = [(['bin/*'], 'bin'), 'lib', 'libexec', 'share'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['configManta.py', 'runMantaWorkflowDemo.py']], + 'dirs': ['libexec'], +} + +modextrapaths = { + 'PATH': '$root/libexec' +} + +moduleclass = 'bio' From 7296f8813c847013a70f4f658d6b602dc181b1d6 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Sun, 10 Sep 2017 11:34:01 +0930 Subject: [PATCH 0002/5331] erratum --- easybuild/easyconfigs/m/manta/manta-1.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/manta/manta-1.1.1.eb b/easybuild/easyconfigs/m/manta/manta-1.1.1.eb index ea00b582a8c..a77d279df20 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.1.1.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.1.1.eb @@ -34,7 +34,7 @@ sanity_check_paths = { } modextrapaths = { - 'PATH': '$root/libexec' + 'PATH': '%(installdir)s/libexec' } moduleclass = 'bio' From ca1693b674d1374895d9b06595d239b71463a216 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 11 Sep 2017 11:27:37 +0200 Subject: [PATCH 0003/5331] {bio}[biary] Transrate 1.0.3 (REVIEW) --- .../BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb | 54 +++++++++++++++++++ .../t/Transrate/Transrate-1.0.3-foss-2017a.eb | 28 ++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb new file mode 100644 index 00000000000..d86e8284e6c --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'cstd': 'c++14'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +patches = [ + 'BLAST+-2.2.30_ictce-fixes.patch', + 'BLAST+-%(version)s_fix-make-install.patch', +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('PCRE', '8.40'), + ('Python', '2.7.13'), + ('Boost', '1.63.0', versionsuffix), + ('GMP', '6.1.2'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.2'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 --with-pcre=$EBROOTPCRE " +configopts += "--with-python=$EBROOTPYTHON --with-boost=$EBROOTBOOST --with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO " + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb new file mode 100644 index 00000000000..1ce38f57d6c --- /dev/null +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb @@ -0,0 +1,28 @@ +easyblock = "PackedBinary" + +name = "Transrate" +version = '1.0.3' + +homepage = 'http://hibberdlab.com/transrate/' +description = """Transrate is software for de-novo transcriptome assembly quality analysis. + It examines your assembly in detail and compares it to experimental evidence + such as the sequencing reads, reporting quality scores for contigs and + assemblies. This allows you to choose between assemblers and parameters, + filter out the bad contigs from an assembly, and help decide when + to stop trying to improve the assembly.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = ['transrate-%(version)s-linux-x86_64.tar.gz'] +source_urls = ['https://bintray.com/artifact/download/blahah/generic'] + +checksums = ['68d034ecd7012f1d3d505a2edd820c1155cd8b64d2acbf2ac833f30d3800141b'] + +dependencies = [('BLAST+', '2.6.0', '-Python-2.7.13')] + +sanity_check_paths = { + 'files': ['transrate', 'bin/bam-read', 'bin/salmon', 'bin/snap-aligner', 'lib/libruby.so'], + 'dirs': ['lib/app/%s' % x for x in ['bin', 'deps', 'lib', 'ruby']] +} + +moduleclass = 'bio' From cccff63081cd3c142951109da48a0129ac1878c0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 11 Sep 2017 11:51:43 +0200 Subject: [PATCH 0004/5331] checksum --- .../b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb index d86e8284e6c..fbe276792f0 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb @@ -26,11 +26,14 @@ toolchainopts = {'cstd': 'c++14'} sources = ['ncbi-blast-%(version)s+-src.tar.gz'] source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + patches = [ 'BLAST+-2.2.30_ictce-fixes.patch', 'BLAST+-%(version)s_fix-make-install.patch', ] +checksums = ['0510e1d607d0fb4389eca50d434d5a0be787423b6850b3a4f315abc2ef19c996'] + dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), From b3dbea2be3b0056a8b8c9f39dcc30f8a1d54fecd Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 11 Sep 2017 13:17:08 +0200 Subject: [PATCH 0005/5331] SHLIB_EXT --- easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb index 1ce38f57d6c..d44b883de37 100644 --- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb @@ -21,7 +21,7 @@ checksums = ['68d034ecd7012f1d3d505a2edd820c1155cd8b64d2acbf2ac833f30d3800141b'] dependencies = [('BLAST+', '2.6.0', '-Python-2.7.13')] sanity_check_paths = { - 'files': ['transrate', 'bin/bam-read', 'bin/salmon', 'bin/snap-aligner', 'lib/libruby.so'], + 'files': ['transrate', 'bin/bam-read', 'bin/salmon', 'bin/snap-aligner', 'lib/libruby.%s' % SHLIB_EXT], 'dirs': ['lib/app/%s' % x for x in ['bin', 'deps', 'lib', 'ruby']] } From 8e381291ff0b2b40bac026ff1999bffae7d667c3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 19 Sep 2017 14:11:34 +0200 Subject: [PATCH 0006/5331] Switched to binary BLAST+ bumbped to Salmon 0.8.2 --- .../easyconfigs/b/BLAST+/BLAST+-2.2.31.eb | 34 ++++++++++ .../easyconfigs/s/Salmon/Salmon-0.8.2.eb | 23 +++++++ ...1.0.3-foss-2017a.eb => Transrate-1.0.3.eb} | 19 ++++-- .../Transrate_1.0.3-salmon-0.8.2.patch | 63 +++++++++++++++++++ 4 files changed, 135 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31.eb create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.8.2.eb rename easybuild/easyconfigs/t/Transrate/{Transrate-1.0.3-foss-2017a.eb => Transrate-1.0.3.eb} (56%) create mode 100644 easybuild/easyconfigs/t/Transrate/Transrate_1.0.3-salmon-0.8.2.patch diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31.eb new file mode 100644 index 00000000000..4f50e7cd657 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'PackedBinary' + +name = 'BLAST+' +version = '2.2.31' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-x64-linux.tar.gz'] +checksums = ['322b951e1bca2e8ef16c76a64d78987443dc13fbbbb7a40f1683a97d98e4f408'] + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2.eb new file mode 100644 index 00000000000..fad5b22e02d --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2.eb @@ -0,0 +1,23 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PackedBinary' + +name = 'Salmon' +version = '0.8.2' + +homepage = 'https://github.com/COMBINE-lab/%(namelower)s' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/COMBINE-lab/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s_linux_x86_64.tar.gz'] +checksums = ['9def7ad603153bc22ca4ed54a607075ccdf513b0e1a8deeaff15d3cdb5563711'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3.eb similarity index 56% rename from easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb rename to easybuild/easyconfigs/t/Transrate/Transrate-1.0.3.eb index d44b883de37..b7ea66d83eb 100644 --- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3-foss-2017a.eb +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3.eb @@ -2,6 +2,7 @@ easyblock = "PackedBinary" name = "Transrate" version = '1.0.3' +sver = '0.8.2' homepage = 'http://hibberdlab.com/transrate/' description = """Transrate is software for de-novo transcriptome assembly quality analysis. @@ -11,17 +12,27 @@ description = """Transrate is software for de-novo transcriptome assembly qualit filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.""" -toolchain = {'name': 'foss', 'version': '2017a'} +toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['transrate-%(version)s-linux-x86_64.tar.gz'] source_urls = ['https://bintray.com/artifact/download/blahah/generic'] -checksums = ['68d034ecd7012f1d3d505a2edd820c1155cd8b64d2acbf2ac833f30d3800141b'] +patches = ['%%(name)s_%%(version)s-salmon-%s.patch' % sver] -dependencies = [('BLAST+', '2.6.0', '-Python-2.7.13')] +checksums = [ + '68d034ecd7012f1d3d505a2edd820c1155cd8b64d2acbf2ac833f30d3800141b', # transrate-1.0.3-linux-x86_64.tar.gz + '0fee41538d4f69e352f2cec25f396bb847c40ada4a15b2260140f4072219e8f6', # Transrate_1.0.3-salmon-0.8.2.patch +] + +dependencies = [ + ('BLAST+', '2.2.31'), + ('Salmon', sver), +] + +postinstallcmds = ['rm %%(installdir)s/bin/%s' % x for x in ['salmon', '*.%s*' % SHLIB_EXT]] sanity_check_paths = { - 'files': ['transrate', 'bin/bam-read', 'bin/salmon', 'bin/snap-aligner', 'lib/libruby.%s' % SHLIB_EXT], + 'files': ['transrate', 'bin/bam-read', 'bin/snap-aligner', 'lib/libruby.%s' % SHLIB_EXT], 'dirs': ['lib/app/%s' % x for x in ['bin', 'deps', 'lib', 'ruby']] } diff --git a/easybuild/easyconfigs/t/Transrate/Transrate_1.0.3-salmon-0.8.2.patch b/easybuild/easyconfigs/t/Transrate/Transrate_1.0.3-salmon-0.8.2.patch new file mode 100644 index 00000000000..a83d6efe8d4 --- /dev/null +++ b/easybuild/easyconfigs/t/Transrate/Transrate_1.0.3-salmon-0.8.2.patch @@ -0,0 +1,63 @@ +# https://github.com/blahah/transrate/commit/622984e7eba69c8222947685c19f4592c8a69a5e +From 622984e7eba69c8222947685c19f4592c8a69a5e Mon Sep 17 00:00:00 2001 +From: Matt MacManes +Date: Tue, 8 Aug 2017 08:12:03 -0400 +Subject: [PATCH] up to Salmon 0.8.2 + +--- + deps/deps.yaml | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/deps/deps.yaml b/deps/deps.yaml +index 956dc53..a39a4ac 100644 +--- a/transrate-1.0.3-linux-x86_64/lib/app/deps/deps.yaml ++++ b/transrate-1.0.3-linux-x86_64/lib/app/deps/deps.yaml +@@ -38,9 +38,9 @@ salmon: + - libtbbmalloc.dylib + - libtbbmalloc_proxy.dylib + version: +- number: '0.6.0' ++ number: '0.8.2' + command: 'salmon -v' + url: + 64bit: +- linux: https://github.com/COMBINE-lab/salmon/releases/download/v0.6.0/SalmonBeta-0.6.0_DebianSqueeze.tar.gz +- macosx: https://github.com/COMBINE-lab/salmon/releases/download/v0.6.0/SalmonBeta-0.6.0_OSX_10.11.tar.gz ++ linux: https://github.com/COMBINE-lab/salmon/releases/download/v0.8.2/Salmon-0.8.2_linux_x86_64.tar.gz ++ macosx: https://github.com/COMBINE-lab/salmon/releases/download/v0.8.2/Salmon-0.8.2_macOS_10.12.tar.gz +# https://github.com/blahah/transrate/pull/212/commits/8d185213bfa7147c5b8ffb4f5489e4c8476a22da +From 8d185213bfa7147c5b8ffb4f5489e4c8476a22da Mon Sep 17 00:00:00 2001 +From: Matt MacManes +Date: Tue, 8 Aug 2017 08:07:46 -0400 +Subject: [PATCH] update salmon command + +to include newer bias correction flags and auto lib type flags +--- + lib/transrate/salmon.rb | 7 +++---- + 1 file changed, 3 insertions(+), 4 deletions(-) + +diff --git a/lib/transrate/salmon.rb b/lib/transrate/salmon.rb +index 4bc8a4d..9e8f81a 100644 +--- a/transrate-1.0.3-linux-x86_64/lib/app/lib/transrate/salmon.rb ++++ b/transrate-1.0.3-linux-x86_64/lib/app/lib/transrate/salmon.rb +@@ -37,17 +37,16 @@ def run assembly, bamfile, threads=8 + + def build_command assembly, bamfile, threads=4 + cmd = "#{@salmon} quant" +- cmd << " --libType IU" + cmd << " --alignments #{bamfile}" + cmd << " --targets #{assembly}" + cmd << " --threads #{threads}" + cmd << " --sampleOut" + cmd << " --sampleUnaligned" # thanks Rob! + cmd << " --output ." ++ cmd << " --seqBias" + cmd << " --useErrorModel" +- cmd << " --biasCorrect" +- cmd << " --noEffectiveLengthCorrection" +- cmd << " --useFSPD" ++ cmd << " --gcBias" ++ cmd << " --libType a" + cmd + end + From 320364433b3c6d7e086fb1f4ba3991d3b784e1aa Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 Sep 2017 17:04:48 +0200 Subject: [PATCH 0007/5331] checksums injected --- .../b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb index fbe276792f0..fc7ac9e2d10 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.6.0-foss-2017a-Python-2.7.13.eb @@ -32,7 +32,11 @@ patches = [ 'BLAST+-%(version)s_fix-make-install.patch', ] -checksums = ['0510e1d607d0fb4389eca50d434d5a0be787423b6850b3a4f315abc2ef19c996'] +checksums = [ + '0510e1d607d0fb4389eca50d434d5a0be787423b6850b3a4f315abc2ef19c996', # ncbi-blast-2.6.0+-src.tar.gz + '8892e8bc0b1020a2e8616594da364c63009839d0d2dc6faf4bae9c44122a78be', # BLAST+-2.2.30_ictce-fixes.patch + 'b3d53e8417406b866e470f1810bdc29649f2d58d7d9d39a466bc33c8c4ff37d1', # BLAST+-2.6.0_fix-make-install.patch +] dependencies = [ ('zlib', '1.2.11'), From bae11a1c9e0c8a079c65fd33c7564c67bfab5a0b Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Tue, 28 Nov 2017 01:37:45 +0000 Subject: [PATCH 0008/5331] erratum --- easybuild/easyconfigs/m/manta/manta-1.1.1.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/manta/manta-1.1.1.eb b/easybuild/easyconfigs/m/manta/manta-1.1.1.eb index a77d279df20..a92a33e46ff 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.1.1.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.1.1.eb @@ -15,14 +15,13 @@ name = 'manta' version = '1.1.1' homepage = 'https://github.com/arq5x/lumpy-sv' -description = """A probabilistic framework for structural variant discovery. -""" +description = """A probabilistic framework for structural variant discovery.""" toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/Illumina/manta/releases/download/v%(version)s'] sources = ['manta-%(version)s.centos5_x86_64.tar.bz2'] -# https://github.com/Illumina/manta/releases/download/v1.1.1/manta-1.1.1.centos5_x86_64.tar.bz2 +checksums = ['48b3327b7cb1ff1b2b60a566c64985ac916a121984346875cae68a36bf63c328'] skipsteps = ['build'] @@ -34,7 +33,7 @@ sanity_check_paths = { } modextrapaths = { - 'PATH': '%(installdir)s/libexec' + 'PATH': 'libexeci', } moduleclass = 'bio' From cfca425c4e1ccf1ae8e9e72e79c1a8a3dc1f8b10 Mon Sep 17 00:00:00 2001 From: Robert Qiao Date: Tue, 28 Nov 2017 02:13:08 +0000 Subject: [PATCH 0009/5331] erratum --- easybuild/easyconfigs/m/manta/manta-1.1.1.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/manta/manta-1.1.1.eb b/easybuild/easyconfigs/m/manta/manta-1.1.1.eb index a92a33e46ff..a6c16583fab 100644 --- a/easybuild/easyconfigs/m/manta/manta-1.1.1.eb +++ b/easybuild/easyconfigs/m/manta/manta-1.1.1.eb @@ -28,12 +28,15 @@ skipsteps = ['build'] files_to_copy = [(['bin/*'], 'bin'), 'lib', 'libexec', 'share'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['configManta.py', 'runMantaWorkflowDemo.py']], + 'files': [ + ['bin/%s' % x for x in ['configManta.py', 'runMantaWorkflowDemo.py']] + + ['libexec/%s' % x for x in ['denovo_scoring.py', 'extractSmallIndelCandidates.py']], + ], 'dirs': ['libexec'], } modextrapaths = { - 'PATH': 'libexeci', + 'PATH': 'libexec', } moduleclass = 'bio' From 0871976f1bce07c9e35be5d8c80d999bbab20be2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 28 Nov 2017 10:41:05 +0100 Subject: [PATCH 0010/5331] {bio}[foss/2017b] MaSuRCA 3.2.2 toolchain bump (REVIEW) --- .../m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb new file mode 100644 index 00000000000..be70066d95a --- /dev/null +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2017 University of Geneva +# Authors:: Yann Sagon +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'MaSuRCA' +version = '3.2.2' + +homepage = 'http://www.genome.umd.edu/masurca.html' + +description = '''MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph + and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing + only short reads from Illumina sequencing or a mixture of short reads and long reads + (Sanger, 454, Pacbio and Nanopore).''' + +toolchain = {'name': 'foss', 'version': '2017b'} + +# need a temporary url to download it. Do it manually here: +# http://www.genome.umd.edu/masurca_form.html +sources = ['%(name)s-%(version)s.tar.gz'] + +dependencies = [ + ('libreadline', '7.0'), + ('Tcl', '8.6.7'), + ('Boost', '1.65.1'), + ('zlib', '1.2.11'), +] + +buildopts = "install-special" +start_dir = "global-1" + +sanity_check_paths = { + 'files': ['bin/masurca'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'bio' From 5ae2a7dddbabe6a4ce343d34495747bdb89f7a84 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 28 Nov 2017 10:45:31 +0100 Subject: [PATCH 0011/5331] checksum injected --- easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb index be70066d95a..46e0015f97c 100644 --- a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb @@ -25,6 +25,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} # need a temporary url to download it. Do it manually here: # http://www.genome.umd.edu/masurca_form.html sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['8c7fd54cd986c11e705171d3932543d3fd51dd3da56bd614a1ab6db3e9fc3333'] dependencies = [ ('libreadline', '7.0'), From 2a63ad8e44645c9538f9aae2d8c45837a12a5a2d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 28 Nov 2017 11:14:16 +0100 Subject: [PATCH 0012/5331] Perl dep added --- .../MaSuRCA-3.2.2-foss-2017b-Perl-5.26.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b-Perl-5.26.0.eb diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b-Perl-5.26.0.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b-Perl-5.26.0.eb new file mode 100644 index 00000000000..431b012f11b --- /dev/null +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b-Perl-5.26.0.eb @@ -0,0 +1,47 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2017 University of Geneva +# Authors:: Yann Sagon +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'MaSuRCA' +version = '3.2.2' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.genome.umd.edu/masurca.html' + +description = '''MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph + and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing + only short reads from Illumina sequencing or a mixture of short reads and long reads + (Sanger, 454, Pacbio and Nanopore).''' + +toolchain = {'name': 'foss', 'version': '2017b'} + +# need a temporary url to download it. Do it manually here: +# http://www.genome.umd.edu/masurca_form.html +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['8c7fd54cd986c11e705171d3932543d3fd51dd3da56bd614a1ab6db3e9fc3333'] + +dependencies = [ + ('Perl', '5.26.0'), + ('libreadline', '7.0'), + ('Tcl', '8.6.7'), + ('Boost', '1.65.1'), + ('zlib', '1.2.11'), +] + +buildopts = "install-special" +start_dir = "global-1" + +sanity_check_paths = { + 'files': ['bin/masurca'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'bio' From 62d5d3c03472a035cb92268086e6f6801f31b172 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 28 Nov 2017 13:27:19 +0100 Subject: [PATCH 0013/5331] delete non-perl file --- .../m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb deleted file mode 100644 index 46e0015f97c..00000000000 --- a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b.eb +++ /dev/null @@ -1,45 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2017 University of Geneva -# Authors:: Yann Sagon -# License:: MIT/GPL -# $Id$ -# -## - -easyblock = 'ConfigureMake' - -name = 'MaSuRCA' -version = '3.2.2' - -homepage = 'http://www.genome.umd.edu/masurca.html' - -description = '''MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph - and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing - only short reads from Illumina sequencing or a mixture of short reads and long reads - (Sanger, 454, Pacbio and Nanopore).''' - -toolchain = {'name': 'foss', 'version': '2017b'} - -# need a temporary url to download it. Do it manually here: -# http://www.genome.umd.edu/masurca_form.html -sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['8c7fd54cd986c11e705171d3932543d3fd51dd3da56bd614a1ab6db3e9fc3333'] - -dependencies = [ - ('libreadline', '7.0'), - ('Tcl', '8.6.7'), - ('Boost', '1.65.1'), - ('zlib', '1.2.11'), -] - -buildopts = "install-special" -start_dir = "global-1" - -sanity_check_paths = { - 'files': ['bin/masurca'], - 'dirs': ['include', 'lib'], -} - -moduleclass = 'bio' From 84d5340b68202539cc8605706bfb4c808038a87e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 28 Nov 2017 13:50:56 +0100 Subject: [PATCH 0014/5331] bzip2 dep added --- .../m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b-Perl-5.26.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b-Perl-5.26.0.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b-Perl-5.26.0.eb index 431b012f11b..85f420d59a4 100644 --- a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b-Perl-5.26.0.eb +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.2-foss-2017b-Perl-5.26.0.eb @@ -34,6 +34,7 @@ dependencies = [ ('Tcl', '8.6.7'), ('Boost', '1.65.1'), ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), ] buildopts = "install-special" From c023542b5c1208b45b0df75cd437135ee47ea102 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 11 Dec 2017 16:19:17 +0200 Subject: [PATCH 0015/5331] New version with patches for hardcoded paths etc. --- ...DTD_Solutions-8.16-fix-install-paths.patch | 86 +++++++++++++++++++ ...tions-8.16-fix-interconnect-api-path.patch | 16 ++++ ..._Solutions-8.16-fix-which-skip-alias.patch | 64 ++++++++++++++ .../FDTD_Solutions/FDTD_Solutions-8.16.982.eb | 18 ++++ 4 files changed, 184 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-install-paths.patch create mode 100644 easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-interconnect-api-path.patch create mode 100644 easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-which-skip-alias.patch create mode 100644 easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-install-paths.patch b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-install-paths.patch new file mode 100644 index 00000000000..f23598b56c9 --- /dev/null +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-install-paths.patch @@ -0,0 +1,86 @@ +# Fix hardcoded paths +# +# Åke Sandgren, 2017-02-07 +diff -ru opt.orig/lumerical/fdtd/mpich/ch_gm/bin/mpirun opt/lumerical/fdtd/mpich/ch_gm/bin/mpirun +--- opt.orig/lumerical/fdtd/mpich/ch_gm/bin/mpirun 2016-09-10 02:54:25.000000000 +0200 ++++ opt/lumerical/fdtd/mpich/ch_gm/bin/mpirun 2017-01-31 16:54:11.454196201 +0100 +@@ -26,8 +26,8 @@ + COMM= + GLOBUSDIR=@GLOBUSDIR@ + CLINKER="gcc" +-prefix=/opt/lumerical/fdtd/mpich/ch_gm +-bindir=/opt/lumerical/fdtd/mpich/ch_gm/bin ++prefix=$EBROOTFDTD_SOLUTIONS/mpich/ch_gm ++bindir=$EBROOTFDTD_SOLUTIONS/mpich/ch_gm/bin + # Record the value of sbindir. Some useful utilities, such as + # cleanipcs (used for cleaning up shared memory segments and semaphores) + # are placed in this directory. +@@ -36,7 +36,7 @@ + sbindir=${exec_prefix}/sbin + # This value for datadir is the default value setup by configure + # This value for datadir is the default value setup by configure +-datadir=/opt/lumerical/fdtd/mpich/ch_gm/share ++datadir=$EBROOTFDTD_SOLUTIONS/mpich/ch_gm/share + DEFAULT_MACHINE=ch_gm + DEFAULT_ARCH=LINUX + +diff -ru opt.orig/lumerical/fdtd/mpich/ch_p4/bin/mpirun opt/lumerical/fdtd/mpich/ch_p4/bin/mpirun +--- opt.orig/lumerical/fdtd/mpich/ch_p4/bin/mpirun 2016-09-10 02:54:25.000000000 +0200 ++++ opt/lumerical/fdtd/mpich/ch_p4/bin/mpirun 2017-01-31 16:54:21.182102363 +0100 +@@ -26,8 +26,8 @@ + COMM= + GLOBUSDIR=@GLOBUSDIR@ + CLINKER="cc" +-prefix=/opt/lumerical/fdtd/mpich/ch_p4 +-bindir=/opt/lumerical/fdtd/mpich/ch_p4/bin ++prefix=$EBROOTFDTD_SOLUTIONS/mpich/ch_p4 ++bindir=$EBROOTFDTD_SOLUTIONS/mpich/ch_p4/bin + # Record the value of sbindir. Some useful utilities, such as + # cleanipcs (used for cleaning up shared memory segments and semaphores) + # are placed in this directory. +@@ -36,7 +36,7 @@ + sbindir=${exec_prefix}/sbin + # This value for datadir is the default value setup by configure + # This value for datadir is the default value setup by configure +-datadir=/opt/lumerical/fdtd/mpich/ch_p4/share ++datadir=$EBROOTFDTD_SOLUTIONS/mpich/ch_p4/share + DEFAULT_MACHINE=ch_p4 + DEFAULT_ARCH=LINUX + +diff -ru opt.orig/lumerical/fdtd/mpich/ch_shmem/bin/mpirun opt/lumerical/fdtd/mpich/ch_shmem/bin/mpirun +--- opt.orig/lumerical/fdtd/mpich/ch_shmem/bin/mpirun 2016-09-10 02:54:25.000000000 +0200 ++++ opt/lumerical/fdtd/mpich/ch_shmem/bin/mpirun 2017-01-31 16:54:28.526031524 +0100 +@@ -26,8 +26,8 @@ + COMM= + GLOBUSDIR=@GLOBUSDIR@ + CLINKER="cc" +-prefix=/opt/lumerical/fdtd/mpich/ch_shmem +-bindir=/opt/lumerical/fdtd/mpich/ch_shmem/bin ++prefix=$EBROOTFDTD_SOLUTIONS/mpich/ch_shmem ++bindir=$EBROOTFDTD_SOLUTIONS/mpich/ch_shmem/bin + # Record the value of sbindir. Some useful utilities, such as + # cleanipcs (used for cleaning up shared memory segments and semaphores) + # are placed in this directory. +@@ -36,7 +36,7 @@ + sbindir=${exec_prefix}/sbin + # This value for datadir is the default value setup by configure + # This value for datadir is the default value setup by configure +-datadir=/opt/lumerical/fdtd/mpich/ch_shmem/share ++datadir=$EBROOTFDTD_SOLUTIONS/mpich/ch_shmem/share + DEFAULT_MACHINE=smp + DEFAULT_ARCH=LINUX + +diff -ru opt.orig/lumerical/fdtd/templates/fdtd-pbs-template.sh opt/lumerical/fdtd/templates/fdtd-pbs-template.sh +--- opt.orig/lumerical/fdtd/templates/fdtd-pbs-template.sh 2016-09-10 02:54:24.000000000 +0200 ++++ opt/lumerical/fdtd/templates/fdtd-pbs-template.sh 2017-01-31 16:55:33.917400758 +0100 +@@ -10,8 +10,8 @@ + NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE` + echo "Starting run at: `date`" + echo "Running on $NUM_PROCS processors." +-MY_PROG="/opt/lumerical/fdtd/bin/fdtd-engine-mpichp4" ++MY_PROG="$EBROOTFDTD_SOLUTIONS/bin/fdtd-engine-mpichp4" + INPUT="" +-/opt/lumerical/fdtd/mpich/ch_p4/bin/mpirun -n $NUM_PROCS $MY_PROG ./${INPUT} ++$EBROOTFDTD_SOLUTIONS/mpich/ch_p4/bin/mpirun -n $NUM_PROCS $MY_PROG ./${INPUT} + echo "Job finished at: `date`" + exit diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-interconnect-api-path.patch b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-interconnect-api-path.patch new file mode 100644 index 00000000000..7612c94cb3d --- /dev/null +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-interconnect-api-path.patch @@ -0,0 +1,16 @@ +# Fix hardcoded paths in python code +# +# Åke Sandgren, 2017-02-07 +diff -ru opt.orig/lumerical/fdtd/api/python/lumapi.py opt/lumerical/fdtd/api/python/lumapi.py +--- opt.orig/lumerical/fdtd/api/python/lumapi.py 2016-09-10 02:54:25.000000000 +0200 ++++ opt/lumerical/fdtd/api/python/lumapi.py 2017-02-02 12:54:37.413273068 +0100 +@@ -1,7 +1,8 @@ + from ctypes import * + from numpy import * ++import os + +-INTEROPLIB = "/opt/lumerical/interconnect/api/c/libinterop-api.so.1" ++INTEROPLIB = os.environ['EBROOTINTERCONNECT'] + "/api/c/libinterop-api.so.1" + + class Session(Structure): + _fields_ = [("p", c_void_p)] diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-which-skip-alias.patch b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-which-skip-alias.patch new file mode 100644 index 00000000000..916ff679062 --- /dev/null +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-which-skip-alias.patch @@ -0,0 +1,64 @@ +# Remove --skip-alias arg to "which", not understood by all versions of +# the command. +# +# Åke Sandgren, 2017-02-07 +diff -ru opt.orig/lumerical/fdtd/bin/fdtd-config.sh opt/lumerical/fdtd/bin/fdtd-config.sh +--- opt.orig/lumerical/fdtd/bin/fdtd-config.sh 2016-09-10 02:54:24.000000000 +0200 ++++ opt/lumerical/fdtd/bin/fdtd-config.sh 2017-01-31 16:46:08.038859599 +0100 +@@ -13,7 +13,7 @@ + echo "Add FDTD Solutions directory to path" + echo + +-BINDIR=`dirname $(readlink -f $(which --skip-alias $0))` ++BINDIR=`dirname $(readlink -f $(which $0))` + + if which CAD &> /dev/null; then + CURPATH=`which CAD |sed 's#/CAD##g'` +diff -ru opt.orig/lumerical/fdtd/bin/fdtd-mpi-status.sh opt/lumerical/fdtd/bin/fdtd-mpi-status.sh +--- opt.orig/lumerical/fdtd/bin/fdtd-mpi-status.sh 2016-09-10 02:54:25.000000000 +0200 ++++ opt/lumerical/fdtd/bin/fdtd-mpi-status.sh 2017-01-31 16:46:15.006792376 +0100 +@@ -20,7 +20,7 @@ + echo " 2) fdtd-engine-mpichp4 MPICH for TCP/IP networked clusters (ch_p4) - included with FDTD Solutions" + echo " 3) fdtd-engine-mpichshmem MPICH for shared memory systems (ch_shmem) - included with FDTD Solutions" + +-MPITESTDIR=`dirname $(readlink -f $(which --skip-alias $0))` ++MPITESTDIR=`dirname $(readlink -f $(which $0))` + + FDTD_PARS=(hpmpi impi infinipath mpich2 mpichp4 ompi scali ) + MPI_NAMES=("HP MPI" "Intel MPI" "Infinipath MPI" MPICH2 MPICH OpenMPI "Scali MPI") +diff -ru opt.orig/lumerical/fdtd/bin/fdtd-process-template.sh opt/lumerical/fdtd/bin/fdtd-process-template.sh +--- opt.orig/lumerical/fdtd/bin/fdtd-process-template.sh 2016-09-10 02:54:24.000000000 +0200 ++++ opt/lumerical/fdtd/bin/fdtd-process-template.sh 2017-01-31 16:46:22.358721449 +0100 +@@ -77,7 +77,7 @@ + FILENAME=`basename $1` + + #Run FDTD to get stats from project file +-SCRIPTDIR=`dirname $(readlink -f $(which --skip-alias $0))` ++SCRIPTDIR=`dirname $(readlink -f $(which $0))` + $SCRIPTDIR/fdtd-engine-mpich2nem -mr $1 > $1.tmp + + #Estimated memory +diff -ru opt.orig/lumerical/fdtd/bin/fdtd-run-local.sh opt/lumerical/fdtd/bin/fdtd-run-local.sh +--- opt.orig/lumerical/fdtd/bin/fdtd-run-local.sh 2016-09-10 02:54:24.000000000 +0200 ++++ opt/lumerical/fdtd/bin/fdtd-run-local.sh 2017-01-31 16:46:25.758688650 +0100 +@@ -20,7 +20,7 @@ + + #Locate the directory of this script so we can find + #utility scripts and templates relative to this path +-SCRIPTDIR=`dirname $(readlink -f $(which --skip-alias $0))` ++SCRIPTDIR=`dirname $(readlink -f $(which $0))` + + #Set path to mpiexec + MPIEXEC=$SCRIPTDIR/../mpich2/nemesis/bin/mpiexec +diff -ru opt.orig/lumerical/fdtd/bin/fdtd-run-pbs.sh opt/lumerical/fdtd/bin/fdtd-run-pbs.sh +--- opt.orig/lumerical/fdtd/bin/fdtd-run-pbs.sh 2016-09-10 02:54:24.000000000 +0200 ++++ opt/lumerical/fdtd/bin/fdtd-run-pbs.sh 2017-01-31 16:46:29.382653688 +0100 +@@ -26,7 +26,7 @@ + + #Locate the directory of this script so we can find + #utility scripts and templates relative to this path +-SCRIPTDIR=`dirname $(readlink -f $(which --skip-alias $0))` ++SCRIPTDIR=`dirname $(readlink -f $(which $0))` + + #The location of the template file to use when submitting jobs + #The line below can be changed to use your own template file diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb new file mode 100644 index 00000000000..c108d214693 --- /dev/null +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb @@ -0,0 +1,18 @@ +name = 'FDTD_Solutions' +version = '8.16.982' + +homepage = 'http://www.lumerical.com/tcad-products/fdtd/' +description = """High performance FDTD-method Maxwell solver for the design, analysis and optimization +of nanophotonic devices, processes and materials.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] + +patches = [ + '%(name)s-%(version_major_minor)s-fix-which-skip-alias.patch', + '%(name)s-%(version_major_minor)s-fix-install-paths.patch', + '%(name)s-%(version_major_minor)s-fix-interconnect-api-path.patch', +] + +moduleclass = 'cae' From d25e9ac169e6591ad3a3d17f71291c43cb1240eb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 12 Jan 2018 13:39:23 +0100 Subject: [PATCH 0016/5331] Fix typo in patch file. --- .../FDTD_Solutions-8.16-fix-interconnect-api-path.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-interconnect-api-path.patch b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-interconnect-api-path.patch index 7612c94cb3d..93979504912 100644 --- a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-interconnect-api-path.patch +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16-fix-interconnect-api-path.patch @@ -10,7 +10,7 @@ diff -ru opt.orig/lumerical/fdtd/api/python/lumapi.py opt/lumerical/fdtd/api/pyt +import os -INTEROPLIB = "/opt/lumerical/interconnect/api/c/libinterop-api.so.1" -+INTEROPLIB = os.environ['EBROOTINTERCONNECT'] + "/api/c/libinterop-api.so.1" ++INTEROPLIB = os.environ['EBROOTFDTD_SOLUTIONS'] + "/api/c/libinterop-api.so.1" class Session(Structure): _fields_ = [("p", c_void_p)] From 0b9772a3c59c3335cb13af4c914a590d68b7b320 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 29 Jan 2018 11:11:37 +0800 Subject: [PATCH 0017/5331] adding easyconfigs: Bader-1.0.3-intel-2018a.eb --- .../b/Bader/Bader-1.0.3-intel-2018a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bader/Bader-1.0.3-intel-2018a.eb diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.0.3-intel-2018a.eb b/easybuild/easyconfigs/b/Bader/Bader-1.0.3-intel-2018a.eb new file mode 100644 index 00000000000..e979838e8a6 --- /dev/null +++ b/easybuild/easyconfigs/b/Bader/Bader-1.0.3-intel-2018a.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'Bader' +version = '1.0.3' + +homepage = 'http://theory.cm.utexas.edu/henkelman/code/bader/' +description = "A fast algorithm for doing Bader's analysis on a charge density grid." + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/'] +sources = ['bader.tar.gz'] +checksums = ['9defc5d005521a3ed8bad7a3e2e557283962269eddf9994864c77b328c179c63'] + +skipsteps = ['configure'] + +buildopts = '-f makefile.lnx_ifort LINK=""' + +files_to_copy = [(['bader'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bader'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'chem' From 96b0a7344c211beba76c25e8d38ce8ecfe74bb85 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 1 Feb 2018 11:31:22 -0600 Subject: [PATCH 0018/5331] adding easyconfigs: ABySS-2.0.2-foss-2016b.eb, ABySS-2.0.2-intel-2016b.eb, sparsehash-2.0.3-GCCcore-5.4.0.eb --- .../a/ABySS/ABySS-2.0.2-foss-2016b.eb | 37 +++++++++++++++++++ .../a/ABySS/ABySS-2.0.2-intel-2016b.eb | 37 +++++++++++++++++++ .../sparsehash-2.0.3-GCCcore-5.4.0.eb | 30 +++++++++++++++ 3 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-foss-2016b.eb create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-intel-2016b.eb create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-foss-2016b.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-foss-2016b.eb new file mode 100644 index 00000000000..16e620b71af --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-foss-2016b.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Maxime Schmitt , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '2.0.2' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df'] + +dependencies = [ + ('Boost', '1.63.0', '-Python-2.7.12'), + ('sparsehash', '2.0.3'), + ('SQLite', '3.13.0'), +] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-intel-2016b.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-intel-2016b.eb new file mode 100644 index 00000000000..ff4e7b87f95 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-intel-2016b.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Maxime Schmitt , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '2.0.2' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df'] + +dependencies = [ + ('Boost', '1.63.0', '-Python-2.7.12'), + ('sparsehash', '2.0.3'), + ('SQLite', '3.13.0'), +] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-5.4.0.eb new file mode 100644 index 00000000000..73749e4a3c2 --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-5.4.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.3' + +homepage = 'https://github.com/sparsehash/sparsehash' + +description = """ + An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! + The SparseHash library contains several hash-map implementations, including + implementations that optimize for space or speed. +""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/sparsehash/sparsehash/archive'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['05e986a5c7327796dad742182b2d10805a8d4f511ad090da0490f146c1ff7a8c'] + +builddependencies = [ + ('binutils', '2.26'), +] + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' From 3b77e34824de5b2eef3574bdaa7571665d8aa877 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 9 Feb 2018 17:22:51 +0200 Subject: [PATCH 0019/5331] Adding patch files --- .../f/FoX/FoX-4.1.2-iomkl-2017b.eb | 26 ++++++++++ .../h/HDF5/HDF5-1.10.1-iomkl-2017b.eb | 20 +++++++ .../QuantumESPRESSO-6.2.1-iomkl-2017b.eb | 52 +++++++++++++++++++ ....1_fix_missing_include_dir_in_COUPLE.patch | 15 ++++++ 4 files changed, 113 insertions(+) create mode 100644 easybuild/easyconfigs/f/FoX/FoX-4.1.2-iomkl-2017b.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-iomkl-2017b.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1_fix_missing_include_dir_in_COUPLE.patch diff --git a/easybuild/easyconfigs/f/FoX/FoX-4.1.2-iomkl-2017b.eb b/easybuild/easyconfigs/f/FoX/FoX-4.1.2-iomkl-2017b.eb new file mode 100644 index 00000000000..794db15bcf3 --- /dev/null +++ b/easybuild/easyconfigs/f/FoX/FoX-4.1.2-iomkl-2017b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'FoX' +version = '4.1.2' + +homepage = 'http://homepages.see.leeds.ac.uk/~earawa/FoX/' +description = """FoX is an XML library written in Fortran 95. +It allows software developers to read, write and modify XML documents from Fortran applications without the +complications of dealing with multi-language development.""" + +toolchain = {'name': 'iomkl', 'version': '2017b'} + +source_urls = ['http://homepages.see.leeds.ac.uk/~earawa/FoX/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3b749138229e7808d0009a97e2ac47815ad5278df6879a9cc64351a7921ba06f'] + +sanity_check_paths = { + 'files': ['lib/libFoX_%s.a' % x for x in ['common', 'dom', 'fsys', 'sax', 'utils', 'wcml', 'wkml', 'wxml']], + 'dirs': ['finclude', 'lib', 'bin'] +} + +modextrapaths = { + 'CPATH': ['finclude'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-iomkl-2017b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-iomkl-2017b.eb new file mode 100644 index 00000000000..c5207050471 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-iomkl-2017b.eb @@ -0,0 +1,20 @@ +name = 'HDF5' +version = '1.10.1' + +homepage = 'https://support.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'iomkl', 'version': '2017b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb new file mode 100644 index 00000000000..dfc2419020b --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb @@ -0,0 +1,52 @@ +name = 'QuantumESPRESSO' +version = '6.2.1' + +homepage = 'http://www.pwscf.org/' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'iomkl', 'version': '2017b'} +toolchainopts = {'usempi': True, 'openmp': True} + +# major part of this list was determined from espresso/install/plugins_list +# - There is currently no plumed version that works for QME 6.1 +# - Yambo is better to install outside of QM-E, there are problems +# building it with openmp turned on and the intel toolchain and there is +# no added benefit to build it inside QM-E +# - Want is never installed in bin/ (since it first shows up in 4.2) so +# don't bother building it here. +sources = [ + 'qe-%(version)s.tar.gz', + 'wannier90-2.1.0.tar.gz', +] + +source_urls = [ +# 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz + 'http://www.wannier.org/code/', # wannier90-2.1.0.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/247/1132/', # qe-6.2.1.tar.gz +] + +patches = ['%(name)s-%(version)s_fix_missing_include_dir_in_COUPLE.patch'] + +dependencies = [ + ('HDF5', '1.10.1'), + ('FoX', '4.1.2'), + +] + +# source checksums +checksums = [ + '6cdd4c8883b4a2262ac98ea452f845ed935294b3988a84b238d833558eb90f0c', # qe-6.2.1.tar.gz + 'ee90108d4bc4aa6a1cf16d72abebcb3087cf6c1007d22dda269eb7e7076bddca', # wannier90-2.1.0.tar.gz + '44751fe9d1e6eede4ba331e7216e222960ff19ba9170aaa0cd4393924aa54fbc', # QuantumESPRESSO-6.2.1_fix_missing_include_dir_in_COUPLE.patch +] + +buildopts = 'all gwl xspectra couple epw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1_fix_missing_include_dir_in_COUPLE.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1_fix_missing_include_dir_in_COUPLE.patch new file mode 100644 index 00000000000..874962756e6 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1_fix_missing_include_dir_in_COUPLE.patch @@ -0,0 +1,15 @@ +# Add missing include directive for fortran module files. +# +# Åke Sandgren, HPC2N +diff -ru qe-6.2.1.orig/COUPLE/src/Makefile qe-6.2.1/COUPLE/src/Makefile +--- qe-6.2.1.orig/COUPLE/src/Makefile 2018-02-09 12:56:01.098532948 +0100 ++++ qe-6.2.1/COUPLE/src/Makefile 2018-02-09 12:56:30.470224052 +0100 +@@ -2,7 +2,7 @@ + include ../../make.inc + + # location of required modules and include files +-MODFLAGS= $(MOD_FLAG)../../iotk/src $(MOD_FLAG)../../Modules $(MOD_FLAG)../../FFTXlib $(MOD_FLAG)../../UtilXlib $(MOD_FLAG)../../CPV/src ++MODFLAGS= $(MOD_FLAG)../../iotk/src $(MOD_FLAG)../../Modules $(MOD_FLAG)../../FFTXlib $(MOD_FLAG)../../UtilXlib $(MOD_FLAG)../../CPV/src $(MOD_FLAG)../../LAXlib + IFLAGS=#-DDEBUG_QECOUPLE + TLDEPS=pw cp + From a126cd69342ec2129ff950c422e07d9b39c40c58 Mon Sep 17 00:00:00 2001 From: Michael Coleman Date: Fri, 9 Feb 2018 10:16:56 -0800 Subject: [PATCH 0020/5331] {bio}[intel/2018a] update SOAPdenovo2-r241 Note that latest source is now on github. Killed 'optarch' (which defaults to True anyway?) and 'pic' (seems unnecessary). --- .../SOAPdenovo2-r241-intel-2018a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-intel-2018a.eb diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-intel-2018a.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-intel-2018a.eb new file mode 100644 index 00000000000..01d11a1130c --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-intel-2018a.eb @@ -0,0 +1,39 @@ +# With <3 for EasyBuild +# +# EasyConfig for SOAPdenovo2: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = "MakeCp" + +name = 'SOAPdenovo2' +version = 'r241' + +homepage = 'http://soap.genomics.org.cn/index.html' +description = """SOAPdenovo is a novel short-read assembly method that can build a + de novo draft assembly for human-sized genomes. The program is specially designed to + assemble Illumina short reads. It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. + SOAPdenovo2 is the successor of SOAPdenovo.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +github_account = 'aquaskyline' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e623b11f78bf885c22ccf265f70b3952828c6cfb05cfb3d17c49c984bcb5eeda'] + +# parallel build is broken +maxparallel = 1 + +files_to_copy = [(['SOAPdenovo-127mer', 'SOAPdenovo-63mer', 'SOAPdenovo-fusion'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer', 'bin/SOAPdenovo-fusion'], + 'dirs': [], +} + +moduleclass = 'bio' From e2d54eacb407bd8c1c53515735613b5e06a4f6e1 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 13 Feb 2018 23:44:59 +0200 Subject: [PATCH 0021/5331] adding easyconfigs: MMseqs2-1-c7a89-foss-2016b.eb --- .../m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb new file mode 100644 index 00000000000..1bebb31f47a --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'MMseqs2' +version = '1-c7a89' + +homepage = 'https://github.com/soedinglab/mmseqs2' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/soedinglab/MMseqs2/archive/'] +sources = ['%(version)s.tar.gz'] + +separate_build_dir = True + +builddependencies = [('CMake', '3.4.3')] + +dependencies = [ + ('zlib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +moduleclass = 'bio' From ee56b6b173dfc545f92f04bc53246e7f91d3b792 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 13 Feb 2018 22:48:12 +0100 Subject: [PATCH 0022/5331] added configopts --- easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb index 1bebb31f47a..595317b6944 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb @@ -20,6 +20,8 @@ separate_build_dir = True builddependencies = [('CMake', '3.4.3')] +configopts = '-DCMAKE_BUILD_TYPE=RELEASE' + dependencies = [ ('zlib', '1.2.8'), ] From 10786961f1495e4608d337cca57120d7c0a02842 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 15 Feb 2018 16:45:02 +0200 Subject: [PATCH 0023/5331] adding easyconfigs: Pilon-1.22-Java-1.8.0_92.eb --- .../p/Pilon/Pilon-1.22-Java-1.8.0_92.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb new file mode 100644 index 00000000000..f8a7d40f48b --- /dev/null +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb @@ -0,0 +1,27 @@ +easyblock = 'JAR' + +name = 'Pilon' +version = '1.22' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/broadinstitute/pilon' +description = "Pilon is an automated genome assembly improvement and variant detection tool" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.jar'] + +dependencies = [('Java', '1.8.0_92')] + +sanity_check_paths = { + 'files': ["%(namelower)s-%(version)s.jar"], + 'dirs': [], +} + +postinstallcmds = ['cd %(installdir)s && ln -s %(namelower)s-%(version)s.jar pilon.jar'] + +modloadmsg = "To execute Pilon run: java -Xmx8G -jar $EBROOTPILON/pilon.jar\n" +modloadmsg += "\rAdjust the memory value according to the size of your input files\n\r" + +moduleclass = 'bio' From 79496adddc38a3146c049fa6d2c07b62444534f3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 16 Feb 2018 08:59:51 +0100 Subject: [PATCH 0024/5331] version 3.2.5 added --- .../MaSuRCA-3.2.5-foss-2017b-Perl-5.26.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.5-foss-2017b-Perl-5.26.0.eb diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.5-foss-2017b-Perl-5.26.0.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.5-foss-2017b-Perl-5.26.0.eb new file mode 100644 index 00000000000..8d192ebbe8a --- /dev/null +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.2.5-foss-2017b-Perl-5.26.0.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2017 University of Geneva +# Authors:: Yann Sagon +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'MaSuRCA' +version = '3.2.5' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.genome.umd.edu/masurca.html' + +description = '''MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph + and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing + only short reads from Illumina sequencing or a mixture of short reads and long reads + (Sanger, 454, Pacbio and Nanopore).''' + +toolchain = {'name': 'foss', 'version': '2017b'} + +# need a temporary url to download it. Do it manually here: +# http://www.genome.umd.edu/masurca_form.html +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['48a7798600456ff4fa90a0f8e5b2011488c58f1712f5c3c1d4a502ea6f252a6e'] + +dependencies = [ + ('Perl', '5.26.0'), + ('libreadline', '7.0'), + ('Tcl', '8.6.7'), + ('Boost', '1.65.1'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), +] + +buildopts = "install-special" +start_dir = "global-1" + +sanity_check_paths = { + 'files': ['bin/masurca'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'bio' From 0551e935b16d5c6a258568723d14af33418afb62 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Fri, 16 Feb 2018 12:26:26 +0100 Subject: [PATCH 0025/5331] added header --- easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb index f8a7d40f48b..df99e147e45 100644 --- a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb @@ -1,3 +1,8 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + easyblock = 'JAR' name = 'Pilon' From b01806c5725abd9c150b9de736f57941610f2d68 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Fri, 16 Feb 2018 12:27:36 +0100 Subject: [PATCH 0026/5331] added checksum --- easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb index df99e147e45..7d4dfca9f06 100644 --- a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(version)s/'] sources = ['%(namelower)s-%(version)s.jar'] +checksums = ['ff738f3bbb964237f6b2cf69243ebf9a21cb7f4edf10bbdcc66fa4ebaad5d13d'] dependencies = [('Java', '1.8.0_92')] From f59b2facf0b045c3bea3b7abf3c59a9971fd2b09 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 16 Feb 2018 13:31:18 +0200 Subject: [PATCH 0027/5331] adding easyconfigs: GATK-4.0.1.2-Java-1.8.0_92.eb --- .../g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb new file mode 100644 index 00000000000..f0ac6a6085f --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.0.1.2' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['%(namelower)s-%(version)s.zip'] +checksums = ['d667c08ec44f4dc2029d00ca16cfcfe7850ae9bfdcdd6e35f3048b8e7e83647b'] + +dependencies = [('Java', '1.8.0_92')] + +# add install dir to PATH +modextrapaths = {'PATH': ''} + +modloadmsg = "To execute GATK run 'gatk'\n" +modloadmsg += "\rTo enable bash completion run 'source $EBROOTGATK/gatk-completion.sh'\n\r" + +sanity_check_paths = { + 'files': ["gatk", "gatk-package-%(version)s-spark.jar", "gatk-package-%(version)s-local.jar"], + 'dirs': [], +} + +moduleclass = 'bio' From a93978f468c82cb491a8a9e10673927ab0f2d30a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Sat, 17 Feb 2018 00:08:36 +0100 Subject: [PATCH 0028/5331] {vis}[intel/2017b] GTK+ 2.24.32 wxPython 3.0.2.0 (REVIEW) --- .../a/ATK/ATK-2.26.1-intel-2017b.eb | 37 ++++++++++++++ .../d/DBus/DBus-1.13.0-intel-2017b.eb | 28 +++++++++++ .../dbus-glib/dbus-glib-0.110-intel-2017b.eb | 26 ++++++++++ .../g/GConf/GConf-3.2.6-intel-2017b.eb | 40 ++++++++++++++++ ...ection-1.53.5-intel-2017b-Python-2.7.14.eb | 48 +++++++++++++++++++ .../GST-plugins-base-0.10.36-intel-2017b.eb | 36 ++++++++++++++ .../GStreamer-0.10.36-intel-2017b.eb | 42 ++++++++++++++++ .../g/GTK+/GTK+-2.24.32-intel-2017b.eb | 28 +++++++++++ ...-Pixbuf-2.36.11-disable-gio-sniffing.patch | 15 ++++++ .../Gdk-Pixbuf-2.36.11-intel-2017b.eb | 46 ++++++++++++++++++ .../h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb | 38 +++++++++++++++ .../p/Pango/Pango-1.40.14-intel-2017b.eb | 35 ++++++++++++++ ...ython-3.0.2.0-intel-2017b-Python-2.7.14.eb | 41 ++++++++++++++++ 13 files changed, 460 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.26.1-intel-2017b.eb create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.13.0-intel-2017b.eb create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-intel-2017b.eb create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-disable-gio-sniffing.patch create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2017b.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.26.1-intel-2017b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.26.1-intel-2017b.eb new file mode 100644 index 00000000000..fe460d6cc4c --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.26.1-intel-2017b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.26.1' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ef00ff6b83851dddc8db38b4d9faeffb99572ba150b0664ee02e46f015ea97cb'] + +builddependencies = [ + ('GObject-Introspection', '1.53.5', '-Python-2.7.14'), +] +dependencies = [ + ('GLib', '2.53.5'), +] + +configopts = "--enable-introspection=yes" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.0-intel-2017b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.0-intel-2017b.eb new file mode 100644 index 00000000000..be0d52b5a2d --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.0-intel-2017b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.13.0' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['837abf414c0cdac4c8586ea6f93a999446470b10abcfeefe19ed8a7921854d2e'] + +dependencies = [('expat', '2.2.4')] + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', + 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-intel-2017b.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-intel-2017b.eb new file mode 100644 index 00000000000..f9e311ef566 --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-intel-2017b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.110' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] +checksums = ['7ce4760cf66c69148f6bd6c92feaabb8812dee30846b24cd0f7395c436d7e825'] + +dependencies = [ + ('GLib', '2.53.5'), + ('DBus', '1.13.0'), + ('expat', '2.2.4'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb new file mode 100644 index 00000000000..4055794a76a --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-intel-2017b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +homepage = 'https://projects.gnome.org/gconf/' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] + +dependencies = [ + ('dbus-glib', '0.110'), + ('GLib', '2.53.5'), + ('GObject-Introspection', '1.53.5', '-Python-2.7.14'), + ('libxml2', '2.9.4'), + ('GTK+', '2.24.32'), + ('intltool', '0.51.0', '-Perl-5.26.0'), +] + +configopts = '--disable-orbit ' + +sanity_check_paths = { + 'files': ['bin/gconf%s' % x for x in['-merge-tree', 'tool-2']] + + ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] + + ['lib/libgconf-2.%s' % x for x in['a', 'so']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..9aee9ea1643 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.53.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.14'), + ('GLib', '2.53.5'), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20170619'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('cairo', '1.14.10'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb new file mode 100644 index 00000000000..034ad54c7b2 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] + +dependencies = [('GStreamer', '0.10.36')] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb new file mode 100644 index 00000000000..3fa10e1d8ed --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2017b.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] + +dependencies = [ + ('GLib', '2.53.5'), + ('GObject-Introspection', '1.53.5', '-Python-2.7.14'), + ('zlib', '1.2.11'), +] + +# does not work with Bison 3.x +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '2.7', '', True) +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['reamer', 'base', + 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'], +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb new file mode 100644 index 00000000000..f2b4b2034a1 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.32' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b6c8a93ddda5eabe3bfee1eb39636c9a03d2a56c7b62828b359bf197943c582e'] + +builddependencies = [ + ('GObject-Introspection', '1.53.5', '-Python-2.7.14'), +] +dependencies = [ + ('ATK', '2.26.1'), + ('Gdk-Pixbuf', '2.36.11'), + ('Pango', '1.40.14'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-disable-gio-sniffing.patch b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-disable-gio-sniffing.patch new file mode 100644 index 00000000000..aadaad222e0 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-disable-gio-sniffing.patch @@ -0,0 +1,15 @@ +hard disable GIO sniffing to avoid relying on shared-mime-info, +and use fallback mechanism to use built-in sniffing based on magic numbers +author: Kenneth Hoste (HPC-UGent) +--- gdk-pixbuf-2.36.11.orig/configure 2017-10-02 17:32:14.000000000 +0200 ++++ gdk-pixbuf-2.36.11/configure 2018-02-16 23:03:51.381732087 +0100 +@@ -19315,6 +19315,9 @@ + fi + + ++# hard disable sniffing, which requires shared-mime-info ++gio_can_sniff=no ++ + if test x$gio_can_sniff = x; then + # Will not run on win32, so require shared-mime-info + diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2017b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2017b.eb new file mode 100644 index 00000000000..7668178e316 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-intel-2017b.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.36.11' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +patches = ['Gdk-Pixbuf-%(version)s-disable-gio-sniffing.patch'] +checksums = [ + 'ae62ab87250413156ed72ef756347b10208c00e76b222d82d9ed361ed9dde2f3', # gdk-pixbuf-2.36.11.tar.xz + '3ea8db8c13c3d2118469ce91c9a399724cb9800c1e96ca4eb2f8cabfb4a116d9', # Gdk-Pixbuf-2.36.11-disable-gio-sniffing.patch +] + +builddependencies = [ + ('GObject-Introspection', '1.53.5', '-Python-2.7.14') +] +dependencies = [ + ('GLib', '2.53.5'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.32'), + ('LibTIFF', '4.0.8'), +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb new file mode 100644 index 00000000000..1ac2bf9a1dd --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.7.1-intel-2017b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.7.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9645a6e83313b690602017f18d4eb2adf81f2e54c6fc4471e19331304965154e'] + +dependencies = [ + ('GLib', '2.53.5'), + ('cairo', '1.14.10'), + ('freetype', '2.8'), +] + +builddependencies = [ + ('GObject-Introspection', '1.53.5', '-Python-2.7.14'), + ('pkg-config', '0.29.2'), +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb new file mode 100644 index 00000000000..040a66af794 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.40.14' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['90af1beaa7bf9e4c52db29ec251ec4fd0a8f2cc185d521ad1f88d01b3a6a17e3'] + +dependencies = [ + ('X11', '20171023'), + ('GLib', '2.53.5'), + ('cairo', '1.14.10'), + ('HarfBuzz', '1.7.1'), +] + +builddependencies = [ + ('GObject-Introspection', '1.53.5', '-Python-2.7.14'), + ('pkg-config', '0.29.2'), +] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..bb1d59e72c6 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,41 @@ +name = 'wxPython' +version = '3.0.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.wxpython.org' +description = """wxPython is a GUI toolkit for the Python programming language. + It allows Python programmers to create programs with a robust, + highly functional graphical user interface, simply and easily. + It is implemented as a Python extension module (native code) + that wraps the popular wxWidgets cross platform GUI library, + which is written in C++.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tar.bz2'] +patches = [ + 'wxPython_%(version)s_intel.patch', + 'wxPython-%(version)s_fix-abs-overload.patch', +] +checksums = [ + 'd54129e5fbea4fb8091c87b2980760b72c22a386cb3b9dd2eebc928ef5e8df61', # wxPython-src-3.0.2.0.tar.bz2 + 'fa7edb55e0c0ad18f636f9d9af7d2ee4cf3be439c78db5cae6d0ee47130f0ec6', # wxPython_3.0.2.0_intel.patch + '7bc2d671af6cd79930275c9e59c42a7c79ee6d66329190ac13df690f5def4d94', # wxPython-3.0.2.0_fix-abs-overload.patch +] + +dependencies = [ + ('Python', '2.7.14'), + ('libpng', '1.6.32'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '1.5.2'), + ('LibTIFF', '4.0.8'), + ('expat', '2.2.4'), + ('GTK+', '2.24.32'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '0.10.36'), + ('Mesa', '17.2.4'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'vis' From c936abc9d61a1b635dcd8a8fd596bc7aa01c2729 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 20 Feb 2018 11:56:51 +0800 Subject: [PATCH 0029/5331] change Bader version to 1.02 --- .../{Bader-1.0.3-intel-2018a.eb => Bader-1.02-intel-2018a.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/b/Bader/{Bader-1.0.3-intel-2018a.eb => Bader-1.02-intel-2018a.eb} (93%) diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.0.3-intel-2018a.eb b/easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb similarity index 93% rename from easybuild/easyconfigs/b/Bader/Bader-1.0.3-intel-2018a.eb rename to easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb index e979838e8a6..3a573275ad2 100644 --- a/easybuild/easyconfigs/b/Bader/Bader-1.0.3-intel-2018a.eb +++ b/easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb @@ -1,14 +1,14 @@ easyblock = 'MakeCp' name = 'Bader' -version = '1.0.3' +version = '1.02' homepage = 'http://theory.cm.utexas.edu/henkelman/code/bader/' description = "A fast algorithm for doing Bader's analysis on a charge density grid." toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/'] +source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] sources = ['bader.tar.gz'] checksums = ['9defc5d005521a3ed8bad7a3e2e557283962269eddf9994864c77b328c179c63'] From 631f5f26034eec7edfda5d5030551979137fdda0 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 20 Feb 2018 12:10:16 +0800 Subject: [PATCH 0030/5331] use download_filename --- easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb b/easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb index 3a573275ad2..379ca31d929 100644 --- a/easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb +++ b/easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb @@ -9,7 +9,10 @@ description = "A fast algorithm for doing Bader's analysis on a charge density g toolchain = {'name': 'intel', 'version': '2018a'} source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] -sources = ['bader.tar.gz'] +sources = [{ + 'filename': 'bader-%(version)s.tar.gz', + 'download_filename': 'bader.tar.gz', +}] checksums = ['9defc5d005521a3ed8bad7a3e2e557283962269eddf9994864c77b328c179c63'] skipsteps = ['configure'] From 1e4ae011072eaa88ae4eddd5ee29dd50af13379b Mon Sep 17 00:00:00 2001 From: Yann Pouillon Date: Tue, 20 Feb 2018 17:51:12 +0100 Subject: [PATCH 0031/5331] adding easyconfigs: xmlf90-1.5.3-foss-2016b.eb, xmlf90-1.5.3-foss-2017a.eb --- .../x/xmlf90/xmlf90-1.5.3-foss-2016b.eb | 20 +++++++++++++++++++ .../x/xmlf90/xmlf90-1.5.3-foss-2017a.eb | 20 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb new file mode 100644 index 00000000000..8f93dff077b --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'xmlf90' +version = '1.5.3' + +homepage = 'https://launchpad.net/xmlf90' +description = """xmlf90 is a basic XML parsing library written in Fortran.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://launchpad.net/xmlf90/trunk/1.5/+download/'] +checksums = ['bf6b8fd83cd1c7fae6f9451a5babde82'] + +sanity_check_paths = { + 'files': ['include/xmlf90_%s.mod' % item for item in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb new file mode 100644 index 00000000000..4226eb86ca8 --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'xmlf90' +version = '1.5.3' + +homepage = 'https://launchpad.net/xmlf90' +description = """xmlf90 is a basic XML parsing library written in Fortran.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://launchpad.net/xmlf90/trunk/1.5/+download/'] +checksums = ['bf6b8fd83cd1c7fae6f9451a5babde82'] + +sanity_check_paths = { + 'files': ['include/xmlf90_%s.mod' % item for item in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' From 2959d7640d7e8f55f1e54a721f0aaf4c4325e848 Mon Sep 17 00:00:00 2001 From: Yann Pouillon Date: Tue, 20 Feb 2018 18:00:31 +0100 Subject: [PATCH 0032/5331] adding easyconfigs: libpsml-1.1.7-foss-2016b.eb, libpsml-1.1.7-foss-2017a.eb --- .../l/libpsml/libpsml-1.1.7-foss-2016b.eb | 26 +++++++++++++++++++ .../l/libpsml/libpsml-1.1.7-foss-2017a.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb create mode 100644 easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb new file mode 100644 index 00000000000..00a552dabf4 --- /dev/null +++ b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpsml' +version = '1.1.7' + +homepage = 'https://launchpad.net/libpsml' +description = """LibPSML provides a Fortran API to parse files in the + PSeudopotential Markup Language (PSML) format.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://launchpad.net/libpsml/trunk/1.1/+download/'] + +checksums = ['3f3189d71ec1ce83e00e477ebbf6c516'] + +dependencies = [ + ('xmlf90', '1.5.3'), +] + +sanity_check_paths = { + 'files': ['include/m_psml.mod', 'lib/libpsml.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb new file mode 100644 index 00000000000..73731f941bc --- /dev/null +++ b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpsml' +version = '1.1.7' + +homepage = 'https://launchpad.net/libpsml' +description = """LibPSML provides a Fortran API to parse files in the + PSeudopotential Markup Language (PSML) format.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://launchpad.net/libpsml/trunk/1.1/+download/'] + +checksums = ['3f3189d71ec1ce83e00e477ebbf6c516'] + +dependencies = [ + ('xmlf90', '1.5.3'), +] + +sanity_check_paths = { + 'files': ['include/m_psml.mod', 'lib/libpsml.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' From dd7ba3198c59c00a770dac03a88f68bb62be9fa0 Mon Sep 17 00:00:00 2001 From: Michael Coleman Date: Tue, 20 Feb 2018 13:34:25 -0800 Subject: [PATCH 0033/5331] {bio}[intel/2018a] update psmc --- .../p/psmc/psmc-0.6.5-foss-2018a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2018a.eb diff --git a/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2018a.eb b/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2018a.eb new file mode 100644 index 00000000000..8dc2d49d710 --- /dev/null +++ b/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2018a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'psmc' +version = '0.6.5' + +homepage = 'https://github.com/lh3/psmc' +description = """This software package infers population size history from a diploid sequence +using the Pairwise Sequentially Markovian Coalescent (PSMC) model.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://github.com/lh3/psmc/archive/'] +sources = ['%(version)s.tar.gz'] + +buildopts = '&& cd utils && make' + +utils = [ + 'avg.pl', 'calD', 'cntcpg', 'ctime_plot.pl', 'dec2ctime.pl', 'decode2bed.pl', 'fq2psmcfa', 'history2ms.pl', + 'ms2psmcfa.pl', 'mutDiff', 'pcnt_bezier.lua', 'psmc2history.pl', 'psmc_plot.pl', 'psmc_trunc.pl', 'splitfa', +] + +files_to_copy = [ + (['psmc'], 'bin'), + (['utils/%s' % util for util in utils], 'bin') +] + +sanity_check_paths = { + 'files': ['bin/psmc'] + ['bin/%s' % util for util in utils], + 'dirs': [], +} + +moduleclass = 'bio' From 8cc74a93047203edc50bc8b62fbe826dd58e6e5b Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Wed, 21 Feb 2018 10:08:11 +0000 Subject: [PATCH 0034/5331] Patch is required to make sure that the Cython extensions properly compile --- .../vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb | 31 +++++++++++++++++++ .../v/vcfnp/vcfnp-2.3.0_numpy_setup.patch | 20 ++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0_numpy_setup.patch diff --git a/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 00000000000..41ed2a50a7f --- /dev/null +++ b/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'vcfnp' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/alimanfoo/vcfnp' +description = """ Load data from a VCF (variant call format) file into numpy arrays, + and (optionally) from there into an HDF5 file.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['vcfnp-%(version)s_numpy_setup.patch'] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': ['bin/vcf2npy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + ('python', "-c 'import vcfnp'"), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0_numpy_setup.patch b/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0_numpy_setup.patch new file mode 100644 index 00000000000..0398ea85298 --- /dev/null +++ b/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0_numpy_setup.patch @@ -0,0 +1,20 @@ +diff -ru vcfnp-2.3.0/setup.py vcfnp-2.3.0.fixed/setup.py +--- vcfnp-2.3.0/setup.py 2016-07-19 16:00:40.000000000 +0000 ++++ vcfnp-2.3.0.fixed/setup.py 2016-08-26 11:55:25.235798000 +0000 +@@ -2,6 +2,7 @@ + from distutils.core import setup + from distutils.extension import Extension + import os ++import numpy + from ast import literal_eval + + try: +@@ -63,7 +64,7 @@ + 'vcfnp.iter', + sources=['vcfnp/iter.pyx'] + get_vcflib_sources(), + language='c++', +- include_dirs=[vcflib_dir, smithwaterman_dir, tabixpp_dir, './vcfnp'], ++ include_dirs=[numpy.get_include(), vcflib_dir, smithwaterman_dir, tabixpp_dir, './vcfnp'], + libraries=['m', 'z'], + extra_compile_args=['-O3'] + ) From e78241ca915310e23af3905cc8a96bfb8953bc37 Mon Sep 17 00:00:00 2001 From: Yann Pouillon Date: Wed, 21 Feb 2018 11:09:32 +0100 Subject: [PATCH 0035/5331] Replaced hard-coded version number and duplicate directory check --- easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb index 8f93dff077b..a208c7edd28 100644 --- a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb @@ -9,12 +9,12 @@ description = """xmlf90 is a basic XML parsing library written in Fortran.""" toolchain = {'name': 'foss', 'version': '2016b'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['https://launchpad.net/xmlf90/trunk/1.5/+download/'] +source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] checksums = ['bf6b8fd83cd1c7fae6f9451a5babde82'] sanity_check_paths = { 'files': ['include/xmlf90_%s.mod' % item for item in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], - 'dirs': ['include', 'lib'], + 'dirs': ['share/org.siesta-project'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb index 4226eb86ca8..d879ad6b46e 100644 --- a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb @@ -9,12 +9,12 @@ description = """xmlf90 is a basic XML parsing library written in Fortran.""" toolchain = {'name': 'foss', 'version': '2017a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['https://launchpad.net/xmlf90/trunk/1.5/+download/'] +source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] checksums = ['bf6b8fd83cd1c7fae6f9451a5babde82'] sanity_check_paths = { 'files': ['include/xmlf90_%s.mod' % item for item in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], - 'dirs': ['include', 'lib'], + 'dirs': ['share/org.siesta-project'], } moduleclass = 'data' From 426141cf668484afe9199a109da7a4aee06d43b8 Mon Sep 17 00:00:00 2001 From: Yann Pouillon Date: Wed, 21 Feb 2018 11:12:40 +0100 Subject: [PATCH 0036/5331] Replaced MD5 checksums by SHA256 ones --- easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb index a208c7edd28..0c841de55ee 100644 --- a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2016b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] -checksums = ['bf6b8fd83cd1c7fae6f9451a5babde82'] +checksums = ['a5378a5d9df4b617f51382092999eb0f20fa1a90ab49afbccfd80aa51650d27c'] sanity_check_paths = { 'files': ['include/xmlf90_%s.mod' % item for item in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb index d879ad6b46e..5d65b010dea 100644 --- a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.3-foss-2017a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2017a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] -checksums = ['bf6b8fd83cd1c7fae6f9451a5babde82'] +checksums = ['a5378a5d9df4b617f51382092999eb0f20fa1a90ab49afbccfd80aa51650d27c'] sanity_check_paths = { 'files': ['include/xmlf90_%s.mod' % item for item in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], From f9586b81280591a73cabb2b5632f2066fe3fb14d Mon Sep 17 00:00:00 2001 From: Yann Pouillon Date: Wed, 21 Feb 2018 11:19:11 +0100 Subject: [PATCH 0037/5331] Replaced hard-coded version number, duplicate directory check, and MD5 sum --- .../easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb | 7 +++---- .../easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb | 7 +++---- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb index 00a552dabf4..057ad7f169c 100644 --- a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb @@ -10,9 +10,8 @@ description = """LibPSML provides a Fortran API to parse files in the toolchain = {'name': 'foss', 'version': '2016b'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['https://launchpad.net/libpsml/trunk/1.1/+download/'] - -checksums = ['3f3189d71ec1ce83e00e477ebbf6c516'] +source_urls = ['https://launchpad.net/libpsml/trunk/%(version_major_minor)s/+download/'] +checksums = ['34ceb4e59efb542360aa4910aae088fd700026c8e1d586806b332dac8b1071a0'] dependencies = [ ('xmlf90', '1.5.3'), @@ -20,7 +19,7 @@ dependencies = [ sanity_check_paths = { 'files': ['include/m_psml.mod', 'lib/libpsml.a'], - 'dirs': ['include', 'lib'], + 'dirs': ['share/org.siesta-project'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb index 73731f941bc..3996d9709df 100644 --- a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb +++ b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb @@ -10,9 +10,8 @@ description = """LibPSML provides a Fortran API to parse files in the toolchain = {'name': 'foss', 'version': '2017a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['https://launchpad.net/libpsml/trunk/1.1/+download/'] - -checksums = ['3f3189d71ec1ce83e00e477ebbf6c516'] +source_urls = ['https://launchpad.net/libpsml/trunk/%(version_major_minor)s/+download/'] +checksums = ['34ceb4e59efb542360aa4910aae088fd700026c8e1d586806b332dac8b1071a0'] dependencies = [ ('xmlf90', '1.5.3'), @@ -20,7 +19,7 @@ dependencies = [ sanity_check_paths = { 'files': ['include/m_psml.mod', 'lib/libpsml.a'], - 'dirs': ['include', 'lib'], + 'dirs': ['share/org.siesta-project'], } moduleclass = 'data' From 817205efd25f2516cc845f24ee415ecd1c8ecfda Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Wed, 21 Feb 2018 13:18:11 +0000 Subject: [PATCH 0038/5331] adding easyconfigs: fastStructure-1.0-foss-2016a-Python-2.7.11.eb, fastStructure-1.0-foss-2016b-Python-2.7.12.eb, fastStructure-1.0-foss-2017a-Python-2.7.13.eb --- ...tStructure-1.0-foss-2016a-Python-2.7.11.eb | 33 +++++++++++++++++++ ...tStructure-1.0-foss-2016b-Python-2.7.12.eb | 33 +++++++++++++++++++ ...tStructure-1.0-foss-2017a-Python-2.7.13.eb | 33 +++++++++++++++++++ 3 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016a-Python-2.7.11.eb create mode 100644 easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016b-Python-2.7.12.eb create mode 100644 easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 00000000000..75bd6f95507 --- /dev/null +++ b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'fastStructure' +version = '1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/rajanil/fastStructure' + +description = """fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. + It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. + Here, we summarize how to setup this software package, compile the C and Cython scripts and run the algorithm + on a test simulated genotype dataset.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/rajanil/fastStructure/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['fastStructure-1.0.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('GSL', '2.1'), +] + +options = {'modulename': 'fastStructure'} + +sanity_check_paths = { + 'files': ['lib/python2.7/site-packages/%s' % x for x in ['fastStructure.so', 'parse_bed.so', 'parse_str.so']] + + ['bin/structure.py', 'bin/distruct.py', 'bin/chooseK.py'], + 'dirs': [] +} +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 00000000000..d4efed0c2de --- /dev/null +++ b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'fastStructure' +version = '1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/rajanil/fastStructure' + +description = """fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. + It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. + Here, we summarize how to setup this software package, compile the C and Cython scripts and run the algorithm + on a test simulated genotype dataset.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/rajanil/fastStructure/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['fastStructure-1.0.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('GSL', '2.3'), +] + +options = {'modulename': 'fastStructure'} + +sanity_check_paths = { + 'files': ['lib/python2.7/site-packages/%s' % x for x in ['fastStructure.so', 'parse_bed.so', 'parse_str.so']] + + ['bin/structure.py', 'bin/distruct.py', 'bin/chooseK.py'], + 'dirs': [] +} +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2017a-Python-2.7.13.eb new file mode 100644 index 00000000000..38b0e62b095 --- /dev/null +++ b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'fastStructure' +version = '1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/rajanil/fastStructure' + +description = """fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. + It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. + Here, we summarize how to setup this software package, compile the C and Cython scripts and run the algorithm + on a test simulated genotype dataset.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://github.com/rajanil/fastStructure/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['fastStructure-1.0.patch'] + +dependencies = [ + ('Python', '2.7.13'), + ('GSL', '2.3'), +] + +options = {'modulename': 'fastStructure'} + +sanity_check_paths = { + 'files': ['lib/python2.7/site-packages/%s' % x for x in ['fastStructure.so', 'parse_bed.so', 'parse_str.so']] + + ['bin/structure.py', 'bin/distruct.py', 'bin/chooseK.py'], + 'dirs': [] +} +moduleclass = 'bio' From 2eb42ba7e4737ca148f69378f32f6f8902397e4a Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Wed, 21 Feb 2018 13:23:18 +0000 Subject: [PATCH 0039/5331] Added patch to make sure that command line scripts are executable and fixes for setup.py --- .../f/fastStructure/fastStructure-1.0.patch | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastStructure/fastStructure-1.0.patch diff --git a/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0.patch b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0.patch new file mode 100644 index 00000000000..e054a02dd24 --- /dev/null +++ b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0.patch @@ -0,0 +1,74 @@ +diff -ru fastStructure-1.0/chooseK.py fastStructure-1.0-fixed/chooseK.py +--- fastStructure-1.0/chooseK.py 2014-12-16 07:43:01.000000000 +0100 ++++ fastStructure-1.0-fixed/chooseK.py 2017-05-30 10:43:40.292104948 +0200 +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python + import numpy as np + import getopt + import vars.utils as utils +diff -ru fastStructure-1.0/distruct.py fastStructure-1.0-fixed/distruct.py +--- fastStructure-1.0/distruct.py 2014-12-16 07:43:01.000000000 +0100 ++++ fastStructure-1.0-fixed/distruct.py 2017-05-30 10:43:37.447999616 +0200 +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python + import numpy as np + import matplotlib.pyplot as plot + import colorsys +diff -ru fastStructure-1.0/setup.py fastStructure-1.0-fixed/setup.py +--- fastStructure-1.0/setup.py 2014-12-16 07:43:01.000000000 +0100 ++++ fastStructure-1.0-fixed/setup.py 2017-05-30 10:57:42.275310140 +0200 +@@ -1,5 +1,6 @@ + + from distutils.core import setup ++from Cython.Build import cythonize + from distutils.extension import Extension + from Cython.Distutils import build_ext + import numpy +@@ -34,3 +35,37 @@ + include_dirs=[numpy.get_include(), '.', 'vars/'], + ext_modules = ext_modules + ) ++ ++setup(name ='structure', ++ scripts=['structure.py', 'distruct.py', 'chooseK.py'] ++ ) ++ ++ ++# setup utility functions ++ext_modules = [Extension("vars.utils", ["vars/utils.pyx"])] ++ ++setup( ++ name = 'utility functions', ++ cmdclass = {'build_ext': build_ext}, ++ include_dirs=[numpy.get_include(), 'vars'], ++ ext_modules = ext_modules ++) ++ ++# setup variable updates ++ext_modules = [Extension("vars.admixprop", sources=["vars/admixprop.pyx", "vars/C_admixprop.c"]), ++ Extension("vars.allelefreq", sources=["vars/allelefreq.pyx", "vars/C_allelefreq.c"], ++ libraries=["gsl","gslcblas"], ++ extra_compile_args=["-O3"]), ++ Extension("vars.marglikehood", sources=["vars/marglikehood.pyx", "vars/C_marglikehood.c"])] ++ext_modules = cythonize(ext_modules) ++ ++setup( ++ name = 'variables', ++ author = 'Anil Raj', ++ version = '1.0', ++ author_email = 'rajanil@stanford.edu', ++ cmdclass = {'build_ext': build_ext}, ++ include_dirs=[numpy.get_include(), 'vars'], ++ ext_modules = ext_modules, ++ packages=['vars'] ++) +diff -ru fastStructure-1.0/structure.py fastStructure-1.0-fixed/structure.py +--- fastStructure-1.0/structure.py 2014-12-16 07:43:01.000000000 +0100 ++++ fastStructure-1.0-fixed/structure.py 2017-05-30 10:43:43.728232207 +0200 +@@ -1,4 +1,4 @@ +- ++#!/usr/bin/env python + import numpy as np + import fastStructure + import parse_bed + From cbf313b42b54b1810b708a597d2fe6b0dd341535 Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Wed, 21 Feb 2018 13:28:31 +0000 Subject: [PATCH 0040/5331] adding easyconfigs: biscuit-0.1.4-foss-2016a.eb --- .../b/biscuit/biscuit-0.1.4-foss-2016a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/biscuit/biscuit-0.1.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/b/biscuit/biscuit-0.1.4-foss-2016a.eb b/easybuild/easyconfigs/b/biscuit/biscuit-0.1.4-foss-2016a.eb new file mode 100644 index 00000000000..8505d22c0fb --- /dev/null +++ b/easybuild/easyconfigs/b/biscuit/biscuit-0.1.4-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'biscuit' +version = '0.1.4' + +homepage = 'https://github.com/zwdzwd/biscuit' +description = """ Utilities to help analyze bisulfite-treated sequence data """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/zwdzwd/%(namelower)s/archive/'] +sources = ['v%(version)s.20160330.tar.gz'] + +dependencies = [('zlib', '1.2.8')] + +buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["bin/biscuit"], "bin"), +] + +sanity_check_paths = { + 'files': ["bin/biscuit"], + 'dirs': [""], +} + +moduleclass = 'bio' From fe4b52e7938e3464aa9468bc601b3f995980e294 Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Wed, 21 Feb 2018 13:38:51 +0000 Subject: [PATCH 0041/5331] adding easyconfigs: CPB-11-4-2011-foss-2017a-Python-2.7.13.eb --- .../CPB-11-4-2011-foss-2017a-Python-2.7.13.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/CPB/CPB-11-4-2011-foss-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/c/CPB/CPB-11-4-2011-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CPB/CPB-11-4-2011-foss-2017a-Python-2.7.13.eb new file mode 100644 index 00000000000..2f48fdd9aec --- /dev/null +++ b/easybuild/easyconfigs/c/CPB/CPB-11-4-2011-foss-2017a-Python-2.7.13.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'CPB' +version = '11-4-2011' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://bmi.osu.edu/hpc/software/cpb/index.html' +description = """CPB is a novel two-step Pearson correlation based biclustering approach to mine genes that are co-regulated with + a given reference gene in order to discover genes that function in a common biological process. + In the first step, the algorithm identifies subsets of genes with high correlation, reducing false negatives + with a nonparametric filtering scheme. + In the second step, biclusters from multiple datasets are used to extract and rank gene correlation information.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['http://bmi.osu.edu/hpc/software/cpb/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.13'), +] + +patches = [('CPB-11-4-2011_makefile.patch', 1)] + +files_to_copy = [(['cpb/init_bicluster', 'cpb/cpb', 'correlation/correlation', '*.py'], 'bin')] + +files_to_check = ['init_bicluster', 'correlation', 'cpb', 'cpb.py', + 'run_correlation.py', 'run_cpb.py', 'shuffle.py', 'bicluster.py'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in files_to_check], + 'dirs': [], +} + +moduleclass = 'bio' From e591926ed5efb89b1f91dcaa10f4180ee359692a Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Wed, 21 Feb 2018 14:00:05 +0000 Subject: [PATCH 0042/5331] Added Makefile to root directory to trigger sub Makefiles --- .../easyconfigs/c/CPB/CPB-11-4-2011_makefile.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/c/CPB/CPB-11-4-2011_makefile.patch diff --git a/easybuild/easyconfigs/c/CPB/CPB-11-4-2011_makefile.patch b/easybuild/easyconfigs/c/CPB/CPB-11-4-2011_makefile.patch new file mode 100644 index 00000000000..cc341dca59a --- /dev/null +++ b/easybuild/easyconfigs/c/CPB/CPB-11-4-2011_makefile.patch @@ -0,0 +1,11 @@ +diff -ruN cpb_source.orig/Makefile cpb_source/Makefile +--- cpb_source.orig/Makefile 1970-01-01 00:00:00.000000000 +0000 ++++ cpb_source/Makefile 2018-02-19 17:31:38.012739000 +0000 +@@ -0,0 +1,7 @@ ++all: ++ $(MAKE) -C correlation ++ $(MAKE) -C cpb ++ ++clean: ++ $(MAKE) -C correlation clean ++ $(MAKE) -C cpb clean From e701d97c406d29438c2eecbbf46abbf012fb9818 Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Wed, 21 Feb 2018 15:00:30 +0000 Subject: [PATCH 0043/5331] adding easyconfigs: GAT-1.2.2-foss-2016a-Python-2.7.11.eb --- .../GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb diff --git a/easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 00000000000..87451fb19d5 --- /dev/null +++ b/easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'GAT' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://gat.readthedocs.io/' +description = """The Genomic Association Tester (GAT) is a tool for computing the significance of overlap between + multiple sets of genomic intervals. GAT estimates significance based on simulation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/gat-run.py', 'bin/gat-great.py', 'bin/gat-compare.py', 'bin/gat-plot.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'bio' From c3da7e59b771e9c53297779e3877ede9ba6f0a57 Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Wed, 21 Feb 2018 15:04:44 +0000 Subject: [PATCH 0044/5331] adding easyconfigs: GenomeMapper-0.4.4-foss-2016a.eb --- .../GenomeMapper-0.4.4-foss-2016a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GenomeMapper/GenomeMapper-0.4.4-foss-2016a.eb diff --git a/easybuild/easyconfigs/g/GenomeMapper/GenomeMapper-0.4.4-foss-2016a.eb b/easybuild/easyconfigs/g/GenomeMapper/GenomeMapper-0.4.4-foss-2016a.eb new file mode 100644 index 00000000000..f18b754b511 --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeMapper/GenomeMapper-0.4.4-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'GenomeMapper' +version = '0.4.4' + +homepage = 'http://1001genomes.org/software/genomemapper_singleref.html' +description = """GenomeMapper is a short read mapping tool designed for accurate read alignments. + It quickly aligns millions of reads either with ungapped or gapped alignments. + This version is used to align against a single reference. + If you are unsure which one is the appropriate GenomeMapper, you might want to use this one.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [('http://1001genomes.org/data/software/genomemapper/genomemapper_%s/' % (version))] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +dependencies = [] + +# buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["gmindex", "genomemapper"], "bin") +] + +sanity_check_paths = { + 'files': ["bin/genomemapper", "bin/gmindex"], + 'dirs': [""], +} + +moduleclass = 'bio' From ac03b696b79b88a547b4ca8b4c986b101546aff6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 22 Feb 2018 09:47:20 +0800 Subject: [PATCH 0045/5331] fix style and simplify (allow static linking) --- .../easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb b/easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb index 379ca31d929..9928ba8d751 100644 --- a/easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb +++ b/easybuild/easyconfigs/b/Bader/Bader-1.02-intel-2018a.eb @@ -9,15 +9,12 @@ description = "A fast algorithm for doing Bader's analysis on a charge density g toolchain = {'name': 'intel', 'version': '2018a'} source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] -sources = [{ - 'filename': 'bader-%(version)s.tar.gz', - 'download_filename': 'bader.tar.gz', -}] +sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] checksums = ['9defc5d005521a3ed8bad7a3e2e557283962269eddf9994864c77b328c179c63'] skipsteps = ['configure'] - -buildopts = '-f makefile.lnx_ifort LINK=""' +buildopts = '-f makefile.lnx_ifort' +parallel = 1 files_to_copy = [(['bader'], 'bin')] @@ -26,6 +23,4 @@ sanity_check_paths = { 'dirs': [], } -parallel = 1 - moduleclass = 'chem' From 74240fddd08012e9d15f1ed96edf851dd92c41da Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Fri, 23 Feb 2018 09:19:10 +0000 Subject: [PATCH 0046/5331] Added checkums --- easybuild/easyconfigs/b/biscuit/biscuit-0.1.4-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/biscuit/biscuit-0.1.4-foss-2016a.eb b/easybuild/easyconfigs/b/biscuit/biscuit-0.1.4-foss-2016a.eb index 8505d22c0fb..676578f6027 100644 --- a/easybuild/easyconfigs/b/biscuit/biscuit-0.1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/b/biscuit/biscuit-0.1.4-foss-2016a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/zwdzwd/%(namelower)s/archive/'] sources = ['v%(version)s.20160330.tar.gz'] +checksums = ['7ca72e316db25987c745d74645c8badc249ff6b379556c5a07f63ddf74b7e8fb'] dependencies = [('zlib', '1.2.8')] From 26f736a9e8169307703e8e98e48befe4b31b8b25 Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Fri, 23 Feb 2018 09:22:36 +0000 Subject: [PATCH 0047/5331] Added checksums --- .../fastStructure-1.0-foss-2016a-Python-2.7.11.eb | 5 ++++- .../fastStructure-1.0-foss-2016b-Python-2.7.12.eb | 5 ++++- .../fastStructure-1.0-foss-2017a-Python-2.7.13.eb | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016a-Python-2.7.11.eb index 75bd6f95507..65e66dc508c 100644 --- a/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016a-Python-2.7.11.eb @@ -15,8 +15,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/rajanil/fastStructure/archive/'] sources = ['v%(version)s.tar.gz'] - patches = ['fastStructure-1.0.patch'] +checksums = [ + 'f1bfb24bb5ecd108bc3a90145fad232012165c1e60608003f1c87d200f867b81', # v1.0.tar.gz + '7f0ec4bdcc1046a2626bb128f985c537e780865004c701518a7e4a28a0aecb70', # fastStructure-1.0.patch +] dependencies = [ ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016b-Python-2.7.12.eb index d4efed0c2de..52d10ee5348 100644 --- a/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2016b-Python-2.7.12.eb @@ -15,8 +15,11 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/rajanil/fastStructure/archive/'] sources = ['v%(version)s.tar.gz'] - patches = ['fastStructure-1.0.patch'] +checksums = [ + 'f1bfb24bb5ecd108bc3a90145fad232012165c1e60608003f1c87d200f867b81', # v1.0.tar.gz + '7f0ec4bdcc1046a2626bb128f985c537e780865004c701518a7e4a28a0aecb70', # fastStructure-1.0.patch +] dependencies = [ ('Python', '2.7.12'), diff --git a/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2017a-Python-2.7.13.eb index 38b0e62b095..e411e7c32fe 100644 --- a/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/f/fastStructure/fastStructure-1.0-foss-2017a-Python-2.7.13.eb @@ -15,8 +15,11 @@ toolchain = {'name': 'foss', 'version': '2017a'} source_urls = ['https://github.com/rajanil/fastStructure/archive/'] sources = ['v%(version)s.tar.gz'] - patches = ['fastStructure-1.0.patch'] +checksums = [ + 'f1bfb24bb5ecd108bc3a90145fad232012165c1e60608003f1c87d200f867b81', # v1.0.tar.gz + '7f0ec4bdcc1046a2626bb128f985c537e780865004c701518a7e4a28a0aecb70', # fastStructure-1.0.patch +] dependencies = [ ('Python', '2.7.13'), From 3690df3ef0fbca43bd3461ed7265faaaa9f2c6f4 Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Fri, 23 Feb 2018 09:24:35 +0000 Subject: [PATCH 0048/5331] Added checksums --- .../easyconfigs/g/GenomeMapper/GenomeMapper-0.4.4-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GenomeMapper/GenomeMapper-0.4.4-foss-2016a.eb b/easybuild/easyconfigs/g/GenomeMapper/GenomeMapper-0.4.4-foss-2016a.eb index f18b754b511..5f44a7f863e 100644 --- a/easybuild/easyconfigs/g/GenomeMapper/GenomeMapper-0.4.4-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GenomeMapper/GenomeMapper-0.4.4-foss-2016a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [('http://1001genomes.org/data/software/genomemapper/genomemapper_%s/' % (version))] sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['800d2a60597d3b9df45268d605f8a97bb7d93b4f1b49faa8c6539bf6a8cd9f78'] dependencies = [] From fb40688275833aa99cfdbb22ab527a2bb11004ff Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Fri, 23 Feb 2018 09:25:26 +0000 Subject: [PATCH 0049/5331] Add checksums --- .../easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb index 87451fb19d5..6b230f100d8 100644 --- a/easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/g/GAT/GAT-1.2.2-foss-2016a-Python-2.7.11.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['e34d80169289e938aefbbebc4c50a3d5cdc8b38bab2cf63ae9716089bfda5968'] dependencies = [ ('Python', '2.7.11'), From fa0fe97920b2416c0a05a8621a45c6f488da321e Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Fri, 23 Feb 2018 09:28:47 +0000 Subject: [PATCH 0050/5331] Added checksums --- .../v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb index 41ed2a50a7f..1619a1d6d32 100644 --- a/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/v/vcfnp/vcfnp-2.3.0-foss-2016a-Python-2.7.11.eb @@ -12,8 +12,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] - patches = ['vcfnp-%(version)s_numpy_setup.patch'] +checksums = [ + '23db095e82ff7108729760b07de91ef3b2d58a543f9ed068eae0bce88b663def', # vcfnp-2.3.0.tar.gz + '920ad7df34a593dcc6a51db1659d70e6a272b4b330c957b4e2a1d50e73213fb9', # vcfnp-2.3.0_numpy_setup.patch +] dependencies = [ ('Python', '2.7.11'), From 2e8150738945058d383bae5999076f500efdf7e2 Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Fri, 23 Feb 2018 09:33:28 +0000 Subject: [PATCH 0051/5331] Added checksums --- .../c/CPB/CPB-11-4-2011-foss-2017a-Python-2.7.13.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CPB/CPB-11-4-2011-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CPB/CPB-11-4-2011-foss-2017a-Python-2.7.13.eb index 2f48fdd9aec..49ddfe451af 100644 --- a/easybuild/easyconfigs/c/CPB/CPB-11-4-2011-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CPB/CPB-11-4-2011-foss-2017a-Python-2.7.13.eb @@ -15,13 +15,16 @@ toolchain = {'name': 'foss', 'version': '2017a'} source_urls = ['http://bmi.osu.edu/hpc/software/cpb/'] sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [('CPB-%(version)s_makefile.patch', 1)] +checksums = [ + '795ae5bff11b9d56b8422e0d7345dfdffcd5cc4ac5cd3db5c6d72669beea785e', # cpb-11-4-2011.tar.gz + 'bbec37b56d7088ef4522cb6bbf742761e07aa4c810aa956caee136ff31897d07', # CPB-11-4-2011_makefile.patch +] dependencies = [ ('Python', '2.7.13'), ] -patches = [('CPB-11-4-2011_makefile.patch', 1)] - files_to_copy = [(['cpb/init_bicluster', 'cpb/cpb', 'correlation/correlation', '*.py'], 'bin')] files_to_check = ['init_bicluster', 'correlation', 'cpb', 'cpb.py', From d49c4ebca0d6bee2e5713ad8d9568f495aa7afa9 Mon Sep 17 00:00:00 2001 From: Ruben Di Battista Date: Thu, 22 Feb 2018 16:03:04 +0100 Subject: [PATCH 0052/5331] Add general (not Lmod) easyconfig for Lua --- .../l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb new file mode 100644 index 00000000000..699b006c2bf --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +buildopts = 'linux' +installopts = 'INSTALL_TOP=%(installdir)s' +skipsteps=['configure'] + +name = "Lua" +version = "5.3.4" + +homepage = "http://www.lua.org/" +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCC', 'version': '7.2.0-2.29'} + +source_urls = ['https://www.lua.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/lua"], + 'dirs': [] +} + +modextravars = { + 'LUA_DIR': '%(installdir)s', +} + +moduleclass = "lang" From 5eb89986b62c015c60c2209f06dd79a5f5a2f75d Mon Sep 17 00:00:00 2001 From: Ruben Di Battista Date: Fri, 23 Feb 2018 14:56:46 +0100 Subject: [PATCH 0053/5331] Fix style --- easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb index 699b006c2bf..c18595c8263 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' buildopts = 'linux' installopts = 'INSTALL_TOP=%(installdir)s' -skipsteps=['configure'] +skipsteps = ['configure'] name = "Lua" version = "5.3.4" From c107f910128f2cb09f8826ba7759835d7a706aec Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Mon, 26 Feb 2018 11:27:50 +0000 Subject: [PATCH 0054/5331] adding easyconfigs: GEMMA-0.97-foss-2017a.eb, Eigen-3.3.3-foss-2017a.eb --- .../e/Eigen/Eigen-3.3.3-foss-2017a.eb | 14 ++++++++ .../g/GEMMA/GEMMA-0.97-foss-2017a.eb | 32 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-foss-2017a.eb create mode 100644 easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2017a.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-foss-2017a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-foss-2017a.eb new file mode 100644 index 00000000000..5e87bd6b968 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.3-foss-2017a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.3.3' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] +checksums = ['a4143fc45e4454b4b98fcea3516b3a79b8cdb3bc7fadf996d088c6a0d805fea1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2017a.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2017a.eb new file mode 100644 index 00000000000..fc3430082a8 --- /dev/null +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2017a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'GEMMA' +version = '0.97' + +homepage = 'https://github.com/genetics-statistics/GEMMA' +description = """GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = ['https://github.com/genetics-statistics/GEMMA/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9b22a61f01af27e60d483cb7bca73e397d8ca4719c741349a8551984c6c33976'] + +builddependencies = [ + ('Eigen', '3.3.3'), +] + +dependencies = [ + ('GSL', '2.3'), +] + +runtest = 'check' + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/gemma'], + 'dirs': [] +} + +moduleclass = 'bio' From e8e4cc1f1bc7df89e80df704839f720ea482f674 Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Mon, 26 Feb 2018 12:26:03 +0000 Subject: [PATCH 0055/5331] Fix style issues --- easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2017a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2017a.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2017a.eb index fc3430082a8..6112d5750a0 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2017a.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2017a.eb @@ -4,7 +4,8 @@ name = 'GEMMA' version = '0.97' homepage = 'https://github.com/genetics-statistics/GEMMA' -description = """GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets.""" +description = """GEMMA is a software toolkit for fast application of linear mixed models (LMMs) + and related models to genome-wide association studies (GWAS) and other large-scale data sets.""" toolchain = {'name': 'foss', 'version': '2017a'} @@ -25,7 +26,7 @@ runtest = 'check' files_to_copy = ['bin'] sanity_check_paths = { - 'files': ['bin/gemma'], + 'files': ['bin/gemma'], 'dirs': [] } From 2edde3f22487d23e6a2833ba6de015eb7743aa77 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 27 Feb 2018 05:50:43 -0500 Subject: [PATCH 0056/5331] GCCcore version --- .../g/gflags/gflags-2.2.1-GCCcore-6.4.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/gflags/gflags-2.2.1-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.1-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..957c6fd7d75 --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.1-GCCcore-6.4.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.1' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ae27cdbcd6a2f935baa78e4f21f675649271634c092b1be01469440495609d0e'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.28'), + ('CMake', '3.10.2'), +] + +configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' From bb77eb0f9792f15b8b5d0aff66ae455ee6425370 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 27 Feb 2018 07:07:11 -0500 Subject: [PATCH 0057/5331] protobuf with gcccore --- .../protobuf/protobuf-3.4.0-GCCcore-6.4.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.4.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.4.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.4.0-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..cfb8515c78a --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.4.0-GCCcore-6.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.4.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f6600abeee3babfa18591961a0ff21e7db6a6d9ef82418a261ec4fee44ee6d44'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.28'), + ('Autotools', '20170619'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From e4a02eeb1ba294635eef0b4d41883d00eeae00c9 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Tue, 27 Feb 2018 07:11:08 -0500 Subject: [PATCH 0058/5331] glog with GCCcore --- .../g/glog/glog-0.3.5-GCCcore-6.4.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/glog/glog-0.3.5-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/glog/glog-0.3.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/glog/glog-0.3.5-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..640c2801ebf --- /dev/null +++ b/easybuild/easyconfigs/g/glog/glog-0.3.5-GCCcore-6.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'glog' +version = '0.3.5' + +homepage = 'https://github.com/google/glog' +description = "A C++ implementation of the Google logging module." + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/google/glog/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7580e408a2c0b5a89ca214739978ce6ff480b5e7d8d7698a2aa92fadc484d1e0'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['include/glog/logging.h', 'include/glog/raw_logging.h', 'lib/libglog.a', 'lib/libglog.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From 748ca785787cfdd89628ab14921e08f5c180cd0e Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 27 Mar 2018 21:59:45 +0200 Subject: [PATCH 0059/5331] added ClonalFrameML-1.11-foss-2016b.eb --- .../ClonalFrameML-1.11-foss-2016b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/ClonalFrameML/ClonalFrameML-1.11-foss-2016b.eb diff --git a/easybuild/easyconfigs/c/ClonalFrameML/ClonalFrameML-1.11-foss-2016b.eb b/easybuild/easyconfigs/c/ClonalFrameML/ClonalFrameML-1.11-foss-2016b.eb new file mode 100644 index 00000000000..4cd4847239a --- /dev/null +++ b/easybuild/easyconfigs/c/ClonalFrameML/ClonalFrameML-1.11-foss-2016b.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'ClonalFrameML' +version = '1.11' + +homepage = 'https://github.com/xavierdidelot/ClonalFrameML' +description = "Efficient Inference of Recombination in Whole Bacterial Genomes" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/xavierdidelot/ClonalFrameML/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['395e2f14a93aa0b999fa152d25668b42450c712f3f4ca305b34533317e81cc84'] + +parallel = 1 + +start_dir = 'src' + +buildopts = 'all' + +files_to_copy = [(['ClonalFrameML'], 'bin'), 'cfml_results.R', 'README.txt'] + +sanity_check_paths = { + 'files': ['bin/ClonalFrameML'], + 'dirs': [] +} + +moduleclass = 'bio' From 745c03e65491569fd2b7010f991a9aaed832312c Mon Sep 17 00:00:00 2001 From: Ruben Di Battista Date: Tue, 3 Apr 2018 15:21:15 +0200 Subject: [PATCH 0060/5331] Fix name --- .../l/Lua/{Lua-5.3.4-GCC-7.2.0-2.29.eb => Lua-5.3.4-GCC-7.2.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/Lua/{Lua-5.3.4-GCC-7.2.0-2.29.eb => Lua-5.3.4-GCC-7.2.0.eb} (100%) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb similarity index 100% rename from easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0-2.29.eb rename to easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb From b4122ea1593dba9bdc4b07f5c63c7ab87ac8e4f6 Mon Sep 17 00:00:00 2001 From: Ruben Di Battista Date: Tue, 3 Apr 2018 15:21:26 +0200 Subject: [PATCH 0061/5331] Add dummy eb for Lua 5.3.4 --- easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb | 32 ++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb new file mode 100644 index 00000000000..da1c106ec07 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +buildopts = 'linux' +installopts = 'INSTALL_TOP=%(installdir)s' +skipsteps = ['configure'] + +name = "Lua" +version = "5.3.4" + +homepage = "http://www.lua.org/" +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://www.lua.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/lua"], + 'dirs': [] +} + +modextravars = { + 'LUA_DIR': '%(installdir)s', +} + +moduleclass = "lang" From d36715e9bad178c5fbf5521f7121c15889b24efb Mon Sep 17 00:00:00 2001 From: Ruben Di Battista Date: Tue, 3 Apr 2018 18:10:37 +0200 Subject: [PATCH 0062/5331] Use Lua easyblock --- easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb index c18595c8263..ec5fe7a6eba 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb @@ -1,8 +1,7 @@ -easyblock = 'ConfigureMake' +easyblock = 'Lua' buildopts = 'linux' installopts = 'INSTALL_TOP=%(installdir)s' -skipsteps = ['configure'] name = "Lua" version = "5.3.4" @@ -29,4 +28,6 @@ modextravars = { 'LUA_DIR': '%(installdir)s', } +runtest='test' + moduleclass = "lang" From e7400c6f3d4792757ea00f55b65c7bb8a6ef3f18 Mon Sep 17 00:00:00 2001 From: Ruben Di Battista Date: Tue, 3 Apr 2018 19:01:16 +0200 Subject: [PATCH 0063/5331] Fix easyblock --- easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb index ec5fe7a6eba..70ddc97853f 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'Lua' +easyblock = 'EB_Lua' buildopts = 'linux' installopts = 'INSTALL_TOP=%(installdir)s' From 5588a6137aab70616f47bfb6f2e1032d072310f4 Mon Sep 17 00:00:00 2001 From: Ruben Di Battista Date: Tue, 3 Apr 2018 19:04:31 +0200 Subject: [PATCH 0064/5331] Use Lua easyblock also for dummy --- easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb index da1c106ec07..5560e9f8422 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb @@ -1,8 +1,7 @@ -easyblock = 'ConfigureMake' +easyblock = 'EB_Lua' buildopts = 'linux' installopts = 'INSTALL_TOP=%(installdir)s' -skipsteps = ['configure'] name = "Lua" version = "5.3.4" @@ -29,4 +28,6 @@ modextravars = { 'LUA_DIR': '%(installdir)s', } +runtest='test' + moduleclass = "lang" From 401c9731438071ac86a3674a7e56ed56bf972603 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 30 Apr 2018 20:21:32 +0200 Subject: [PATCH 0065/5331] fix for AMD CPUs --- .../t/TensorFlow/TensorFlow-1.7.0-foss-2018a-Python-3.6.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0-foss-2018a-Python-3.6.4.eb index be4c5dce797..f39515e6ac1 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0-foss-2018a-Python-3.6.4.eb @@ -13,12 +13,14 @@ patches = [ 'TensorFlow-1.5.0_swig-env.patch', 'TensorFlow-1.6.0_remove-msse-hardcoding.patch', 'TensorFlow-1.6.0_lrt-flag.patch', + 'TensorFlow-%(version)s_fix_mkl-dnn.patch', ] checksums = [ 'c676a96fc8700722816b2b98c85578b2f99fac7a7b2484c9c7f0641484f8d50d', # v1.7.0.tar.gz '53807290f1acb6a0f2a84f1a0ad9f917ee131c304b3e08679f3cbd335b22c7ef', # TensorFlow-1.5.0_swig-env.patch '0ad82aab981721b1ed4881106d9accd43fe38b863ec147f6a16b278605012099', # TensorFlow-1.6.0_remove-msse-hardcoding.patch 'd8b262eea9ff94c94c90b8c51219d8f56085ccee4370525cce8beba3b2b91d38', # TensorFlow-1.6.0_lrt-flag.patch + '1badaee647107206baeb3160dcbd58bd82d27033ac0defa8d953c853b09f0f65', # TensorFlow-1.7.0_fix_mkl-dnn.patch ] builddependencies = [ From d5af3653580d35267f90bda34dfd70b6b6d51d8f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 30 Apr 2018 20:24:52 +0200 Subject: [PATCH 0066/5331] add patch --- .../TensorFlow-1.7.0_fix_mkl-dnn.patch | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0_fix_mkl-dnn.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0_fix_mkl-dnn.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0_fix_mkl-dnn.patch new file mode 100644 index 00000000000..634d891ad0e --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.7.0_fix_mkl-dnn.patch @@ -0,0 +1,21 @@ +fix error on AMD CPUs: terminate called after throwing an instance of 'Xbyak::Error' what(): internal error +author: Samuel Moors (Vrije Universiteit Brussel VUB) +diff -ur tensorflow-1.7.0.orig/tensorflow/workspace.bzl tensorflow-1.7.0/tensorflow/workspace.bzl +--- tensorflow-1.7.0.orig/tensorflow/workspace.bzl 2018-03-29 06:18:40.000000000 +0200 ++++ tensorflow-1.7.0/tensorflow/workspace.bzl 2018-04-30 16:50:44.336648345 +0200 +@@ -105,11 +105,11 @@ + tf_http_archive( + name = "mkl_dnn", + urls = [ +- "https://mirror.bazel.build/github.com/01org/mkl-dnn/archive/e0bfcaa7fcb2b1e1558f5f0676933c1db807a729.tar.gz", +- "https://github.com/01org/mkl-dnn/archive/e0bfcaa7fcb2b1e1558f5f0676933c1db807a729.tar.gz", ++ "https://mirror.bazel.build/github.com/intel/mkl-dnn/archive/v0.13.tar.gz", ++ "https://github.com/intel/mkl-dnn/archive/v0.13.tar.gz", + ], +- sha256 = "02e244f63dd95402691a361392504c143eede9a89043426f174836638a9cbf09", +- strip_prefix = "mkl-dnn-e0bfcaa7fcb2b1e1558f5f0676933c1db807a729", ++ sha256 = "d2cfd93a70cfe86ebe054477c530c9b5c1218b70f75856eb6d1956c68ee89e8f", ++ strip_prefix = "mkl-dnn-0.13", + build_file = str(Label("//third_party/mkl_dnn:mkldnn.BUILD")), + ) + From e6b06f275807336a3f99aff149b69b7830b720ef Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 16 May 2018 12:44:59 +0200 Subject: [PATCH 0067/5331] Add OPARI2 2.0.3 easyconfig (GCCcore-6.4.0) --- .../o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..12de3831d71 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2018 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.3' + +homepage = 'http://www.score-p.org' +description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, + is a source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls to + the POMP2 measurement interface.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '7e2efcfbc99152ee6e31454ef4fb747f77165691539d5d2c1df2abc4612de86c', # opari2-2.0.3.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +moduleclass = 'perf' From ab65fa86d90b1185ed4f9264c41bf37a2de9d652 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 16 May 2018 14:01:36 +0200 Subject: [PATCH 0068/5331] Add OTF2 2.1.1 easyconfig + deps (GCCcore-6.4.0) --- ...0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb | 25 ++++++++ .../o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb | 58 +++++++++++++++++++ .../SIONlib-1.7.2-GCCcore-6.4.0-tools.eb | 51 ++++++++++++++++ ...1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb | 27 +++++++++ 4 files changed, 161 insertions(+) create mode 100644 easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.2-GCCcore-6.4.0-tools.eb create mode 100644 easybuild/easyconfigs/s/Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb b/easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb new file mode 100644 index 00000000000..d12775bb5a2 --- /dev/null +++ b/easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'future' +version = '0.16.0' +versionsuffix = '-Python-%(pyver)s-bare' + +homepage = 'http://python-future.org/' +description = """ + python-future is the missing compatibility layer between Python 2 and Python 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'] + +dependencies = [('Python', '2.7.14', '-bare')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..7cb87dae0a9 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb @@ -0,0 +1,58 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2018 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '2.1.1' + +homepage = 'http://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '01591b42e76f396869ffc84672f4eaa90ee8ec2a8939755d9c0b5b8ecdcf47d3', # otf2-2.1.1.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), + # SIONlib container support (optional): + ('SIONlib', '1.7.2', '-tools'), +] + +dependencies = [ + # Python bindings (optional) + ('Python', '2.7.14', '-bare'), + ('future', '0.16.0', '-Python-2.7.14-bare'), + ('Six', '1.11.0', '-Python-2.7.14-bare'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + ('lib/libotf2.a', 'lib64/libotf2.a'), + ('lib/libotf2.%s' % SHLIB_EXT, 'lib64/libotf2.%s' % SHLIB_EXT)], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.2-GCCcore-6.4.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.2-GCCcore-6.4.0-tools.eb new file mode 100644 index 00000000000..3faf89a4302 --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.2-GCCcore-6.4.0-tools.eb @@ -0,0 +1,51 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2018 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +## + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.2' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)sl'] +sources = ['sionlib-%(version)sl.tar.gz'] +checksums = [ + '7d94fc9a285f407e4e80b49fa618a6d68c7c78dacf3ce45512bbffbbd96500ed', # sionlib-1.7.2l.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb b/easybuild/easyconfigs/s/Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb new file mode 100644 index 00000000000..ae3a207e769 --- /dev/null +++ b/easybuild/easyconfigs/s/Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Six' +version = '1.11.0' +versionsuffix = '-Python-%(pyver)s-bare' + +homepage = 'http://pypi.python.org/pypi/six/' +description = """ + Six is a Python 2 and 3 compatibility library. It provides utility functions + for smoothing over the differences between the Python versions with the goal + of writing Python code that is compatible on both Python versions. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'] + +dependencies = [('Python', '2.7.14', '-bare')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 48ae425fd1e879b502117622d0c0e45bb241f3ac Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 16 May 2018 14:12:08 +0200 Subject: [PATCH 0069/5331] Add PDT 3.25 easyconfig (GCCcore-6.4.0) --- .../p/PDT/PDT-3.25-GCCcore-6.4.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..2942a9934d1 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-6.4.0.eb @@ -0,0 +1,39 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2018 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'PDT' +version = '3.25' + +homepage = 'http://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +checksums = [ + '1037628d854edfeded3d847150d3e8fbd3774e8146407ce32f5021c80f6299be', # pdtoolkit-3.25.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), +] + +moduleclass = 'perf' From de8eeb8efe817bbc2de58ac617b2a56f9954f0e5 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 16 May 2018 14:18:33 +0200 Subject: [PATCH 0070/5331] Add CubeW 4.4 easyconfig (GCCcore-6.4.0) --- .../CubeWriter-4.4-GCCcore-6.4.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..d06bce19cf4 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb @@ -0,0 +1,56 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2018 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.4' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This component provides the Cube high-performance C writer library. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = [ + 'b1d6fecb546bc645ced430ea3fc166e85835f3b997d4e5f0dece71919fc95a99', # cubew-4.4.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + ('lib/libcube4w.a', 'lib64/libcube4w.a'), + ('lib/libcube4w.%s' % SHLIB_EXT, 'lib64/libcube4w.%s' % SHLIB_EXT)], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' From 41a83c46a07b3602f8217ff2989ed4c73ba92237 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 16 May 2018 14:28:36 +0200 Subject: [PATCH 0071/5331] Add CubeLib 4.4 easyconfig (GCCcore-6.4.0) --- .../c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..06d0a21480f --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb @@ -0,0 +1,56 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2018 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.4' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This component provides the Cube general purpose C++ library and tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '77548e1732fa5e82b13cc8465c8a21349bf42b45a382217d2e70d18576741d5c', # cubelib-4.4.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + ('lib/libcube4.a', 'lib64/libcube4.a'), + ('lib/libcube4.%s' % SHLIB_EXT, 'lib64/libcube4.%s' % SHLIB_EXT)], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' From ddfb03f704b6e0af9135070e68b255f3a96c09df Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 16 May 2018 16:37:38 +0200 Subject: [PATCH 0072/5331] Add CubeGUI 4.4 + deps easyconfigs (GCCcore-6.4.0) --- .../c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb | 54 ++++++++++++++ .../l/libGLU/libGLU-9.0.0-GCCcore-6.4.0.eb | 30 ++++++++ ...-1.0.7-GCCcore-6.4.0-Python-2.7.14-bare.eb | 33 +++++++++ .../m/Mesa/Mesa-17.3.6-GCCcore-6.4.0.eb | 74 +++++++++++++++++++ .../q/Qt5/Qt5-5.10.1-GCCcore-6.4.0.eb | 34 +++++++++ ...39.1.0-GCCcore-6.4.0-Python-2.7.14-bare.eb | 33 +++++++++ 6 files changed, 258 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-6.4.0-Python-2.7.14-bare.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-39.1.0-GCCcore-6.4.0-Python-2.7.14-bare.eb diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..9a8745cb7fc --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb @@ -0,0 +1,54 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2018 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeGUI' +version = '4.4' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube graphical report explorer. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '0620bae3ac357d0486ce7f5f97e448eeb2494c9a31865b679380ee08c6750e70', # cubegui-4.4.tar.gz +] + +dependencies = [ + ('CubeLib', '4.4'), + ('Qt5', '5.10.1'), +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['bin/cube', 'bin/cubegui-config', + ('lib/libcube4gui.a', 'lib64/libcube4gui.a'), + ('lib/libcube4gui.%s' % SHLIB_EXT, 'lib64/libcube4gui.%s' % SHLIB_EXT)], + 'dirs': ['include/cubegui', 'lib/cube-plugins'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..135a591a322 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-6.4.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] +checksums = ['1f7ad0d379a722fcbd303aa5650c6d7d5544fde83196b42a73d1193568a4df12'] + +dependencies = [ + ('Mesa', '17.3.6'), +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-6.4.0-Python-2.7.14-bare.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-6.4.0-Python-2.7.14-bare.eb new file mode 100644 index 00000000000..45ff68131ce --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-6.4.0-Python-2.7.14-bare.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.7' +versionsuffix = '-Python-%(pyver)s-bare' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + '4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae', # Mako-1.0.7.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), +] + +dependencies = [ + ('Python', '2.7.14', '-bare'), + ('setuptools', '39.1.0', '-Python-2.7.14-bare'), +] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..9a0af02523b --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-GCCcore-6.4.0.eb @@ -0,0 +1,74 @@ +# Automatically converted from Mesa-17.2.4-intel-2017b.eb +# Original message: +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '17.3.6' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. +toolchainopts = {'optarch': False} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] +sources = [SOURCELOWER_TAR_XZ] +patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] +checksums = [ + 'e5915680d44ac9d05defdec529db7459ac9edd441c9845266eff2e2d3e57fbf8', # mesa-17.3.6.tar.xz + '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.3.6_fix-strip-llvm-flags.patch +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('Autotools', '20170619'), + ('pkg-config', '0.29.2'), + ('Mako', '1.0.7', '-Python-2.7.14-bare'), + ('libxml2', '2.9.7'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('nettle', '3.4'), + ('libdrm', '2.4.91'), + ('LLVM', '5.0.1'), + ('X11', '20180131'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..b5f1ad5b5a5 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-GCCcore-6.4.0.eb @@ -0,0 +1,34 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.10.1' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +checksums = ['05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a'] + +dependencies = [ + ('GLib', '2.54.3'), + ('libpng', '1.6.34'), + ('X11', '20180131'), + ('libGLU', '9.0.0'), +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), + ('pkg-config', '0.29.2'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-39.1.0-GCCcore-6.4.0-Python-2.7.14-bare.eb b/easybuild/easyconfigs/s/setuptools/setuptools-39.1.0-GCCcore-6.4.0-Python-2.7.14-bare.eb new file mode 100644 index 00000000000..ac33003e7ae --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools/setuptools-39.1.0-GCCcore-6.4.0-Python-2.7.14-bare.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'setuptools' +version = '39.1.0' +versionsuffix = '-Python-%(pyver)s-bare' + +homepage = 'http://pypi.python.org/pypi/setuptools/' +description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] +checksums = [ + 'c5484e13b89927b44fd15897f7ce19dded8e7f035466a4fa7b946c0bdd86edd7', # setuptools-39.1.0.zip +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), +] + +dependencies = [ + ('Python', '2.7.14', '-bare'), +] + +sanity_check_paths = { + 'files': ['bin/easy_install', + 'lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': [], +} + +moduleclass = 'devel' From a7b46c7458ffe1056a0a82ff7101f690972c1d81 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 16 May 2018 16:38:14 +0200 Subject: [PATCH 0073/5331] Cleanup --- .../easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb | 3 ++- .../c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb | 2 +- .../future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb | 9 ++++++++- .../easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb | 10 ++++++---- .../Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb | 9 ++++++++- 5 files changed, 25 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb index 06d0a21480f..cd5e804916a 100644 --- a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb @@ -23,7 +23,8 @@ description = """ non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. - This component provides the Cube general purpose C++ library and tools. + This module provides the Cube general purpose C++ library component and + command-line tools. """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb index d06bce19cf4..31c04d8f44e 100644 --- a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb @@ -23,7 +23,7 @@ description = """ non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. - This component provides the Cube high-performance C writer library. + This module provides the Cube high-performance C writer library component. """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb b/easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb index d12775bb5a2..9553a94e0a0 100644 --- a/easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb +++ b/easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb @@ -13,7 +13,14 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'] +checksums = [ + 'e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb', # future-0.16.0.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), +] dependencies = [('Python', '2.7.14', '-bare')] diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb index 12de3831d71..b1d0a5dbcdc 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb @@ -16,10 +16,12 @@ name = 'OPARI2' version = '2.0.3' homepage = 'http://www.score-p.org' -description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, - is a source-to-source instrumentation tool for OpenMP and hybrid codes. - It surrounds OpenMP directives and runtime library calls with calls to - the POMP2 measurement interface.""" +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} diff --git a/easybuild/easyconfigs/s/Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb b/easybuild/easyconfigs/s/Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb index ae3a207e769..3b0fabce728 100644 --- a/easybuild/easyconfigs/s/Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb +++ b/easybuild/easyconfigs/s/Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb @@ -15,7 +15,14 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'] +checksums = [ + '70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9', # six-1.11.0.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.28'), +] dependencies = [('Python', '2.7.14', '-bare')] From c8175e36785b898e2f42c7e3e8b1275a5a605435 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 16 May 2018 16:43:29 +0200 Subject: [PATCH 0074/5331] Add Cube 4.4 bundle easyconfig (GCCcore-6.4.0) --- .../c/Cube/Cube-4.4-GCCcore-6.4.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cube/Cube-4.4-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/Cube/Cube-4.4-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..5e0a4c3961a --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.4-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2018 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'Bundle' + +name = 'Cube' +version = '4.4' + +homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides a convenience bundle comprised of the Cube + high-performance C writer library, the general purpose C++ library and + command-line tools, and the graphical report explorer. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +dependencies = [ + ('CubeWriter', '4.4'), + ('CubeLib', '4.4'), + ('CubeGUI', '4.4'), +] + +moduleclass = 'perf' From 8c7d1f9fc26a1232af32287d3b19d8d7af1dbe8b Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 17 May 2018 14:00:55 +0200 Subject: [PATCH 0075/5331] Renamed package `Six` to `six` as requested --- easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb | 2 +- .../six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb} | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/s/{Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb => six/six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb} (95%) diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb index 7cb87dae0a9..cce8a8c3fd3 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb @@ -41,7 +41,7 @@ dependencies = [ # Python bindings (optional) ('Python', '2.7.14', '-bare'), ('future', '0.16.0', '-Python-2.7.14-bare'), - ('Six', '1.11.0', '-Python-2.7.14-bare'), + ('six', '1.11.0', '-Python-2.7.14-bare'), ] configopts = '--enable-shared' diff --git a/easybuild/easyconfigs/s/Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb b/easybuild/easyconfigs/s/six/six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb similarity index 95% rename from easybuild/easyconfigs/s/Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb rename to easybuild/easyconfigs/s/six/six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb index 3b0fabce728..5ae72ef53ab 100644 --- a/easybuild/easyconfigs/s/Six/Six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb +++ b/easybuild/easyconfigs/s/six/six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'Six' +name = 'six' version = '1.11.0' versionsuffix = '-Python-%(pyver)s-bare' @@ -14,7 +14,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] checksums = [ '70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9', # six-1.11.0.tar.gz ] From 760d196025e8eb3e273acdbf2ef7e5c962dd8b77 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 17 May 2018 16:47:22 +0200 Subject: [PATCH 0076/5331] Don't try to build OTF2 Python bindings; it has to be done in a different way --- ...0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb | 32 ----------------- .../o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb | 11 +----- ...1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb | 34 ------------------- 3 files changed, 1 insertion(+), 76 deletions(-) delete mode 100644 easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb delete mode 100644 easybuild/easyconfigs/s/six/six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb b/easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb deleted file mode 100644 index 9553a94e0a0..00000000000 --- a/easybuild/easyconfigs/f/future/future-0.16.0-GCCcore-6.4.0-Python-2.7.14-bare.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'future' -version = '0.16.0' -versionsuffix = '-Python-%(pyver)s-bare' - -homepage = 'http://python-future.org/' -description = """ - python-future is the missing compatibility layer between Python 2 and Python 3. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = [ - 'e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb', # future-0.16.0.tar.gz -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), -] - -dependencies = [('Python', '2.7.14', '-bare')] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb index cce8a8c3fd3..82e53e6dcc0 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb @@ -37,22 +37,13 @@ builddependencies = [ ('SIONlib', '1.7.2', '-tools'), ] -dependencies = [ - # Python bindings (optional) - ('Python', '2.7.14', '-bare'), - ('future', '0.16.0', '-Python-2.7.14-bare'), - ('six', '1.11.0', '-Python-2.7.14-bare'), -] - configopts = '--enable-shared' sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', ('lib/libotf2.a', 'lib64/libotf2.a'), ('lib/libotf2.%s' % SHLIB_EXT, 'lib64/libotf2.%s' % SHLIB_EXT)], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], + 'dirs': [], } -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/six/six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb b/easybuild/easyconfigs/s/six/six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb deleted file mode 100644 index 5ae72ef53ab..00000000000 --- a/easybuild/easyconfigs/s/six/six-1.11.0-GCCcore-6.4.0-Python-2.7.14-bare.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'six' -version = '1.11.0' -versionsuffix = '-Python-%(pyver)s-bare' - -homepage = 'http://pypi.python.org/pypi/six/' -description = """ - Six is a Python 2 and 3 compatibility library. It provides utility functions - for smoothing over the differences between the Python versions with the goal - of writing Python code that is compatible on both Python versions. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = [ - '70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9', # six-1.11.0.tar.gz -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), -] - -dependencies = [('Python', '2.7.14', '-bare')] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'lib' From e70b39e3f109eb4d46689a6f41a7ac316de567fc Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 18 May 2018 10:22:35 +0200 Subject: [PATCH 0077/5331] Make CubeLib a build dependency of CubeGUI; it's properly rpath'ed --- .../easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb index 9a8745cb7fc..391ad730c4a 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb @@ -34,14 +34,14 @@ checksums = [ '0620bae3ac357d0486ce7f5f97e448eeb2494c9a31865b679380ee08c6750e70', # cubegui-4.4.tar.gz ] -dependencies = [ - ('CubeLib', '4.4'), - ('Qt5', '5.10.1'), -] - builddependencies = [ # use same binutils version that was used when building GCCcore ('binutils', '2.28'), + ('CubeLib', '4.4'), +] + +dependencies = [ + ('Qt5', '5.10.1'), ] sanity_check_paths = { From b95dc598ee35f3de3b51706942f64cddd9830ec9 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 18 May 2018 11:05:06 +0200 Subject: [PATCH 0078/5331] Add Score-P 4.0 easyconfig (gompi-2018a) --- .../s/Score-P/Score-P-4.0-gompi-2018a.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-4.0-gompi-2018a.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-4.0-gompi-2018a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-4.0-gompi-2018a.eb new file mode 100644 index 00000000000..3e5c793655c --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-4.0-gompi-2018a.eb @@ -0,0 +1,62 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2018 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Score-P' +version = '4.0' + +homepage = 'http://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2018a'} + +source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = [ + 'c050525606965950ad9b35c14077b88571bcf9bfca08599279a3d8d1bb00e655', # scorep-4.0.tar.gz +] + +builddependencies = [ + ('CubeLib', '4.4'), + ('CubeWriter', '4.4'), + # Unwinding/sampling support (optional): + ('libunwind', '1.2.1'), +] + +dependencies = [ + # binutils is implicitly available via GCC toolchain + # ('binutils', '2.28'), + ('OPARI2', '2.0.3'), + ('OTF2', '2.1.1'), + # Hardware counter support (optional): + ('PAPI', '5.5.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/scorep', 'include/scorep/SCOREP_User.h', + ('lib/libscorep_adapter_mpi_event.a', 'lib64/libscorep_adapter_mpi_event.a'), + ('lib/libscorep_adapter_mpi_event.%s' % SHLIB_EXT, 'lib64/libscorep_adapter_mpi_event.%s' % SHLIB_EXT)], + 'dirs': [], +} + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From e3873b12b0d4d5e19b6b91b96d6a8c4fc20bc004 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 18 May 2018 11:28:49 +0200 Subject: [PATCH 0079/5331] Add Scalasca 2.4 easyconfig (gompi-2018a) --- .../s/Scalasca/Scalasca-2.4-gompi-2018a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalasca/Scalasca-2.4-gompi-2018a.eb diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.4-gompi-2018a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.4-gompi-2018a.eb new file mode 100644 index 00000000000..016bd7a4273 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.4-gompi-2018a.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2018 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Scalasca' +version = '2.4' + +homepage = 'http://www.scalasca.org/' +description = """ + Scalasca is a software tool that supports the performance optimization of + parallel programs by measuring and analyzing their runtime behavior. The + analysis identifies potential performance bottlenecks -- in particular + those concerning communication and synchronization -- and offers guidance + in exploring their causes. +""" + +toolchain = {'name': 'gompi', 'version': '2018a'} + +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '4a895868258030f700a635eac93d36764f60c8c63673c7db419ea4bcc6b0b760', # scalasca-2.4.tar.gz +] + +builddependencies = [ + ('CubeWriter', '4.4'), +] + +dependencies = [ + ('CubeGUI', '4.4'), + ('CubeLib', '4.4'), + ('OTF2', '2.1.1'), + ('Score-P', '4.0'), +] + +sanity_check_paths = { + 'files': ['bin/scalasca', ('lib/libpearl.replay.a', 'lib64/libpearl.replay.a')], + 'dirs': [], +} + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scalasca/patterns'} + +moduleclass = 'perf' From c4a25ccd90bebe245f0085f39cac8f00399febf5 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 May 2018 22:35:07 +0200 Subject: [PATCH 0080/5331] fixed conflict with develop --- .../GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb index 9aee9ea1643..614806b791d 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.53.5-intel-2017b-Python-2.7.14.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['b8271d3e3e3044289d06e824605a53b2518593bc2b071db6c90485c837ff437d'] dependencies = [ ('Python', '2.7.14'), @@ -27,6 +28,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), ('cairo', '1.14.10'), + ('pkg-config', '0.29.2'), ] preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " From 630455108636989219643ec21dbf49796dfd025a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Sat, 2 Jun 2018 13:43:57 +0200 Subject: [PATCH 0081/5331] Python 2.7 as buildep for dbus-glib --- .../easyconfigs/d/dbus-glib/dbus-glib-0.110-intel-2017b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-intel-2017b.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-intel-2017b.eb index f9e311ef566..d7be0dd8d49 100644 --- a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-intel-2017b.eb +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-intel-2017b.eb @@ -12,6 +12,10 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] sources = [SOURCE_TAR_GZ] checksums = ['7ce4760cf66c69148f6bd6c92feaabb8812dee30846b24cd0f7395c436d7e825'] +# DBus' dbus-binding-tool needs Python 2.7. Adding Python to DBus as dependency +# would cause lots of conflicts, so Python 2.7 is here added as builddep. +builddependencies = [('Python', '2.7.14', '-bare')] + dependencies = [ ('GLib', '2.53.5'), ('DBus', '1.13.0'), From 153aa4b9fe352bbdd576a3e4adec3d1fad05aeee Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 8 Jun 2018 09:00:55 +0200 Subject: [PATCH 0082/5331] First eb file for libutempter v1.1.6 --- .../libutempter-1.1.6.2-GCC-6.4.0-2.28.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..5a9f46496e9 --- /dev/null +++ b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libutempter' +version = '1.1.6.2' + +homepage = 'http://git.altlinux.org/people/ldv/packages/?p=libutempter.git' +description = """libutempter is library that provides an interface for terminal + emulators such as screen and xterm to record user sessions to utmp and wtmp files.""" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = [ + 'http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h=' + + version[0:5] + '-alt' + version[6:7] + ';sf=tgz'] +sources = [{ + 'filename': '%s-%s-alt%s.tar.gz' % (name, version[0:5], version[6:7]), + 'extract_cmd': "tar xfvz %s --strip 1", +}] + +checksums = ['b7e55b666c575d8f2d294c82655b6af21f0c7339625ba6707e5edc2883a2b09a'] + +skipsteps = ['configure'] + +preinstallopts = 'sed -i "s#/usr##g" Makefile && ' + +installopts = 'DESTDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['include/utempter.h', 'lib/libutempter.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib', 'share/man/man3'], +} + +moduleclass = 'devel' From 264bc6c29383c29142dbca3e5161ad1e1533f89e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 18 Jun 2018 18:36:44 +0200 Subject: [PATCH 0083/5331] Style improvements for libutempter v1.1.6.2 for GCC/6.4.0-2.28 --- .../l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb index 5a9f46496e9..e3eb1409e77 100644 --- a/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb @@ -10,8 +10,8 @@ description = """libutempter is library that provides an interface for terminal toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = [ - 'http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h=' - + version[0:5] + '-alt' + version[6:7] + ';sf=tgz'] + 'http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h=' + + version[0:5] + '-alt' + version[6:7] + ';sf=tgz'] sources = [{ 'filename': '%s-%s-alt%s.tar.gz' % (name, version[0:5], version[6:7]), 'extract_cmd': "tar xfvz %s --strip 1", From f0c71db11d301cdf685d4d8566ec2a3f56a040bc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 20 Jun 2018 16:47:04 +0200 Subject: [PATCH 0084/5331] PyCUDA v2017.1.1 for intel/2018a and Python/2.7.14 --- .../Boost-1.67.0-intel-2018a-Python-2.7.14.eb | 24 ++++++++++++++ ...CUDA-2017.1.1-intel-2018a-Python-2.7.14.eb | 32 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.67.0-intel-2018a-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.67.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/b/Boost/Boost-1.67.0-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..6fc6f19b3c6 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.67.0-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,24 @@ +name = 'Boost' +version = '1.67.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8aa4e330c870ef50a896634c931adf468b21f8a69b77007e45c444151229f665'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.14'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..c7cc9b57b85 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'PyCUDA' +version = '2017.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mathema.tician.de/software/pycuda' +description = """PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6b5a9384e38c603ee429f8a6bee424532db7b3505027ce22f7e18ad19564b563'] + +dependencies = [ + ('Python', '2.7.14'), + ('CUDA', '9.1.85', '', True), + ('Boost', '1.67.0', versionsuffix), +] + +prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " +prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python27 && " + +options = {'modulename': '%(namelower)s'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lang' From 2277caede61c10c5829e8a2ca17760caa1e7c69b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 22 Jun 2018 11:12:59 +0200 Subject: [PATCH 0085/5331] Use Boost v1.66 with PyCUDA v2017.1.1 and intel/2018a --- .../p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb index c7cc9b57b85..50f46f90bca 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb @@ -16,11 +16,11 @@ checksums = ['6b5a9384e38c603ee429f8a6bee424532db7b3505027ce22f7e18ad19564b563'] dependencies = [ ('Python', '2.7.14'), ('CUDA', '9.1.85', '', True), - ('Boost', '1.67.0', versionsuffix), + ('Boost', '1.66.0', versionsuffix), ] prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " -prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python27 && " +prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " options = {'modulename': '%(namelower)s'} From 5475c5a0f880025fc25131ef681dda48d9b99ee8 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 22 Jun 2018 16:34:44 +0200 Subject: [PATCH 0086/5331] Remove Boost v1.67 for intel/2018a --- .../Boost-1.67.0-intel-2018a-Python-2.7.14.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.67.0-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.67.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/b/Boost/Boost-1.67.0-intel-2018a-Python-2.7.14.eb deleted file mode 100644 index 6fc6f19b3c6..00000000000 --- a/easybuild/easyconfigs/b/Boost/Boost-1.67.0-intel-2018a-Python-2.7.14.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'Boost' -version = '1.67.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.boost.org/' -description = """Boost provides free peer-reviewed portable C++ source libraries.""" - -toolchain = {'name': 'intel', 'version': '2018a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['8aa4e330c870ef50a896634c931adf468b21f8a69b77007e45c444151229f665'] - -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.11'), - ('Python', '2.7.14'), -] - -# also build boost_mpi -boost_mpi = True - -moduleclass = 'devel' From d8e4a802003aea9aef7b155accfdd0567a7a6d41 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Thu, 12 Jul 2018 09:26:24 +0200 Subject: [PATCH 0087/5331] adding easyconfigs: buildenv-default-foss-2017b.eb --- .../b/buildenv/buildenv-default-foss-2017b.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2017b.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2017b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2017b.eb new file mode 100644 index 00000000000..906ab864332 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2017b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2017b'} + +moduleclass = 'devel' From bbcf57bd565a87630394883a51c41a8570a319f5 Mon Sep 17 00:00:00 2001 From: crubb Date: Sun, 2 Sep 2018 08:29:08 +0000 Subject: [PATCH 0088/5331] Add ownCloud-2.4.3 and QtKeychain-0.9.1; update dependencies --- .../GLib-2.54.3-foss-2018b-Python-3.6.6.eb | 43 +++++++++++++++++++ .../o/ownCloud/ownCloud-2.4.3-foss-2018b.eb | 35 +++++++++++++++ .../q/Qt5/Qt5-5.11.1-foss-2018b.eb | 30 +++++++++++++ .../QtKeychain/QtKeychain-0.9.1-foss-2018b.eb | 30 +++++++++++++ 4 files changed, 138 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.54.3-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/o/ownCloud/ownCloud-2.4.3-foss-2018b.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.11.1-foss-2018b.eb create mode 100644 easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.9.1-foss-2018b.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.54.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GLib/GLib-2.54.3-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..3926f2002fd --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.54.3-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'GLib' +version = '2.54.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['963fdc6685dc3da8e5381dfb9f15ca4b5709b28be84d9d05a9bb8e446abac0a8'] + +builddependencies = [ + ('binutils', '2.30'), + ('util-linux', '2.32'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.8.1'), + ('libxml2', '2.9.8'), + ('PCRE', '8.41'), + ('Python', '3.6.6'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " +configopts += "--enable-static --enable-shared" + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/ownCloud/ownCloud-2.4.3-foss-2018b.eb b/easybuild/easyconfigs/o/ownCloud/ownCloud-2.4.3-foss-2018b.eb new file mode 100644 index 00000000000..77134200383 --- /dev/null +++ b/easybuild/easyconfigs/o/ownCloud/ownCloud-2.4.3-foss-2018b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'ownCloud' +version = '2.4.3' + +homepage = 'https://github.com/owncloud/client' +description = """The ownCloud Desktop Client is a tool to synchronize files from ownCloud Server with your computer.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/owncloud/client/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6dc25bc790d4de82207dde13035e856c8932c8aec59fe8aa114af946fafe6530'] + +builddependencies = [ + ('CMake', '3.11.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('SQLite', '3.24.0'), + ('QtKeychain', '0.9.1'), + ('Qt5', '5.11.1'), +] + +configopts = "-DCMAKE_INSTALL_LIBDIR=lib/ " +configopts += "-DNO_SHIBBOLETH:BOOL=ON " + +sanity_check_paths = { + 'files': ['bin/owncloud', 'bin/owncloudcmd', 'lib/libowncloudsync.%s' % SHLIB_EXT], + 'dirs': [''], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.11.1-foss-2018b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.11.1-foss-2018b.eb new file mode 100644 index 00000000000..fc6e6050f4d --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.11.1-foss-2018b.eb @@ -0,0 +1,30 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.11.1' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +checksums = ['39602cb08f9c96867910c375d783eed00fc4a244bffaa93b801225d17950fb2b'] + +builddependencies = [('pkg-config', '0.29.2')] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +dependencies = [ + ('GLib', '2.54.3'), + ('libpng', '1.6.34'), + ('X11', '20180604'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.9.1-foss-2018b.eb b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.9.1-foss-2018b.eb new file mode 100644 index 00000000000..95b0d7a904d --- /dev/null +++ b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.9.1-foss-2018b.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'QtKeychain' +version = '0.9.1' + +homepage = 'https://github.com/frankosterfeld/qtkeychain' +description = "Platform-independent Qt API for storing passwords securely." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/frankosterfeld/qtkeychain/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9c2762d9d0759a65cdb80106d547db83c6e9fdea66f1973c6e9014f867c6f28e'] + +builddependencies = [ + ('CMake', '3.11.4'), +] + +dependencies = [ + ('Qt5', '5.11.1'), +] + +configopts = "-DCMAKE_INSTALL_LIBDIR=lib/ " + +sanity_check_paths = { + 'files': ['lib/libqt5keychain.%s' % SHLIB_EXT], + 'dirs': [''], +} + +moduleclass = 'tools' From bd80117eea7148eec6cc2ba21f5a2cdfde9ff410 Mon Sep 17 00:00:00 2001 From: crubb Date: Sat, 8 Sep 2018 09:47:11 +0000 Subject: [PATCH 0089/5331] Depend on Qt5-5.10.1 instead of Qt5-5.11.1 --- .../GLib-2.54.3-foss-2018b-Python-3.6.6.eb | 43 ------------------- .../o/ownCloud/ownCloud-2.4.3-foss-2018b.eb | 2 +- .../q/Qt5/Qt5-5.11.1-foss-2018b.eb | 30 ------------- .../QtKeychain/QtKeychain-0.9.1-foss-2018b.eb | 2 +- 4 files changed, 2 insertions(+), 75 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.54.3-foss-2018b-Python-3.6.6.eb delete mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.11.1-foss-2018b.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.54.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GLib/GLib-2.54.3-foss-2018b-Python-3.6.6.eb deleted file mode 100644 index 3926f2002fd..00000000000 --- a/easybuild/easyconfigs/g/GLib/GLib-2.54.3-foss-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GLib' -version = '2.54.3' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.gtk.org/' -description = """GLib is one of the base libraries of the GTK+ project""" - -toolchain = {'name': 'foss', 'version': '2018b'} -toolchainopts = {'pic': True} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['963fdc6685dc3da8e5381dfb9f15ca4b5709b28be84d9d05a9bb8e446abac0a8'] - -builddependencies = [ - ('binutils', '2.30'), - ('util-linux', '2.32'), - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('libffi', '3.2.1'), - ('gettext', '0.19.8.1'), - ('libxml2', '2.9.8'), - ('PCRE', '8.41'), - ('Python', '3.6.6'), -] - -# avoid using hardcoded path to Python binary in build step -preconfigopts = "export PYTHON=python && " - -configopts = "--disable-maintainer-mode --disable-silent-rules --disable-libelf --disable-systemtap " -configopts += "--enable-static --enable-shared" - -postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] - -sanity_check_paths = { - 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/ownCloud/ownCloud-2.4.3-foss-2018b.eb b/easybuild/easyconfigs/o/ownCloud/ownCloud-2.4.3-foss-2018b.eb index 77134200383..6dc2e12b126 100644 --- a/easybuild/easyconfigs/o/ownCloud/ownCloud-2.4.3-foss-2018b.eb +++ b/easybuild/easyconfigs/o/ownCloud/ownCloud-2.4.3-foss-2018b.eb @@ -21,7 +21,7 @@ dependencies = [ ('zlib', '1.2.11'), ('SQLite', '3.24.0'), ('QtKeychain', '0.9.1'), - ('Qt5', '5.11.1'), + ('Qt5', '5.10.1'), ] configopts = "-DCMAKE_INSTALL_LIBDIR=lib/ " diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.11.1-foss-2018b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.11.1-foss-2018b.eb deleted file mode 100644 index fc6e6050f4d..00000000000 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.11.1-foss-2018b.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'EB_Qt' - -name = 'Qt5' -version = '5.11.1' - -homepage = 'http://qt.io/' -description = "Qt is a comprehensive cross-platform C++ application framework." - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = [ - 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', - 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' -] -sources = ['qt-everywhere-src-%(version)s.tar.xz'] -checksums = ['39602cb08f9c96867910c375d783eed00fc4a244bffaa93b801225d17950fb2b'] - -builddependencies = [('pkg-config', '0.29.2')] - -# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) -configopts = '-skip qtgamepad' - -dependencies = [ - ('GLib', '2.54.3'), - ('libpng', '1.6.34'), - ('X11', '20180604'), - ('libGLU', '9.0.0'), -] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.9.1-foss-2018b.eb b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.9.1-foss-2018b.eb index 95b0d7a904d..3810181302b 100644 --- a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.9.1-foss-2018b.eb +++ b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.9.1-foss-2018b.eb @@ -17,7 +17,7 @@ builddependencies = [ ] dependencies = [ - ('Qt5', '5.11.1'), + ('Qt5', '5.10.1'), ] configopts = "-DCMAKE_INSTALL_LIBDIR=lib/ " From 5df37af2dcac633970336b009903731ea76951dd Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 10 Sep 2018 10:32:10 +0200 Subject: [PATCH 0090/5331] Add manual download link for libutempter v1.1.6.2 [GCC/6.4.0-2.28] --- .../l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb index e3eb1409e77..639b634539e 100644 --- a/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb @@ -9,9 +9,10 @@ description = """libutempter is library that provides an interface for terminal toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} -source_urls = [ - 'http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h=' + - version[0:5] + '-alt' + version[6:7] + ';sf=tgz'] +# Download link: http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h=1.1.6-alt2;sf=tgz +# source_urls = [ +# 'http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h='; + +# version[0:5] + '-alt' + version[6:7] + ';sf=tgz'] sources = [{ 'filename': '%s-%s-alt%s.tar.gz' % (name, version[0:5], version[6:7]), 'extract_cmd': "tar xfvz %s --strip 1", From 7d9ac8010b8d9817375ab2168e906dc60180b91f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 17 Sep 2018 10:13:16 +0200 Subject: [PATCH 0091/5331] Update manual download instructions for libutempter v1.1.6.2 [GCC/6.4.0-2.28] --- .../l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb index 639b634539e..e198858862b 100644 --- a/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb @@ -9,12 +9,10 @@ description = """libutempter is library that provides an interface for terminal toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} -# Download link: http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h=1.1.6-alt2;sf=tgz -# source_urls = [ -# 'http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h='; + -# version[0:5] + '-alt' + version[6:7] + ';sf=tgz'] +# download via http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h=1.1.6-alt2;sf=tgz +# and rename libutempter-1.1.6-alt2-3c6e555.tar.gz to libutempter-1.1.6.2.tar.gz sources = [{ - 'filename': '%s-%s-alt%s.tar.gz' % (name, version[0:5], version[6:7]), + 'filename': SOURCE_TAR_GZ, 'extract_cmd': "tar xfvz %s --strip 1", }] From 2c9d073f94eac0a04ae10e786f07770a3abae0b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Sep 2018 13:26:18 +0200 Subject: [PATCH 0092/5331] adding easyconfigs: Seurat-2.3.4-foss-2018b-R-3.5.1.eb --- .../Seurat/Seurat-2.3.4-foss-2018b-R-3.5.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-2.3.4-foss-2018b-R-3.5.1.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-2.3.4-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-2.3.4-foss-2018b-R-3.5.1.eb new file mode 100644 index 00000000000..603c4bd2db1 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-2.3.4-foss-2018b-R-3.5.1.eb @@ -0,0 +1,26 @@ +easyblock = 'RPackage' + +name = 'Seurat' +version = '2.3.4' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [('R', '3.5.1')] + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['%(name)s_%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 278dd6e8db0dc33d6658609a6f96ba8058e79ab1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Sep 2018 15:30:22 +0200 Subject: [PATCH 0093/5331] add missing checksum for Seurat --- .../easyconfigs/s/Seurat/Seurat-2.3.4-foss-2018b-R-3.5.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-2.3.4-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-2.3.4-foss-2018b-R-3.5.1.eb index 603c4bd2db1..73a2c7d8dfd 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-2.3.4-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-2.3.4-foss-2018b-R-3.5.1.eb @@ -17,6 +17,7 @@ source_urls = [ 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ] sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['0d0a92c8ecc7beebddbefbcc4d845cb1c66b7005416d9b6335e27f9b22d90b51'] sanity_check_paths = { 'files': [], From f43064ed5ced5db5f5b9f076091da6c5fcb0e387 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 7 Oct 2018 13:11:29 +0200 Subject: [PATCH 0094/5331] adding easyconfigs: Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb, Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb, Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb and patches: Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch --- ...use_FFTW_FFT_instead_of_PUBFFT_part2.patch | 16 ++++ ...ss-2018b-AmberTools-17-patchlevel-10-15.eb | 84 ++++++++++++++++++ ...da-2018b-AmberTools-17-patchlevel-10-15.eb | 88 +++++++++++++++++++ ...el-2018b-AmberTools-17-patchlevel-10-15.eb | 81 +++++++++++++++++ .../netCDF-Fortran-4.4.4-fosscuda-2018b.eb | 18 ++++ .../n/netCDF/netCDF-4.6.1-fosscuda-2018b.eb | 34 +++++++ 6 files changed, 321 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-fosscuda-2018b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.6.1-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch new file mode 100644 index 00000000000..b319066796c --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch @@ -0,0 +1,16 @@ +Use FFTW_FFT with FFTW3 instead of PUBFFT for pmemd. +This fixes linking with FFTW3 as opposed to using MKL. + +Åke Sandgren, 20181006 +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2018-10-06 19:30:27.186868451 +0200 +@@ -3765,7 +3765,7 @@ + PMEMD_FOPTFLAGS=$pmemd_foptflags \$(AMBERBUILDFLAGS) + PMEMD_CC=$cc + PMEMD_COPTFLAGS=$pmemd_coptflags $mpi_flag \$(AMBERBUILDFLAGS) +-PMEMD_FLIBSF=$flibs_mkl $win_mpilibs $emillib ++PMEMD_FLIBSF=$flibs_mkl $win_mpilibs $emillib $flibs_fftw3 + PMEMD_LD=$ld \$(AMBERBUILDFLAGS) + LDOUT=$ldout + PMEMD_GNU_BUG303=$pmemd_gnu_bug303 diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb new file mode 100644 index 00000000000..777748a7e36 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb @@ -0,0 +1,84 @@ +name = 'Amber' +version = '16' +ambertools_ver = '17' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (10, 15) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] +patches = [ + 'Amber-%%(version)s-AT-%s_fix-hardcoding.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_intel_mpi_compiler_version_detection.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_mkl_include_path.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_fftw_from_mkl_or_external.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_FFTW_FFT_instead_of_PUBFFT.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_sander_link_with_external_fftw.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix-cpptraj-dont-use-static.patch' % ambertools_ver, + # Must come after fix-cpptraj-dont-use-static.patch + 'Amber-%%(version)s-AT-%s_cpptraj_use_mkl_fft.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_incorrect_omp_directive_rism.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_openmp_at_link.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_CUSTOMBUILDFLAGS_for_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_do_parallel_in_checkrismunsupported.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_fixed_size_cmd_in_nab.patch' % ambertools_ver, + 'Amber-%(version)s-fix_missing_build_target.patch', + 'Amber-%(version)s-dont_use_ipo.patch', + 'Amber-%%(version)s-AT-%s_use_FFTW_FFT_instead_of_PUBFFT_part2.patch' % ambertools_ver, +] +checksums = [ + '3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d', # Amber16.tar.bz2 + '4fbb2cf57d27422949909cc6f7e434c9855333366196a1d539264617c8bc5dec', # AmberTools17.tar.bz2 + '5bf43acaa720815640e54f0872e119dd33bb223e7e1c2f01b459b86efc71ae6e', # Amber-16-AT-17_fix-hardcoding.patch + # Amber-16-AT-17-fix_intel_mpi_compiler_version_detection.patch + '43e79b40388caa2bc14f80acbe72e520b245459dde519d528c07928909dd3c08', + '35fc82573ede194d11090f1df8fdef36d681bf78d2107a495e57a7f1d5ca0b69', # Amber-16-AT-17-fix_mkl_include_path.patch + # Amber-16-AT-17-use_fftw_from_mkl_or_external.patch + '645f4ec6aacfc316c97f936d6549d91d1664b915ab7311c00c5c4591787753af', + # Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch + '8a377c87f95756bb072664a77d417eec66912872c4c02e354f4068104ee2a51c', + # Amber-16-AT-17-fix_sander_link_with_external_fftw.patch + '092d70bec83b4383fd2722095026e069acac0f6bf57a9ac8ae030fe537bc64f9', + # Amber-16-AT-17-fix-cpptraj-dont-use-static.patch + '9ae4d6ac172d30a9b3a48992ad4217e8e21336c94107ae2435850c0f77dc0993', + '17bb30c77e204c57cfb6e78f0a7a70994df206d6309f425d83ca0a026323b955', # Amber-16-AT-17_cpptraj_use_mkl_fft.patch + # Amber-16-AT-17-fix_incorrect_omp_directive_rism.patch + '46455dd23f93bdb657f27edc9f92fad503f12048184b926711ee41a6f28b916c', + # Amber-16-AT-17-fix_missing_openmp_at_link.patch + '2116f52b5051eb07cfe74fe5bd751e237d1792c248dc0e5a204a19aea25ed337', + # Amber-16-AT-17-use_CUSTOMBUILDFLAGS_for_nab.patch + '5de8b3e93bd1b36c5d57b64089fc40f14b00c6503fdc7437a005d545c4c16282', + # Amber-16-AT-17-fix_missing_do_parallel_in_checkrismunsupported.patch + '5cf41b908b730efee760e623465e180d8aa93f0c50b688093bd4258cf508eba7', + '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch + '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch + # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch + 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch + 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch + # Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch + '129752ba327559951d79abc3d7d15fe919897b063edcd29f79112861bdd8d9ec', +] + +dependencies = [ + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.15'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('X11', '20180604'), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb new file mode 100644 index 00000000000..e1369411f00 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb @@ -0,0 +1,88 @@ +name = 'Amber' +version = '16' +ambertools_ver = '17' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (10, 15) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] +patches = [ + 'Amber-%%(version)s-AT-%s_fix-hardcoding.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_intel_mpi_compiler_version_detection.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_mkl_include_path.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_fftw_from_mkl_or_external.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_FFTW_FFT_instead_of_PUBFFT.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_sander_link_with_external_fftw.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix-cpptraj-dont-use-static.patch' % ambertools_ver, + # Must come after fix-cpptraj-dont-use-static.patch + 'Amber-%%(version)s-AT-%s_cpptraj_use_mkl_fft.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_incorrect_omp_directive_rism.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_openmp_at_link.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_CUSTOMBUILDFLAGS_for_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_do_parallel_in_checkrismunsupported.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_fixed_size_cmd_in_nab.patch' % ambertools_ver, + 'Amber-%(version)s-fix_missing_build_target.patch', + 'Amber-%(version)s-dont_use_ipo.patch', + 'Amber-%%(version)s-AT-%s_use_FFTW_FFT_instead_of_PUBFFT_part2.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_allow_cuda9.patch' % ambertools_ver, + 'Amber-%(version)s_test_cuda.patch', +] +checksums = [ + '3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d', # Amber16.tar.bz2 + '4fbb2cf57d27422949909cc6f7e434c9855333366196a1d539264617c8bc5dec', # AmberTools17.tar.bz2 + '5bf43acaa720815640e54f0872e119dd33bb223e7e1c2f01b459b86efc71ae6e', # Amber-16-AT-17_fix-hardcoding.patch + # Amber-16-AT-17-fix_intel_mpi_compiler_version_detection.patch + '43e79b40388caa2bc14f80acbe72e520b245459dde519d528c07928909dd3c08', + '35fc82573ede194d11090f1df8fdef36d681bf78d2107a495e57a7f1d5ca0b69', # Amber-16-AT-17-fix_mkl_include_path.patch + # Amber-16-AT-17-use_fftw_from_mkl_or_external.patch + '645f4ec6aacfc316c97f936d6549d91d1664b915ab7311c00c5c4591787753af', + # Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch + '8a377c87f95756bb072664a77d417eec66912872c4c02e354f4068104ee2a51c', + # Amber-16-AT-17-fix_sander_link_with_external_fftw.patch + '092d70bec83b4383fd2722095026e069acac0f6bf57a9ac8ae030fe537bc64f9', + # Amber-16-AT-17-fix-cpptraj-dont-use-static.patch + '9ae4d6ac172d30a9b3a48992ad4217e8e21336c94107ae2435850c0f77dc0993', + '17bb30c77e204c57cfb6e78f0a7a70994df206d6309f425d83ca0a026323b955', # Amber-16-AT-17_cpptraj_use_mkl_fft.patch + # Amber-16-AT-17-fix_incorrect_omp_directive_rism.patch + '46455dd23f93bdb657f27edc9f92fad503f12048184b926711ee41a6f28b916c', + # Amber-16-AT-17-fix_missing_openmp_at_link.patch + '2116f52b5051eb07cfe74fe5bd751e237d1792c248dc0e5a204a19aea25ed337', + # Amber-16-AT-17-use_CUSTOMBUILDFLAGS_for_nab.patch + '5de8b3e93bd1b36c5d57b64089fc40f14b00c6503fdc7437a005d545c4c16282', + # Amber-16-AT-17-fix_missing_do_parallel_in_checkrismunsupported.patch + '5cf41b908b730efee760e623465e180d8aa93f0c50b688093bd4258cf508eba7', + '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch + '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch + # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch + 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch + 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch + # Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch + '129752ba327559951d79abc3d7d15fe919897b063edcd29f79112861bdd8d9ec', + '9f57711fe607920a48fcff2f2523230a13fbbb354ab683795247fc6dd8848192', # Amber-16-AT-17_allow_cuda9.patch + 'b870417a0aad5b220dca9f590ec5cf857e06f44b7ee43165c4ace9901ae9a0f7', # Amber-16_test_cuda.patch +] + +dependencies = [ + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.15'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('X11', '20180604'), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb new file mode 100644 index 00000000000..4a20d0a047b --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb @@ -0,0 +1,81 @@ +name = 'Amber' +version = '16' +ambertools_ver = '17' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (10, 15) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] +patches = [ + 'Amber-%%(version)s-AT-%s_fix-hardcoding.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_intel_mpi_compiler_version_detection.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_mkl_include_path.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_fftw_from_mkl_or_external.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_FFTW_FFT_instead_of_PUBFFT.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_sander_link_with_external_fftw.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix-cpptraj-dont-use-static.patch' % ambertools_ver, + # Must come after fix-cpptraj-dont-use-static.patch + 'Amber-%%(version)s-AT-%s_cpptraj_use_mkl_fft.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_incorrect_omp_directive_rism.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_openmp_at_link.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_CUSTOMBUILDFLAGS_for_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_do_parallel_in_checkrismunsupported.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_fixed_size_cmd_in_nab.patch' % ambertools_ver, + 'Amber-%(version)s-fix_missing_build_target.patch', + 'Amber-%(version)s-dont_use_ipo.patch', +] +checksums = [ + '3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d', # Amber16.tar.bz2 + '4fbb2cf57d27422949909cc6f7e434c9855333366196a1d539264617c8bc5dec', # AmberTools17.tar.bz2 + '5bf43acaa720815640e54f0872e119dd33bb223e7e1c2f01b459b86efc71ae6e', # Amber-16-AT-17_fix-hardcoding.patch + # Amber-16-AT-17-fix_intel_mpi_compiler_version_detection.patch + '43e79b40388caa2bc14f80acbe72e520b245459dde519d528c07928909dd3c08', + '35fc82573ede194d11090f1df8fdef36d681bf78d2107a495e57a7f1d5ca0b69', # Amber-16-AT-17-fix_mkl_include_path.patch + # Amber-16-AT-17-use_fftw_from_mkl_or_external.patch + '645f4ec6aacfc316c97f936d6549d91d1664b915ab7311c00c5c4591787753af', + # Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch + '8a377c87f95756bb072664a77d417eec66912872c4c02e354f4068104ee2a51c', + # Amber-16-AT-17-fix_sander_link_with_external_fftw.patch + '092d70bec83b4383fd2722095026e069acac0f6bf57a9ac8ae030fe537bc64f9', + # Amber-16-AT-17-fix-cpptraj-dont-use-static.patch + '9ae4d6ac172d30a9b3a48992ad4217e8e21336c94107ae2435850c0f77dc0993', + '17bb30c77e204c57cfb6e78f0a7a70994df206d6309f425d83ca0a026323b955', # Amber-16-AT-17_cpptraj_use_mkl_fft.patch + # Amber-16-AT-17-fix_incorrect_omp_directive_rism.patch + '46455dd23f93bdb657f27edc9f92fad503f12048184b926711ee41a6f28b916c', + # Amber-16-AT-17-fix_missing_openmp_at_link.patch + '2116f52b5051eb07cfe74fe5bd751e237d1792c248dc0e5a204a19aea25ed337', + # Amber-16-AT-17-use_CUSTOMBUILDFLAGS_for_nab.patch + '5de8b3e93bd1b36c5d57b64089fc40f14b00c6503fdc7437a005d545c4c16282', + # Amber-16-AT-17-fix_missing_do_parallel_in_checkrismunsupported.patch + '5cf41b908b730efee760e623465e180d8aa93f0c50b688093bd4258cf508eba7', + '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch + '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch + # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch + 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch + 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch +] + +dependencies = [ + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.15'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('X11', '20180604'), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-fosscuda-2018b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-fosscuda-2018b.eb new file mode 100644 index 00000000000..3d1be7a36c3 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-fosscuda-2018b.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.4.4' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['44b1986c427989604df9925dcdbf6c1a977e4ecbde6dd459114bca20bf5e9e67'] + +dependencies = [('netCDF', '4.6.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.6.1-fosscuda-2018b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.6.1-fosscuda-2018b.eb new file mode 100644 index 00000000000..faa8ae9a631 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.6.1-fosscuda-2018b.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.6.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a2fabf27c72a5ee746e3843e1debbaad37cd035767eaede2045371322211eebb'] + +dependencies = [ + ('HDF5', '1.10.2'), + ('cURL', '7.60.0'), + ('Szip', '2.1.1'), +] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.11.4'), + ('Doxygen', '1.8.14'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' From e54d150c155d2563af2876938a8ccb00b9a1c903 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 7 Oct 2018 13:53:08 +0200 Subject: [PATCH 0095/5331] Amber16: Add missing patch to allow CUDA 9 to be used --- .../a/Amber/Amber-16-AT-17_allow_cuda9.patch | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-AT-17_allow_cuda9.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_allow_cuda9.patch b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_allow_cuda9.patch new file mode 100644 index 00000000000..893e5e75fa7 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_allow_cuda9.patch @@ -0,0 +1,16 @@ +Allow use of all CUDA 9 versions + +Åke Sandgren, 20180727 +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2018-07-27 10:27:34.745642223 +0200 ++++ amber16/AmberTools/src/configure2 2018-07-27 10:30:05.442542975 +0200 +@@ -1203,7 +1203,8 @@ + #SM2.0 = All GF variants = C2050, 2075, M2090, GTX480, GTX580 etc. + sm20flags='-gencode arch=compute_20,code=sm_20' + cudaversion=`$nvcc --version | grep 'release' | cut -d' ' -f5 | cut -d',' -f1` +- if [ "$cudaversion" = "9.0" ]; then ++ cudamajversion=`echo $cudaversion | cut -d. -f1` ++ if [ $cudamajversion -ge 9 ]; then + echo "CUDA Version $cudaversion detected" + echo "Configuring for SM3.0, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1 and SM7.0" + nvccflags="$sm30flags $sm50flags $sm52flags $sm53flags $sm60flags $sm61flags $sm70flags -Wno-deprecated-declarations" From 30bf9fb93e4117bbf8ea1bfce9c886a9c9a98e0f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 16 Oct 2018 16:40:39 +0200 Subject: [PATCH 0096/5331] Unzip libutempter compressed tarball to get consistent checksum --- .../libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb index e198858862b..13cb6c68203 100644 --- a/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb @@ -9,14 +9,13 @@ description = """libutempter is library that provides an interface for terminal toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} -# download via http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h=1.1.6-alt2;sf=tgz -# and rename libutempter-1.1.6-alt2-3c6e555.tar.gz to libutempter-1.1.6.2.tar.gz +# Download from http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h=1.1.6-alt2;sf=tgz +# and unzip / rename libutempter-1.1.6-alt2-3c6e555.tar.gz to libutempter-1.1.6.2.tar sources = [{ - 'filename': SOURCE_TAR_GZ, - 'extract_cmd': "tar xfvz %s --strip 1", + 'filename': SOURCE_TAR, + 'extract_cmd': "tar xfv %s --strip 1", }] - -checksums = ['b7e55b666c575d8f2d294c82655b6af21f0c7339625ba6707e5edc2883a2b09a'] +checksums = ['4a55a5859a824e40af0844c8fb4bc951026edc83e529739f738a9f07c6c5751b'] skipsteps = ['configure'] From 0384bc77a1db3ce98a9024c812cc517b8b9b8307 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 30 Oct 2018 09:51:37 +0800 Subject: [PATCH 0097/5331] adding easyconfigs: FDTD_Solutions-8.20.1731.eb --- .../f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb new file mode 100644 index 00000000000..ce223b5c241 --- /dev/null +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb @@ -0,0 +1,12 @@ +name = 'FDTD_Solutions' +version = '8.20.1731' + +homepage = 'http://www.lumerical.com/tcad-products/fdtd/' +description = """High performance FDTD-method Maxwell solver for the design, analysis and optimization +of nanophotonic devices, processes and materials.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] + +moduleclass = 'cae' From 725256b3111078041890f06d2eb860ed7eada9e1 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 30 Oct 2018 11:44:14 +0800 Subject: [PATCH 0098/5331] add checksum --- .../easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb index ce223b5c241..05deb18ba6c 100644 --- a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb @@ -8,5 +8,6 @@ of nanophotonic devices, processes and materials.""" toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCE_TAR_GZ] +checksums = ['e742bd5a7a64d04d6aa6ee99cbafd77fb63a0388951cd83431e4da4ce84f6a48'] moduleclass = 'cae' From 7e5911a849de57a6d585816ff8cbdfabeb0879af Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 31 Oct 2018 22:02:16 +0200 Subject: [PATCH 0099/5331] adding easyconfigs: Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb, Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb --- ...oss-2018b-AmberTools-18-patchlevel-10-8.eb | 91 +++++++++++++++++++ ...tel-2017b-AmberTools-18-patchlevel-10-8.eb | 91 +++++++++++++++++++ ...Python-1.65.1-intel-2017b-Python-2.7.14.eb | 25 +++++ ....Python-1.67.0-foss-2018b-Python-2.7.15.eb | 25 +++++ 4 files changed, 232 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb b/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb new file mode 100644 index 00000000000..bd8df90856d --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb @@ -0,0 +1,91 @@ +name = 'Amber' +version = '18' +ambertools_ver = '18' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (10, 8) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] +patches = [ + 'Amber-%%(version)s-AT-%s_fix_hardcoding.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_intel_mpi_compiler_version_detection.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_mkl_include_path.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_use_fftw_from_mkl_or_external.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_use_FFTW_FFT_instead_of_PUBFFT.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_sander_link_with_external_fftw.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix-cpptraj-dont-use-static.patch' % ambertools_ver, + # Must come after fix-cpptraj-dont-use-static.patch + 'Amber-%%(version)s-AT-%s_cpptraj_use_mkl_fft.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_incorrect_omp_directive_rism.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_missing_openmp_at_link.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_use_CUSTOMBUILDFLAGS_for_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_missing_do_parallel_in_checkrismunsupported.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_use_easybuild_pythonpath.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_use_external_boost_in_packmol_memembed.patch' % ambertools_ver, + 'Amber-%(version)s_fix_missing_build_target.patch', + 'Amber-%(version)s_dont_use_ipo.patch', +] +checksums = [ + '2060897c0b11576082d523fb63a51ba701bc7519ff7be3d299d5ec56e8e6e277', # Amber18.tar.bz2 + 'c630fc3d251fcefe19bb81c8c617e0547f1687b6aef68ea526e4e5fff65bea1c', # AmberTools18.tar.bz2 + 'd1bad000dc155b77cd20787fbe7da5552dfb1d3e2834407824208b51f9518ad1', # Amber-18-AT-18_fix_hardcoding.patch + # Amber-18-AT-18_fix_intel_mpi_compiler_version_detection.patch + 'f25d0353b045bc769d3938aa698aea40e9e7bd152a2acca4b7fa1d790cf96297', + 'c95db1c296c3512b818a1b34a65c2ea4cbce46acf70689919c5f42c3bb0799d3', # Amber-18-AT-18_fix_mkl_include_path.patch + # Amber-18-AT-18_use_fftw_from_mkl_or_external.patch + '10e18ddd1218e73cb10531d8426c3568d8bdc255da92e682fffd2ee2a4ad1867', + # Amber-18-AT-18_use_FFTW_FFT_instead_of_PUBFFT.patch + 'ebe85219f22869ec22e531592b785d68c15337171acd479660ab4e3ecd07655f', + # Amber-18-AT-18_fix_sander_link_with_external_fftw.patch + '6f8eefc905a6817062a65ec1ed757b9d782e4ffc250511e750e6d87110e00c52', + # Amber-18-AT-18_fix-cpptraj-dont-use-static.patch + 'c142011166a26164d65287e7bea2e14d6df62c1984caada48410e62af0d5c3da', + '7ace48e6e24aa061737506d08e435e2053ca7074eb78fc47888183aabf71cd44', # Amber-18-AT-18_cpptraj_use_mkl_fft.patch + # Amber-18-AT-18_fix_incorrect_omp_directive_rism.patch + '9639dcc8d7b4053950f16d2a1706787bbf5748dead05773a7b53ec47ce8817d2', + # Amber-18-AT-18_fix_missing_openmp_at_link.patch + '2116f52b5051eb07cfe74fe5bd751e237d1792c248dc0e5a204a19aea25ed337', + # Amber-18-AT-18_use_CUSTOMBUILDFLAGS_for_nab.patch + '5de8b3e93bd1b36c5d57b64089fc40f14b00c6503fdc7437a005d545c4c16282', + # Amber-18-AT-18_fix_missing_do_parallel_in_checkrismunsupported.patch + '5cf41b908b730efee760e623465e180d8aa93f0c50b688093bd4258cf508eba7', + '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-18-AT-18_fix_rism_fftw_lib.patch + '9854a15537353d26d5ebd3d3b711c46d30b50c3dae830e5bf5c9cce489f449e1', # Amber-18-AT-18_ignore_X11_checks.patch + 'dcfdf064e774b4a55802b660146f1cdebb1226bdd75713de7a783848fc23526e', # Amber-18-AT-18_use_easybuild_pythonpath.patch + # Amber-18-AT-18_use_external_boost_in_packmol_memembed.patch + '9493a3dfddf62d6aa1bbb0a92a39e766a2b76a9ff8a9006e0fcc9ee3e5d94aac', + '6b09a6548fa18127245e05c79bdca143adf31db349349cb39bfdb8c4f60772a7', # Amber-18_fix_missing_build_target.patch + 'a4c12ad39088ce6e9e7bad39e8d9a736989e6ae4a380c70535a5451eb3060903', # Amber-18_dont_use_ipo.patch +] + +builddependencies = [ + ('flex', '2.6.4'), +] + +dependencies = [ + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.15'), + ('Boost.Python', '1.67.0', '-Python-%(pyver)s'), + ('matplotlib', '2.2.3', '-Python-%(pyver)s'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('X11', '20180604'), +] + +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb b/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb new file mode 100644 index 00000000000..838e5e5c3ae --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb @@ -0,0 +1,91 @@ +name = 'Amber' +version = '18' +ambertools_ver = '18' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (10, 8) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] +patches = [ + 'Amber-%%(version)s-AT-%s_fix_hardcoding.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_intel_mpi_compiler_version_detection.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_mkl_include_path.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_use_fftw_from_mkl_or_external.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_use_FFTW_FFT_instead_of_PUBFFT.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_sander_link_with_external_fftw.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix-cpptraj-dont-use-static.patch' % ambertools_ver, + # Must come after fix-cpptraj-dont-use-static.patch + 'Amber-%%(version)s-AT-%s_cpptraj_use_mkl_fft.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_incorrect_omp_directive_rism.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_missing_openmp_at_link.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_use_CUSTOMBUILDFLAGS_for_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_missing_do_parallel_in_checkrismunsupported.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_use_easybuild_pythonpath.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_use_external_boost_in_packmol_memembed.patch' % ambertools_ver, + 'Amber-%(version)s_fix_missing_build_target.patch', + 'Amber-%(version)s_dont_use_ipo.patch', +] +checksums = [ + '2060897c0b11576082d523fb63a51ba701bc7519ff7be3d299d5ec56e8e6e277', # Amber18.tar.bz2 + 'c630fc3d251fcefe19bb81c8c617e0547f1687b6aef68ea526e4e5fff65bea1c', # AmberTools18.tar.bz2 + 'd1bad000dc155b77cd20787fbe7da5552dfb1d3e2834407824208b51f9518ad1', # Amber-18-AT-18_fix_hardcoding.patch + # Amber-18-AT-18_fix_intel_mpi_compiler_version_detection.patch + 'f25d0353b045bc769d3938aa698aea40e9e7bd152a2acca4b7fa1d790cf96297', + 'c95db1c296c3512b818a1b34a65c2ea4cbce46acf70689919c5f42c3bb0799d3', # Amber-18-AT-18_fix_mkl_include_path.patch + # Amber-18-AT-18_use_fftw_from_mkl_or_external.patch + '10e18ddd1218e73cb10531d8426c3568d8bdc255da92e682fffd2ee2a4ad1867', + # Amber-18-AT-18_use_FFTW_FFT_instead_of_PUBFFT.patch + 'ebe85219f22869ec22e531592b785d68c15337171acd479660ab4e3ecd07655f', + # Amber-18-AT-18_fix_sander_link_with_external_fftw.patch + '6f8eefc905a6817062a65ec1ed757b9d782e4ffc250511e750e6d87110e00c52', + # Amber-18-AT-18_fix-cpptraj-dont-use-static.patch + 'c142011166a26164d65287e7bea2e14d6df62c1984caada48410e62af0d5c3da', + '7ace48e6e24aa061737506d08e435e2053ca7074eb78fc47888183aabf71cd44', # Amber-18-AT-18_cpptraj_use_mkl_fft.patch + # Amber-18-AT-18_fix_incorrect_omp_directive_rism.patch + '9639dcc8d7b4053950f16d2a1706787bbf5748dead05773a7b53ec47ce8817d2', + # Amber-18-AT-18_fix_missing_openmp_at_link.patch + '2116f52b5051eb07cfe74fe5bd751e237d1792c248dc0e5a204a19aea25ed337', + # Amber-18-AT-18_use_CUSTOMBUILDFLAGS_for_nab.patch + '5de8b3e93bd1b36c5d57b64089fc40f14b00c6503fdc7437a005d545c4c16282', + # Amber-18-AT-18_fix_missing_do_parallel_in_checkrismunsupported.patch + '5cf41b908b730efee760e623465e180d8aa93f0c50b688093bd4258cf508eba7', + '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-18-AT-18_fix_rism_fftw_lib.patch + '9854a15537353d26d5ebd3d3b711c46d30b50c3dae830e5bf5c9cce489f449e1', # Amber-18-AT-18_ignore_X11_checks.patch + 'dcfdf064e774b4a55802b660146f1cdebb1226bdd75713de7a783848fc23526e', # Amber-18-AT-18_use_easybuild_pythonpath.patch + # Amber-18-AT-18_use_external_boost_in_packmol_memembed.patch + '9493a3dfddf62d6aa1bbb0a92a39e766a2b76a9ff8a9006e0fcc9ee3e5d94aac', + '6b09a6548fa18127245e05c79bdca143adf31db349349cb39bfdb8c4f60772a7', # Amber-18_fix_missing_build_target.patch + 'a4c12ad39088ce6e9e7bad39e8d9a736989e6ae4a380c70535a5451eb3060903', # Amber-18_dont_use_ipo.patch +] + +builddependencies = [ + ('flex', '2.6.4'), +] + +dependencies = [ + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.14'), + ('Boost.Python', '1.65.1', '-Python-%(pyver)s'), + ('matplotlib', '2.1.1', '-Python-%(pyver)s'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('X11', '20171023'), +] + +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..486dddb670b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,25 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.65.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.sourceforge.net/boost/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['a13de2c8fbad635e6ba9c8f8714a0e6b4264b60a29b964b940a22554705b6b60'] + +dependencies = [ + ('Python', '2.7.14'), + ('Boost', version), +] + +only_python_bindings = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..b599c07fc89 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,25 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.67.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.sourceforge.net/boost/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8aa4e330c870ef50a896634c931adf468b21f8a69b77007e45c444151229f665'] + +dependencies = [ + ('Python', '2.7.15'), + ('Boost', version), +] + +only_python_bindings = True + +moduleclass = 'lib' From b97d83a638f504d137145e56cf255c180cefc362 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Nov 2018 15:37:48 +0100 Subject: [PATCH 0100/5331] adding easyconfigs: Trilinos-12.12.1-intel-2018a-Python-3.6.4.eb, ParMETIS-4.0.3-intel-2018a.eb --- .../p/ParMETIS/ParMETIS-4.0.3-intel-2018a.eb | 23 +++++++ ...ilinos-12.12.1-intel-2018a-Python-3.6.4.eb | 62 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2018a.eb create mode 100644 easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-intel-2018a-Python-3.6.4.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2018a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2018a.eb new file mode 100644 index 00000000000..ef7d45d50d0 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-intel-2018a.eb @@ -0,0 +1,23 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.12.1')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..47e9ea4fa18 --- /dev/null +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,62 @@ +name = 'Trilinos' +version = '12.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://trilinos.org' +description = """The Trilinos Project is an effort to develop algorithms and enabling technologies + within an object-oriented software framework for the solution of large-scale, complex multi-physics + engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'usempi': True, 'pic': True, 'strict': True} + +source_urls = [ + 'http://trilinos.csbsju.edu/download/files/', + 'https://trilinos.org/oldsite/download/files/', +] +sources = ['%(namelower)s-%(version)s-Source.tar.gz'] +patches = [ + ('Trilinos-%(version)s_fix-CEpetra-LAPACK.patch', 'packages/CTrilinos'), + 'Trilinos-%(version)s_fix-Py3.patch', + 'Trilinos-%(version)s_muelu-fix-function-signature.patch', + 'Trilinos-%(version)s_fix-Sundance.patch', +] +checksums = [ + '7c67d83befbeabc773661bcdfee2850c404d249160b755d3f1be2e96f564f9fd', # trilinos-12.12.1-Source.tar.gz + 'de2e989bf9e7cbe7cab9126a464b5b1569983de4060956e7a95dccb9e0bad039', # Trilinos-12.12.1_fix-CEpetra-LAPACK.patch + '5505645b712056403263860de86efccfb343cb5e5bf8d65697526d65ea5df099', # Trilinos-12.12.1_fix-Py3.patch + # Trilinos-12.12.1_muelu-fix-function-signature.patch + '253191cc6f6a6ebcc893e2684c64cfefa62c1cd0cc6b03b5f83646856fbdfe8a', + 'df7924c207c1fab98d5aeec1333c4e2da5c07117daf2c72279f894552087e391', # Trilinos-12.12.1_fix-Sundance.patch +] + +builddependencies = [ + ('CMake', '3.10.2'), + ('SWIG', '3.0.12', versionsuffix), +] +dependencies = [ + ('Python', '3.6.4'), + ('Boost', '1.66.0'), + ('Boost.Python', '1.66.0', versionsuffix), + ('SCOTCH', '6.0.5'), + ('SuiteSparse', '5.1.2', '-METIS-5.1.0'), + ('ParMETIS', '4.0.3'), + ('netCDF', '4.6.0'), + ('MATIO', '1.5.12'), + ('GLM', '0.9.9.0'), + ('X11', '20180131'), +] + +# disable TrilinosCouplings package, doesn't build correctly (examples fail to compile) +skip_exts = ['TrilinosCouplings'] + +# workaround for Teuchos.pyc not being found during "make install" +# see https://github.com/trilinos/Trilinos/issues/1749 +preinstallopts = "cd %(builddir)s/trilinos-%(version)s-Source/packages/PyTrilinos/src/PyTrilinos && " +preinstallopts += "python -m compileall -b -l -f . && cd - && " + +# too parallel is too slow because of memory requirements (results in swapping), and may cause build/tests to fail +# building with 20 cores seems to require about 100GB of memory (peak usage) +maxparallel = 10 + +moduleclass = 'numlib' From e213b9731b93a8d617beb727e4e5afdadb363792 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Nov 2018 16:05:05 +0100 Subject: [PATCH 0101/5331] {vis}[intel/2018a] p4vasp v0.3.30 + deps w/ Python 2.7.14 --- .../Glade-3.8.6-intel-2018a-Python-2.7.14.eb | 38 +++++++++++++ ...ITSTool-2.0.5-intel-2018a-Python-2.7.14.eb | 27 +++++++++ .../l/libglade/libglade-2.6.4-intel-2018a.eb | 28 ++++++++++ ...-python-2.9.7-intel-2018a-Python-2.7.14.eb | 27 +++++++++ ...yCairo-1.18.0-intel-2018a-Python-2.7.14.eb | 35 ++++++++++++ ...Object-2.28.7-intel-2018a-Python-2.7.14.eb | 46 +++++++++++++++ .../PyGTK-2.24.0-intel-2018a-Python-2.7.14.eb | 51 +++++++++++++++++ ...penGL-3.1.3b2-intel-2018a-Python-2.7.14.eb | 31 ++++++++++ ...p4vasp-0.3.30-intel-2018a-Python-2.7.14.eb | 56 +++++++++++++++++++ 9 files changed, 339 insertions(+) create mode 100644 easybuild/easyconfigs/g/Glade/Glade-3.8.6-intel-2018a-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.5-intel-2018a-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/l/libglade/libglade-2.6.4-intel-2018a.eb create mode 100644 easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.7-intel-2018a-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-intel-2018a-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.7-intel-2018a-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2018a-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-intel-2018a-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.30-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/g/Glade/Glade-3.8.6-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/g/Glade/Glade-3.8.6-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..70408326699 --- /dev/null +++ b/easybuild/easyconfigs/g/Glade/Glade-3.8.6-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Glade' +version = '3.8.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://glade.gnome.org/' +description = """Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit + and the GNOME desktop environment.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [FTPGNOME_SOURCE] +sources = ['%(namelower)s%(version_major)s-%(version)s.tar.xz'] +checksums = ['aaeeebffaeb3068fb23757a2eede46adeb4c7cecc740feed7654e065491f5449'] + +builddependencies = [ + ('intltool', '0.51.0', '-Perl-5.26.1'), + ('pkg-config', '0.29.2'), + ('X11', '20180131'), + ('ITSTool', '2.0.5', versionsuffix), +] + +dependencies = [ + ('Python', '2.7.14'), + ('GTK+', '2.24.32'), + ('PyGTK', '2.24.0', versionsuffix), + ('gettext', '0.19.8.1', '-libxml2-2.9.7'), + ('libxml2', '2.9.7'), +] +sanity_check_paths = { + 'files': ['bin/glade-%(version_major)s', 'lib/libgladeui-1.%s' % SHLIB_EXT, 'lib/pkgconfig/gladeui-1.0.pc', + 'lib/glade%%(version_major)s/modules/libgladegtk.%s' % SHLIB_EXT, + 'lib/glade%%(version_major)s/modules/libgladepython.%s' % SHLIB_EXT], + 'dirs': ['include/libgladeui-1.0/gladeui', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.5-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.5-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..a8f4791e467 --- /dev/null +++ b/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.5-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'ITSTool' +version = '2.0.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://itstool.org/' +description = "ITS Tool allows you to translate your XML documents with PO files" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://files.itstool.org/itstool/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['100506f8df62cca6225ec3e631a8237e9c04650c77495af4919ac6a100d4b308'] + +dependencies = [ + ('Python', '2.7.14'), + ('libxml2-python', '2.9.7', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/itstool'], + 'dirs': ['share/itstool/its', 'share/man'], +} +sanity_check_commands = ["itstool --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libglade/libglade-2.6.4-intel-2018a.eb b/easybuild/easyconfigs/l/libglade/libglade-2.6.4-intel-2018a.eb new file mode 100644 index 00000000000..6c9b26c1c41 --- /dev/null +++ b/easybuild/easyconfigs/l/libglade/libglade-2.6.4-intel-2018a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libglade' +version = '2.6.4' + +homepage = 'https://developer.gnome.org/libglade/' +description = """Libglade is a library for constructing user interfaces dynamically from XML descriptions.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c41d189b68457976069073e48d6c14c183075d8b1d8077cb6dfb8b7c5097add3'] + +dependencies = [ + ('ATK', '2.28.1'), + ('GTK+', '2.24.32'), + ('GLib', '2.54.3'), + ('libxml2', '2.9.7'), +] + +sanity_check_paths = { + 'files': ['bin/libglade-convert', 'lib/libglade-2.0.a', 'lib/libglade-2.0.%s' % SHLIB_EXT, + 'lib/pkgconfig/libglade-2.0.pc'], + 'dirs': ['include/libglade-2.0/glade', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.7-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.7-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..a90f6920e9c --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.7-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_libxml2' + +name = 'libxml2-python' +version = '2.9.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = ['libxml2-%(version)s.tar.gz'] +checksums = ['f63c5e7d30362ed28b38bfa1ac6313f9a80230720b7fb6c80575eeab3ff5900c'] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.3'), + ('Python', '2.7.14'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..803eb7e98e2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.0-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'PyCairo' +version = '1.18.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://cairographics.org/pycairo/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abd42a4c9c2069febb4c38fe74bfc4b4a9d3a89fea3bc2e4ba7baff7a20f783f'] + +dependencies = [ + ('Python', '2.7.14'), + ('cairo', '1.14.12'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'cairo'} + +sanity_check_paths = { + 'files': ['include/pycairo/pycairo.h', 'lib/pkgconfig/pycairo.pc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages', 'lib64/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.7-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.7-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..bc50bb164fe --- /dev/null +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-2.28.7-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'PyGObject' +version = '2.28.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pygtk.org/' +description = """Python Bindings for GLib/GObject/GIO/GTK+""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['bb9d25a3442ca7511385a7c01b057492095c263784ef31231ffe589d83a96a5a'] + +dependencies = [ + ('Python', '2.7.14'), + ('GLib', '2.54.3'), + ('GObject-Introspection', '1.54.1', versionsuffix), + ('PyCairo', '1.18.0', versionsuffix), +] + +configopts = "--disable-introspection" + +modextrapaths = { + 'PYTHONPATH': [ + 'lib/python%(pyshortver)s/site-packages', + 'lib/python%(pyshortver)s/site-packages/gtk-2.0', + 'lib64/python%(pyshortver)s/site-packages', + 'lib64/python%(pyshortver)s/site-packages/gtk-2.0', + ], +} + +sanity_check_paths = { + 'files': ['include/pygtk-%(version_major)s.0/pyglib.h', 'include/pygtk-%(version_major)s.0/pygobject.h', + 'lib/libpyglib-%(version_major)s.0-python.so'], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + ('python', "-c 'import gobject'"), + ('python', "-c 'import glib'"), + ('python', "-c 'import gio'"), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..eb00d15db0c --- /dev/null +++ b/easybuild/easyconfigs/p/PyGTK/PyGTK-2.24.0-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'PyGTK' +version = '2.24.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pygtk.org/' +description = """PyGTK lets you to easily create programs with a graphical user interface + using the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['cd1c1ea265bd63ff669e92a2d3c2a88eb26bcd9e5363e0f82c896e649f206912'] + +dependencies = [ + ('Python', '2.7.14'), + ('GLib', '2.54.3'), + ('PyGObject', '2.28.7', versionsuffix), + ('GTK+', '2.24.32'), + ('ATK', '2.28.1'), + ('PyCairo', '1.18.0', versionsuffix), + ('libglade', '2.6.4'), +] + +postinstallcmds = [ + "sed -i s#'codegendir=${datadir}'#codegendir=$EBROOTPYGOBJECT/share# %(installdir)s/lib/pkgconfig/pygtk-2.0.pc", + "sed -i s#'exec_prefix=${prefix}'#exec_prefix=$EBROOTPYGOBJECT# %(installdir)s/bin/pygtk-codegen-2.0", +] + +modextrapaths = { + 'PYTHONPATH': [ + 'lib/python%(pyshortver)s/site-packages', + 'lib64/python%(pyshortver)s/site-packages', + 'lib/python%(pyshortver)s/site-packages/gtk-%(version_major)s.0', + 'lib64/python%(pyshortver)s/site-packages/gtk-%(version_major)s.0', + ], +} + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pygtk-%(version_major)s.0.pc'], + 'dirs': ['lib/pygtk'], +} + +sanity_check_commands = [ + "python -c 'import gtk'", + "python -c 'import gtk.glade'", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..44c15149da2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyOpenGL' +version = '3.1.3b2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ac73b4c0b433be02d6a55b9ed768acf07003a92a3315ba9d62bc8f8da5f0c291'] + +dependencies = [ + ('Python', '2.7.14'), + ('Mesa', '17.3.6'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'OpenGL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.30-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.30-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..1bc5282f6f8 --- /dev/null +++ b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.30-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'p4vasp' +version = '0.3.30' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.p4vasp.at/' +description = """Visualization suite for VASP""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://www.p4vasp.at/files'] +sources = [SOURCE_TGZ] +patches = [ + ('p4vasp-%(version)s_drop_fltk_from_makefile.patch'), + ('p4vasp-%(version)s_fix_compiler_spec.patch'), + ('p4vasp-%(version)s_fix_fltk-config_usage.patch'), + ('p4vasp-%(version)s_dont_preload_libstdc_nor_set_PYTHONPATH_again.patch'), +] +checksums = [ + '7052926f70a799f87c2d3a5d52c86575422113e3f589776b071dfc554969df7d', # p4vasp-0.3.30.tgz + '1a7b4a59d4605bd022af0b90b20922137a0a90b077e512041a0091221daf26a1', # p4vasp-0.3.30_drop_fltk_from_makefile.patch + 'b73f6f99261fa3399b673c27f0d3e2164bf7f5da0018e536a0c5a1349a341aa3', # p4vasp-0.3.30_fix_compiler_spec.patch + 'ca226baeb49abb681beb057b781c059e41d1988d16dae1aca38d1e6b2d425801', # p4vasp-0.3.30_fix_fltk-config_usage.patch + # p4vasp-0.3.30_dont_preload_libstdc_nor_set_PYTHONPATH_again.patch + '94ac59b261789ea197380678703bacdddbcf6722b7fb302408984a2d7e25ce3c', +] + +dependencies = [ + ('Python', '2.7.14'), + ('PyGTK', '2.24.0', versionsuffix), + ('PyOpenGL', '3.1.3b2', versionsuffix), + # stick to Glade 3.8.x, more recent versions require GTK+ 3.x + ('Glade', '3.8.6', versionsuffix), + ('X11', '20180131'), + ('FLTK', '1.3.4'), +] + +skipsteps = ['configure', 'build'] + +# redefine $HOME to specify installation prefix O_o +preinstallopts = "make cleanall && env HOME=%(installdir)s make local && " + +sanity_check_paths = { + 'files': ['p4vasp/bin/p4v', 'p4vasp/lib/libODP.a', 'p4vasp/lib/libp4vasp.a'], + 'dirs': ['p4vasp/data', 'p4vasp/include/ODP', 'p4vasp/include/p4vasp', 'p4vasp/python-packages', 'p4vasp/utils'], +} + +modextrapaths = { + 'CPATH': ['p4vasp/include'], + 'LIBRARY_PATH': ['p4vasp/lib'], + 'PATH': ['p4vasp/bin'], + 'PYTHONPATH': ['p4vasp/python-packages'], +} + +moduleclass = 'vis' From ea06c215907da88cee750a178504221862c39334 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Nov 2018 15:46:04 +0100 Subject: [PATCH 0102/5331] adding easyconfigs: JiTCODE-1.3.2-intel-2018a-Python-3.6.4.eb, SymEngine-0.3.0-intel-2018a-20181006.eb --- .../JiTCODE-1.3.2-intel-2018a-Python-3.6.4.eb | 56 +++++++++++++++++++ .../SymEngine-0.3.0-intel-2018a-20181006.eb | 26 +++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.3.2-intel-2018a-Python-3.6.4.eb create mode 100644 easybuild/easyconfigs/s/SymEngine/SymEngine-0.3.0-intel-2018a-20181006.eb diff --git a/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.3.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.3.2-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..3dee7acee08 --- /dev/null +++ b/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.3.2-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'JiTCODE' +version = '1.3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://jitcde-common.readthedocs.io' +description = "Just-in-time compilation for ordinary/delay/stochastic differential equations (DDEs)" + +toolchain = {'name': 'intel', 'version': '2018a'} + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '3.6.4'), + ('SymEngine', '0.3.0', '-20181006'), +] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('symengine', '0.3.1.dev0', { + 'source_tmpl': '511453a.tar.gz', + 'source_urls': ['https://github.com/symengine/symengine.py/archive/'], + 'checksums': ['b822c0cb677bfde033815e672425dfd93469a47e13ab3268937f822a972f2c9d'], + 'preinstallopts': "export SymEngine_DIR=$EBROOTSYMENGINE/lib/cmake/symengine && ", + }), + ('jitcxde-common', '1.3.0', { + 'source_tmpl': 'jitcxde_common-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/j/jitcxde-common'], + 'checksums': ['db9ff40b3a73d05b95f28eee89a00dedbdf398f3d9d4eda4edd70c26d5f5ed49'], + 'modulename': 'jitcxde_common', + }), + ('jitcdde', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jitcdde'], + 'checksums': ['68e9fcc2bb0da764fc17c77666e2de6cecbaf480003086a775a241a308f9669a'], + }), + ('jitcsde', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jitcsde'], + 'checksums': ['863cf30483e124dbba6c8f31496ae21b0507ba7f07952df5566bb9842f17d009'], + }), + ('jitcode', version, { + 'source_urls': ['https://pypi.python.org/packages/source/j/jitcode'], + 'checksums': ['84348cfecba84e3865a864259e9c98417e4facdcb2963d1fe27565c6994ea7c2'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SymEngine/SymEngine-0.3.0-intel-2018a-20181006.eb b/easybuild/easyconfigs/s/SymEngine/SymEngine-0.3.0-intel-2018a-20181006.eb new file mode 100644 index 00000000000..a1fa280a540 --- /dev/null +++ b/easybuild/easyconfigs/s/SymEngine/SymEngine-0.3.0-intel-2018a-20181006.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'SymEngine' +version = '0.3.0' +versionsuffix = '-20181006' + +homepage = 'https://github.com/symengine/symengine' +description = "SymEngine is a standalone fast C++ symbolic manipulation library." + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/symengine/symengine/archive/'] +sources = [{'download_filename': '9b604b2.tar.gz', 'filename': '%(name)s-%(version)s%(versionsuffix)s.tar.gz'}] +checksums = ['a91cf118fc3967fbd831d662ed0d10c66b748ab98414d87623c513d1d3131a97'] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [('GMP', '6.1.2')] + +sanity_check_paths = { + 'files': ['lib/libsymengine.a'], + 'dirs': ['include/symengine', 'lib/cmake/symengine'], +} + +moduleclass = 'lib' From e71e22f5e80faf5653ca5429cbca63fd799d2342 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Nov 2018 16:28:54 +0100 Subject: [PATCH 0103/5331] adding easyconfigs: netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb --- ...f4-python-1.4.2-foss-2018a-Python-3.6.4.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..3799b7e0856 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.6.4'), + ('netCDF', '4.6.0'), + ('cURL', '7.58.0'), +] + +use_pip = True + +exts_list = [ + ('cftime', '1.0.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cftime'], + 'checksums': ['2c81d4879a2c1753961d647e55e0125039ddeda195944c3d526f2cf087dfb7bb'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'v%(version)srel.tar.gz', + 'source_urls': ['https://github.com/Unidata/netcdf4-python/archive/'], + 'checksums': [ + 'd87ae1554b108a7bda490fe3b637de678846e5437bdd5b83844fada5347cff7d', # v1.4.2rel.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +moduleclass = 'data' From 63c40bea894726c168ab74db0ed9eebcfb67e471 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Nov 2018 16:44:19 +0100 Subject: [PATCH 0104/5331] add patch to fix failing test for netcdf4-python 1.4.2 --- ...f4-python-1.4.2-foss-2018a-Python-3.6.4.eb | 9 +++- ...etcdf4-python-1.4.2_fix-opendap-test.patch | 50 +++++++++++++++++++ 2 files changed, 57 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2_fix-opendap-test.patch diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb index 3799b7e0856..f010055ca79 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2-foss-2018a-Python-3.6.4.eb @@ -24,13 +24,18 @@ exts_list = [ 'checksums': ['2c81d4879a2c1753961d647e55e0125039ddeda195944c3d526f2cf087dfb7bb'], }), (name, version, { - 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], - 'source_tmpl': 'v%(version)srel.tar.gz', 'source_urls': ['https://github.com/Unidata/netcdf4-python/archive/'], + 'source_tmpl': 'v%(version)srel.tar.gz', + 'patches': [ + 'netcdf4-python-1.1.8-avoid-diskless-test.patch', + 'netcdf4-python-1.4.2_fix-opendap-test.patch', + ], 'checksums': [ 'd87ae1554b108a7bda490fe3b637de678846e5437bdd5b83844fada5347cff7d', # v1.4.2rel.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + # netcdf4-python-1.4.2_fix-opendap-test.patch + '3466b768de483f9f9a59a93e57966d02bc31bc2b212bcd1d273eb4f5f630e5f9', ], }), ] diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2_fix-opendap-test.patch b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2_fix-opendap-test.patch new file mode 100644 index 00000000000..b8930da15f7 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.2_fix-opendap-test.patch @@ -0,0 +1,50 @@ +see https://github.com/Unidata/netcdf4-python/issues/856 and https://github.com/Unidata/netcdf4-python/pull/857 + +From 43ac0ad9060c723ee5d5fe3e6c131a0683dc7f1c Mon Sep 17 00:00:00 2001 +From: Jeff Whitaker +Date: Wed, 7 Nov 2018 06:49:47 -0700 +Subject: [PATCH 1/2] run opendap test first from run_all.py (issue #856) + +--- + test/run_all.py | 6 ++++++ + 1 file changed, 6 insertions(+) + +diff --git a/test/run_all.py b/test/run_all.py +index f06590cf..82b505e9 100755 +--- a/test/run_all.py ++++ b/test/run_all.py +@@ -29,6 +29,12 @@ + if os.getenv('NO_NET'): + test_files.remove('tst_dap.py'); + sys.stdout.write('not running tst_dap.py ...\n') ++else: ++ # run opendap test first (issue #856). ++ test_files.remove('tst_dap.py') ++ test_files.insert(0,'tst_dap.py') ++ print(test_files) ++ + + # Build the test suite from the tests found in the test files. + testsuite = unittest.TestSuite() + +From dcf701552056a803734710f8648e039fbedfd056 Mon Sep 17 00:00:00 2001 +From: Jeff Whitaker +Date: Wed, 7 Nov 2018 06:53:31 -0700 +Subject: [PATCH 2/2] remove debug print + +--- + test/run_all.py | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/test/run_all.py b/test/run_all.py +index 82b505e9..036b6ce9 100755 +--- a/test/run_all.py ++++ b/test/run_all.py +@@ -33,7 +33,6 @@ + # run opendap test first (issue #856). + test_files.remove('tst_dap.py') + test_files.insert(0,'tst_dap.py') +- print(test_files) + + + # Build the test suite from the tests found in the test files. From db0b2c770ab5f7ca77682cbb65fc42165cebf487 Mon Sep 17 00:00:00 2001 From: ec2-user Date: Thu, 15 Nov 2018 06:35:18 +0000 Subject: [PATCH 0105/5331] adding easyconfigs: AMD-BLIS-1.2-GCC-7.3.0-2.30.eb --- .../a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb diff --git a/easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..0b8690ced99 --- /dev/null +++ b/easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'AMD-BLIS' +version = 1.2 + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' +description = """AMD fork of BLIS. BLIS is a portable software framework for instantiating high-performance + BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} + +source_urls = ['https://github.com/amd/blis/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b2e7d055c37faa5bfda5a1be63a35d1e612108a9809d7726cedbdd4722d76b1d'] + +builddependencies = [('Python', '2.7.15', '-bare')] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' From 9041ebfaa58418354916e47eb6b360b0bbc7d851 Mon Sep 17 00:00:00 2001 From: ec2-user Date: Thu, 15 Nov 2018 06:36:26 +0000 Subject: [PATCH 0106/5331] adding easyconfigs: AMD-LibM-3.2.2-GCC-7.3.0-2.30.eb --- .../AMD-LibM/AMD-LibM-3.2.2-GCC-7.3.0-2.30.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMD-LibM/AMD-LibM-3.2.2-GCC-7.3.0-2.30.eb diff --git a/easybuild/easyconfigs/a/AMD-LibM/AMD-LibM-3.2.2-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/a/AMD-LibM/AMD-LibM-3.2.2-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..02c413a9efd --- /dev/null +++ b/easybuild/easyconfigs/a/AMD-LibM/AMD-LibM-3.2.2-GCC-7.3.0-2.30.eb @@ -0,0 +1,26 @@ +easyblock = 'Binary' + +name = 'AMD-LibM' +version = '3.2.2' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/amd-math-library-libm/' +description = """AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor based machines.""" + +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} + +sources = ['%(name)s-Linux-%(version)s.tar.gz'] +checksums = ['b62c2571cf611baec6d2b6f01cbfe44460eca13a594747f33962723f0b00099d'] + +extract_sources = True + +postinstallcmds = [ + "ln -s %(installdir)s/lib/dynamic/libamdlibm.so %(installdir)s/lib/libamdlibm.so", + "ln -s %(installdir)s/lib/static/libamdlibm.a %(installdir)s/lib/libamdlibm.a", +] + +sanity_check_paths = { + 'files': ['lib/libamdlibm.so', 'lib/libamdlibm.a'], + 'dirs': ['lib'] +} + +moduleclass = 'numlib' From 21d750e7a746114d8e81a3bb8684a97b5332a75c Mon Sep 17 00:00:00 2001 From: ec2-user Date: Thu, 15 Nov 2018 06:41:10 +0000 Subject: [PATCH 0107/5331] fix style --- .../easyconfigs/a/AMD-LibM/AMD-LibM-3.2.2-GCC-7.3.0-2.30.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AMD-LibM/AMD-LibM-3.2.2-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/a/AMD-LibM/AMD-LibM-3.2.2-GCC-7.3.0-2.30.eb index 02c413a9efd..58ad5c19f41 100644 --- a/easybuild/easyconfigs/a/AMD-LibM/AMD-LibM-3.2.2-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/a/AMD-LibM/AMD-LibM-3.2.2-GCC-7.3.0-2.30.eb @@ -4,7 +4,8 @@ name = 'AMD-LibM' version = '3.2.2' homepage = 'https://developer.amd.com/amd-cpu-libraries/amd-math-library-libm/' -description = """AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor based machines.""" +description = """AMD LibM is a software library containing a collection of basic math functions + optimized for x86-64 processor based machines.""" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} From 4d4bc9315998b1e951bf343556f40c00ccd56fd6 Mon Sep 17 00:00:00 2001 From: ec2-user Date: Thu, 15 Nov 2018 07:00:45 +0000 Subject: [PATCH 0108/5331] adding easyconfigs: AMD-RNG-1.0-GCC-7.3.0-2.30.eb, AMD-SecureRNG-1.0-GCC-7.3.0-2.30.eb --- .../a/AMD-RNG/AMD-RNG-1.0-GCC-7.3.0-2.30.eb | 21 ++++++++++++++++++ .../AMD-SecureRNG-1.0-GCC-7.3.0-2.30.eb | 22 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMD-RNG/AMD-RNG-1.0-GCC-7.3.0-2.30.eb create mode 100644 easybuild/easyconfigs/a/AMD-SecureRNG/AMD-SecureRNG-1.0-GCC-7.3.0-2.30.eb diff --git a/easybuild/easyconfigs/a/AMD-RNG/AMD-RNG-1.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/a/AMD-RNG/AMD-RNG-1.0-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..6981d470afc --- /dev/null +++ b/easybuild/easyconfigs/a/AMD-RNG/AMD-RNG-1.0-GCC-7.3.0-2.30.eb @@ -0,0 +1,21 @@ +easyblock = 'Binary' + +name = 'AMD-RNG' +version = '1.0' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/rng-library/' +description = """AMD Random Number Generator Library is a pseudorandom number generator library.""" + +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} + +sources = ['%(name)s-Linux-%(version)s.tar.gz'] +checksums = ['55ca89a8b3bfe5ad84700b0a7659612286d8b3f1853a1dc28fedea577edb61d6'] + +extract_sources = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['rng-1.0/lib', 'rng-omp-1.0/lib', 'rng-omp-1.0/lib_omp'] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/AMD-SecureRNG/AMD-SecureRNG-1.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/a/AMD-SecureRNG/AMD-SecureRNG-1.0-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..a7ffd6ab5f6 --- /dev/null +++ b/easybuild/easyconfigs/a/AMD-SecureRNG/AMD-SecureRNG-1.0-GCC-7.3.0-2.30.eb @@ -0,0 +1,22 @@ +easyblock = 'Binary' + +name = 'AMD-SecureRNG' +version = '1.0' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/rng-library/' +description = """The AMD Secure Random Number Generator (RNG) is a library that provides APIs to access the + cryptographically secure random numbers generated by AMD’s hardware-based random number generator implementation.""" + +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} + +sources = ['%(name)s-Linux-%(version)s.tar.gz'] +checksums = ['9c599d49deb3a0fc2c8787a8c8f950d5abf0b2c2424f172120025e27e1bde934'] + +extract_sources = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib'], +} + +moduleclass = 'numlib' From ed57d1f40e2a2dfe721e49793aaa8f5ae5413eef Mon Sep 17 00:00:00 2001 From: ec2-user Date: Thu, 15 Nov 2018 07:06:28 +0000 Subject: [PATCH 0109/5331] fix style --- easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb index 0b8690ced99..a7295a5fb52 100644 --- a/easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'AMD-BLIS' -version = 1.2 +version = '1.2' homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' description = """AMD fork of BLIS. BLIS is a portable software framework for instantiating high-performance From 8e271ffbb0287b7c7acf3d89899129b4f1ef4cdd Mon Sep 17 00:00:00 2001 From: ec2-user Date: Thu, 15 Nov 2018 07:40:18 +0000 Subject: [PATCH 0110/5331] add easyconfig for AMD-libFLAME --- .../AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb diff --git a/easybuild/easyconfigs/a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..812cf63fa01 --- /dev/null +++ b/easybuild/easyconfigs/a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'AMD-libFLAME' +version = '1.0' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame' +description = """AMD fork of libFLAME. libFLAME is a portable library for dense matrix computations, + providing much of the functionality present in LAPACK.""" + +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} + +source_urls = ['https://github.com/amd/libflame/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['11e7b21b59849416ac372ef2c2b38beb73e62bead85d0ae3ffd0f4f1f6f760cf'] + +dependencies = [('AMD-BLIS', '1.2')] + +configopts = '--enable-max-arg-list-hack --enable-lapack2flame --enable-cblas-interfaces' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/FLAME.h', 'lib/libflame.a'], + 'dirs': ['lib'], +} + +moduleclass = 'numlib' From 7a975a028311147dccc416a9144df8058605dfd5 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 15 Nov 2018 13:02:47 +0100 Subject: [PATCH 0111/5331] Fix long lines. Used inject-checksum so some code got moved around. --- .../QuantumESPRESSO-6.2.1-iomkl-2017b.eb | 21 +++++++++---------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb index dfc2419020b..8ced07dde78 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb @@ -18,18 +18,22 @@ toolchainopts = {'usempi': True, 'openmp': True} # no added benefit to build it inside QM-E # - Want is never installed in bin/ (since it first shows up in 4.2) so # don't bother building it here. -sources = [ - 'qe-%(version)s.tar.gz', - 'wannier90-2.1.0.tar.gz', -] - source_urls = [ # 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.wannier.org/code/', # wannier90-2.1.0.tar.gz 'http://qe-forge.org/gf/download/frsrelease/247/1132/', # qe-6.2.1.tar.gz ] - +sources = [ + 'qe-%(version)s.tar.gz', + 'wannier90-2.1.0.tar.gz', +] patches = ['%(name)s-%(version)s_fix_missing_include_dir_in_COUPLE.patch'] +checksums = [ + '6cdd4c8883b4a2262ac98ea452f845ed935294b3988a84b238d833558eb90f0c', # qe-6.2.1.tar.gz + 'ee90108d4bc4aa6a1cf16d72abebcb3087cf6c1007d22dda269eb7e7076bddca', # wannier90-2.1.0.tar.gz + # QuantumESPRESSO-6.2.1_fix_missing_include_dir_in_COUPLE.patch + '44751fe9d1e6eede4ba331e7216e222960ff19ba9170aaa0cd4393924aa54fbc', +] dependencies = [ ('HDF5', '1.10.1'), @@ -38,11 +42,6 @@ dependencies = [ ] # source checksums -checksums = [ - '6cdd4c8883b4a2262ac98ea452f845ed935294b3988a84b238d833558eb90f0c', # qe-6.2.1.tar.gz - 'ee90108d4bc4aa6a1cf16d72abebcb3087cf6c1007d22dda269eb7e7076bddca', # wannier90-2.1.0.tar.gz - '44751fe9d1e6eede4ba331e7216e222960ff19ba9170aaa0cd4393924aa54fbc', # QuantumESPRESSO-6.2.1_fix_missing_include_dir_in_COUPLE.patch -] buildopts = 'all gwl xspectra couple epw w90' From a984f5b516f76343d8dee2e810763d22984714c5 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 15 Nov 2018 14:18:07 +0100 Subject: [PATCH 0112/5331] Fix style complaint from hound. --- .../q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb index 8ced07dde78..609daae07d2 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb @@ -19,9 +19,9 @@ toolchainopts = {'usempi': True, 'openmp': True} # - Want is never installed in bin/ (since it first shows up in 4.2) so # don't bother building it here. source_urls = [ -# 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz +# 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.wannier.org/code/', # wannier90-2.1.0.tar.gz - 'http://qe-forge.org/gf/download/frsrelease/247/1132/', # qe-6.2.1.tar.gz + 'http://qe-forge.org/gf/download/frsrelease/247/1132/', # qe-6.2.1.tar.gz ] sources = [ 'qe-%(version)s.tar.gz', From 3220cd93cd05765f22301f0e302e6bdff040b243 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 15 Nov 2018 16:06:42 +0100 Subject: [PATCH 0113/5331] Fix one more style complaint from hound. --- .../q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb index 609daae07d2..876f8992213 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb @@ -20,7 +20,7 @@ toolchainopts = {'usempi': True, 'openmp': True} # don't bother building it here. source_urls = [ # 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz - 'http://www.wannier.org/code/', # wannier90-2.1.0.tar.gz + 'http://www.wannier.org/code/', # wannier90-2.1.0.tar.gz 'http://qe-forge.org/gf/download/frsrelease/247/1132/', # qe-6.2.1.tar.gz ] sources = [ From c674a3dd5db77db0d47e36d6a2d5b7c61e27bb1a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 15 Nov 2018 17:59:10 +0100 Subject: [PATCH 0114/5331] Fix one more style complaint from hound. --- .../q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb index 876f8992213..797a71243fb 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb @@ -19,7 +19,7 @@ toolchainopts = {'usempi': True, 'openmp': True} # - Want is never installed in bin/ (since it first shows up in 4.2) so # don't bother building it here. source_urls = [ -# 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz + # 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.wannier.org/code/', # wannier90-2.1.0.tar.gz 'http://qe-forge.org/gf/download/frsrelease/247/1132/', # qe-6.2.1.tar.gz ] From 46e61a5e0ec6ef5d21c37366ece045927d1dab99 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 16 Nov 2018 18:09:03 +0800 Subject: [PATCH 0115/5331] also build libflame dynamic lib --- .../AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb | 8 +++-- .../m/make/make-4.2.1-GCC-7.3.0-2.30.eb | 31 +++++++++++++++++++ 2 files changed, 37 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb diff --git a/easybuild/easyconfigs/a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb index 812cf63fa01..db6eae93ded 100644 --- a/easybuild/easyconfigs/a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb @@ -8,19 +8,23 @@ description = """AMD fork of libFLAME. libFLAME is a portable library for dense providing much of the functionality present in LAPACK.""" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} +toolchainopts = {'pic': True} source_urls = ['https://github.com/amd/libflame/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['11e7b21b59849416ac372ef2c2b38beb73e62bead85d0ae3ffd0f4f1f6f760cf'] +# '--enable-max-arg-list-hack --enable-dynamic-build' requires 'file' function from GNU Make 4.x +builddependencies = [('make', '4.2.1')] + dependencies = [('AMD-BLIS', '1.2')] -configopts = '--enable-max-arg-list-hack --enable-lapack2flame --enable-cblas-interfaces' +configopts = '--enable-max-arg-list-hack --enable-lapack2flame --enable-cblas-interfaces --enable-dynamic-build' runtest = 'check' sanity_check_paths = { - 'files': ['include/FLAME.h', 'lib/libflame.a'], + 'files': ['include/FLAME.h', 'lib/libflame.a', 'lib/libflame.%s' % SHLIB_EXT], 'dirs': ['lib'], } diff --git a/easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..a25d9bda13b --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.2.1' + +homepage = 'http://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['d6e262bf3601b42d2b1e4ef8310029e1dcf20083c5446b4b7aa67081fdffc589'] + +sanity_check_paths = { + 'files': ['bin/make'], + 'dirs': [] +} + +moduleclass = 'devel' From 2540e941207c70fc3af589985b35e875ff7de334 Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Sun, 28 Oct 2018 14:38:46 +0100 Subject: [PATCH 0116/5331] ENH: support WRF and WPS v4.0.1 (intel-2018b) --- .../w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb | 34 +++ .../w/WPS/WPS-4.0.1_find-wrfdir.patch | 20 ++ ...S-4.0.1_netCDF-Fortran_seperate_path.patch | 70 +++++ .../w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb | 38 +++ ...F-4.0.1_netCDF-Fortran_separate_path.patch | 254 ++++++++++++++++++ 5 files changed, 416 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb new file mode 100644 index 00000000000..4528b3ee5fd --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb @@ -0,0 +1,34 @@ +name = 'WPS' +version = '4.0.1' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'opt': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/wrf-model/WPS/archive/'] + +checksums = ['1379cee8029818e7a69376a7c425d1a00801284182dd0f56a58a753703d5fb2b'] + +patches = [ + 'WPS-%(version)s_netCDF-Fortran_seperate_path.patch', + 'WPS-%(version)s_find-wrfdir.patch', +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +dependencies = [ + ('WRF', version, '%s' % versionsuffix), + ('JasPer', '2.0.14'), + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('zlib', '1.2.11'), + ('libpng', '1.6.34'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch new file mode 100644 index 00000000000..982ddd0845b --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch @@ -0,0 +1,20 @@ +diff -uNr WPS-4.0.1.orig/arch/preamble WPS-4.0.1/arch/preamble +--- WPS-4.0.1.orig/arch/preamble 2018-10-02 18:21:14.000000000 +0200 ++++ WPS-4.0.1/arch/preamble 2018-10-26 16:05:10.676021080 +0200 +@@ -39,13 +39,13 @@ + # repository, or an older WRF v3.x tar file. + # To override the path to the compiled WRF code, just set the WRF_DIR variable after the "endif" below + # +-ifneq ($(wildcard $(DEV_TOP)/../WRF-4.0.1), ) # Check for WRF v4.0.1 directory (probably GitHub archive) ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF-4.0.1), ) # Check for WRF v4.0.1 directory (probably GitHub archive) + WRF_DIR = ../WRF-4.0.1 + else +-ifneq ($(wildcard $(DEV_TOP)/../WRF-4.0), ) # Check for WRF v4.0 directory (probably GitHub archive) ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF-4.0), ) # Check for WRF v4.0 directory (probably GitHub archive) + WRF_DIR = ../WRF-4.0 + else +-ifneq ($(wildcard $(DEV_TOP)/../WRF), ) # Check for clone of the WRF repository ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF), ) # Check for clone of the WRF repository + WRF_DIR = ../WRF + else # Check for old WRF v3.x directory + WRF_DIR = ../WRFV3 diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch new file mode 100644 index 00000000000..d4584dde87c --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch @@ -0,0 +1,70 @@ +diff -uNr WPS.orig/arch/Config.pl WPS/arch/Config.pl +--- WPS.orig/arch/Config.pl 2017-07-13 01:16:49.000000000 +0200 ++++ WPS/arch/Config.pl 2017-10-05 15:09:46.656317470 +0200 +@@ -36,6 +36,7 @@ + if(substr( $ARGV[0], 1, 8 ) eq "netcdff=") + { + $sw_netcdff_lib = substr( $ARGV[0], 9); ++ $sw_netcdff_lib =~ s/!/ /g ; + } + if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") + { +diff -uNr WPS.orig/configure WPS/configure +--- WPS.orig/configure 2017-07-13 01:16:49.000000000 +0200 ++++ WPS/configure 2017-10-05 15:11:12.749218059 +0200 +@@ -119,9 +119,14 @@ + echo "Will use NETCDF in dir: $NETCDF" + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available +- NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then +- NETCDFF="-lnetcdff" ++ USENETCDFF=" " ++ # for netCDF 4.2 and greater, the Fortran library is a seperate install ++ if [ -z "$NETCDFF" ] ++ then ++ NETCDFF=$NETCDF ++ fi ++ if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-lnetcdff" + fi + else + echo "Will configure for use without NetCDF" +@@ -151,7 +156,7 @@ + fi + + # Found perl, so proceed with configuration +-perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$NETCDFF -os=$os -mach=$mach ++perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$USENETCDFF -os=$os -mach=$mach + + + #Checking cross-compiling capability for some particular environment +@@ -317,9 +322,9 @@ + end program + EOF + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -lnetcdf $USENETCDFF > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + ./fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then +diff -uNr WPS.orig/util/src/Makefile WPS/util/src/Makefile +--- WPS.orig/util/src/Makefile 2017-07-13 01:16:50.000000000 +0200 ++++ WPS/util/src/Makefile 2017-10-05 15:12:07.359886380 +0200 +@@ -41,11 +41,11 @@ + write_met_module.o misc_definitions_module.o met_data_module.o + $(SFC) $(LDFLAGS) -o $@ elev_angle.o cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o met_data_module.o \ +- -L$(NETCDF)/lib -I$(NETCDF)/include -lnetcdf ++ -L$(NETCDFF)/lib -I$(NETCDFF)/include -lnetcdff + + elev_angle.o: elev_angle.F cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o +- $(SFC) -c elev_angle.F -I$(NETCDF)/include ++ $(SFC) -c elev_angle.F -I$(NETCDFF)/include + + calc_ecmwf_p.exe: calc_ecmwf_p.o cio.o module_debug.o module_stringutil.o gridinfo_module.o read_met_module.o \ + write_met_module.o module_date_pack.o misc_definitions_module.o met_data_module.o constants_module.o diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb new file mode 100644 index 00000000000..19bb8bc2cda --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb @@ -0,0 +1,38 @@ +name = 'WRF' +version = '4.0.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/wrf-model/WRF/archive/'] + +checksums = ['a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe'] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.20.00')] + +dependencies = [ + ('JasPer', '2.0.14'), + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', +# 'WRF-%(version)s_known_problems.patch', # no known problems as of 2018-10-19 +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..607bfdad074 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch @@ -0,0 +1,254 @@ +diff -uNr WRF-4.0.1.orig/arch/Config.pl WRF-4.0.1/arch/Config.pl +--- WRF-4.0.1.orig/arch/Config.pl 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/arch/Config.pl 2018-10-25 00:03:03.060958813 +0200 +@@ -8,6 +8,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; # for netCDF 4.2 and greater, Fortran lib might be in a different path + $sw_pnetcdf_path = "" ; + $sw_hdf5_path=""; + $sw_phdf5_path=""; +@@ -90,6 +91,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -117,6 +122,7 @@ + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { + $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -439,6 +445,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ; + $_ =~ s/CONFIGURE_PHDF5_PATH/$sw_phdf5_path/g ; +@@ -485,7 +492,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +diff -uNr WRF-4.0.1.orig/arch/configure.defaults WRF-4.0.1/arch/configure.defaults +--- WRF-4.0.1.orig/arch/configure.defaults 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/arch/configure.defaults 2018-10-19 17:57:23.437418176 +0200 +@@ -1598,6 +1598,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +diff -uNr WRF-4.0.1.orig/arch/conf_tokens WRF-4.0.1/arch/conf_tokens +--- WRF-4.0.1.orig/arch/conf_tokens 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/arch/conf_tokens 2018-10-23 10:19:00.867135754 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDFF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -uNr WRF-4.0.1.orig/arch/postamble WRF-4.0.1/arch/postamble +--- WRF-4.0.1.orig/arch/postamble 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/arch/postamble 2018-10-24 08:53:53.042677598 +0200 +@@ -47,7 +47,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/wrftladj \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ +- -I$(NETCDFPATH)/include \ ++ -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include \ + CONFIGURE_RTTOV_INC + REGISTRY = Registry + CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE +@@ -70,6 +70,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + RTTOVPATH = CONFIGURE_RTTOV_PATH +@@ -101,13 +102,13 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_pnf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \ +- make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ ++ make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ + FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_grib_share : +diff -uNr WRF-4.0.1.orig/configure WRF-4.0.1/configure +--- WRF-4.0.1.orig/configure 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/configure 2018-10-19 18:39:36.232467326 +0200 +@@ -183,12 +183,20 @@ + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" ] ; then + USENETCDFF="-lnetcdff" + else +- USENETCDFF=" " ++ if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++ else ++ USENETCDFF=" " ++ fi + fi +- if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" ] ; then ++ if [ -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then + USENETCDF="-lnetcdf" + else +- USENETCDF=" " ++ if [ -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then ++ USENETCDF="-L$NETCDF/lib!-L$NETCDF/lib64!-lnetcdf" # ! will be replaced with space ++ else ++ USENETCDF=" " ++ fi + fi + export USENETCDF=$USENETCDF + export USENETCDFF=$USENETCDFF +@@ -629,14 +637,14 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +diff -uNr WRF-4.0.1.orig/external/io_netcdf/makefile WRF-4.0.1/external/io_netcdf/makefile +--- WRF-4.0.1.orig/external/io_netcdf/makefile 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/external/io_netcdf/makefile 2018-10-19 18:11:19.135941823 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib64/libnetcdff.a -o -f $(NETCDFFPATH)/lib64/libnetcdff.so \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -uNr WRF-4.0.1.orig/external/io_pnetcdf/Makefile WRF-4.0.1/external/io_pnetcdf/Makefile +--- WRF-4.0.1.orig/external/io_pnetcdf/Makefile 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/external/io_pnetcdf/Makefile 2018-10-19 18:11:49.369236552 +0200 +@@ -9,8 +9,8 @@ + ext_pnc_put_var_td.code \ + ext_pnc_put_var_ti.code \ + transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = -L$(NETCDFPATH)/lib -lpnetcdf ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = -L$(NETCDFFPATH)/lib -lpnetcdf + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -25,15 +25,15 @@ + $(RANLIB) libwrfio_pnf.a + + wrf_io.o: wrf_io.F90 $(CODE) +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f + $(FC) $(FFLAGS) -c wrf_io.f + + module_wrfsi_static.o: module_wrfsi_static.F90 +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f + $(FC) $(FFLAGS) -c module_wrfsi_static.f + + field_routines.o: field_routines.F90 wrf_io.o +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f + $(FC) $(FFLAGS) -c field_routines.f + + superclean: +diff -uNr WRF-4.0.1.orig/Makefile WRF-4.0.1/Makefile +--- WRF-4.0.1.orig/Makefile 2018-10-03 00:17:21.000000000 +0200 ++++ WRF-4.0.1/Makefile 2018-10-19 18:23:30.857876650 +0200 +@@ -906,7 +906,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \ + FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ +@@ -1036,7 +1036,7 @@ + + # rule used by configure to test if this will compile with netcdf4 + nc4_test: +- @cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib $(USENETCDF) ; cd .. ++ @cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 $(USENETCDF) ; cd .. + + # rule used by configure to test if Fortran 2003 IEEE signaling is available + fortran_2003_ieee_test: From e567a1f07173fb9f9c5d3047df680827e226bb89 Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Sun, 28 Oct 2018 15:58:52 +0100 Subject: [PATCH 0117/5331] ENH: add tcsh-6.20.00 (GCCcore-7.3.0) --- .../t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..a4366a50622 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.20.00' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.30', '', True)] + +dependencies = [('ncurses', '6.1')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' From 57f2286570e804a53ff97bb07a4a357344d1364f Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Sun, 28 Oct 2018 18:56:07 +0100 Subject: [PATCH 0118/5331] STY: fix style, add checksums --- .../t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb | 6 +++--- .../w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb | 10 ++++++---- .../w/WPS/WPS-4.0.1_find-wrfdir.patch | 8 ++++++++ ...S-4.0.1_netCDF-Fortran_seperate_path.patch | 5 +++++ .../w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb | 20 ++++++++++--------- ...F-4.0.1_netCDF-Fortran_separate_path.patch | 5 +++++ 6 files changed, 38 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb index a4366a50622..5bd9169ede5 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb @@ -22,14 +22,14 @@ description = """Tcsh is an enhanced, but completely compatible version of the B toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -sources = [SOURCELOWER_TAR_GZ] source_urls = [ 'ftp://ftp.astron.com/pub/%(namelower)s', 'ftp://ftp.astron.com/pub/%(namelower)s/old', ] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b89de7064ab54dac454a266cfe5d8bf66940cb5ed048d0c30674ea62e7ecef9d'] -# use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.30', '', True)] +builddependencies = [('binutils', '2.30')] dependencies = [('ncurses', '6.1')] diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb index 4528b3ee5fd..5a74b38bd1f 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb @@ -9,15 +9,17 @@ description = """WRF Preprocessing System (WPS) for WRF. The Weather Research an toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'opt': True} -sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/wrf-model/WPS/archive/'] - -checksums = ['1379cee8029818e7a69376a7c425d1a00801284182dd0f56a58a753703d5fb2b'] - +sources = ['v%(version)s.tar.gz'] patches = [ 'WPS-%(version)s_netCDF-Fortran_seperate_path.patch', 'WPS-%(version)s_find-wrfdir.patch', ] +checksums = [ + '1379cee8029818e7a69376a7c425d1a00801284182dd0f56a58a753703d5fb2b', # v4.0.1.tar.gz + 'ca8e931847658b0fe24283dc16a87479c8093571f4bae9a04fa1ab6cad49bcb1', # WPS-4.0.1_netCDF-Fortran_seperate_path.patch + '279fc79909a3eb0370fea0bdf5690e0d5bfb9c5d04350f10ae0bf48680238111', # WPS-4.0.1_find-wrfdir.patch +] buildtype = "dmpar" versionsuffix = '-%s' % buildtype diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch index 982ddd0845b..50413e35aff 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_find-wrfdir.patch @@ -1,3 +1,11 @@ +# Allow WRF source code directory to be located in EasyBuild module tree +# ============================================================================ +# Since WPS v4.0, the WPS build system seems to make strong assumptions on +# where to find the WRF source code. This patch allows the WRF source code to +# be found also when WRF is located in the EasyBuild module tree. $WRF_DIR_PRE +# is being set from the wps EasyBlock. +# Patch written by @andreas-h (Oct 2018) + diff -uNr WPS-4.0.1.orig/arch/preamble WPS-4.0.1/arch/preamble --- WPS-4.0.1.orig/arch/preamble 2018-10-02 18:21:14.000000000 +0200 +++ WPS-4.0.1/arch/preamble 2018-10-26 16:05:10.676021080 +0200 diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch index d4584dde87c..432299fbcaf 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch @@ -1,3 +1,8 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since 2013; it was committed by +# @boegel then. + diff -uNr WPS.orig/arch/Config.pl WPS/arch/Config.pl --- WPS.orig/arch/Config.pl 2017-07-13 01:16:49.000000000 +0200 +++ WPS/arch/Config.pl 2017-10-05 15:09:46.656317470 +0200 diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb index 19bb8bc2cda..0b5fb87e213 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb @@ -9,10 +9,18 @@ description = """The Weather Research and Forecasting (WRF) Model is a next-gene toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 -sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/wrf-model/WRF/archive/'] - -checksums = ['a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', + # 'WRF-%(version)s_known_problems.patch', # no known problems as of 2018-10-19 + ] +checksums = [ + 'a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe', # v4.0.1.tar.gz + 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + 'c5287268f0f1f4f8816c3384a59ff10649f68ceee11d24238149ea27620f5ba1', # WRF-4.0.1_netCDF-Fortran_separate_path.patch +] # csh is used by WRF install scripts builddependencies = [('tcsh', '6.20.00')] @@ -23,12 +31,6 @@ dependencies = [ ('netCDF-Fortran', '4.4.4'), ] -patches = [ - 'WRF_parallel_build_fix.patch', - 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', -# 'WRF-%(version)s_known_problems.patch', # no known problems as of 2018-10-19 -] - # limit parallel build to 20 maxparallel = 20 diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch index 607bfdad074..3196108ca09 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch @@ -1,3 +1,8 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since WRF3.5; it was committed by +# @boegel then. + diff -uNr WRF-4.0.1.orig/arch/Config.pl WRF-4.0.1/arch/Config.pl --- WRF-4.0.1.orig/arch/Config.pl 2018-10-03 00:17:21.000000000 +0200 +++ WRF-4.0.1/arch/Config.pl 2018-10-25 00:03:03.060958813 +0200 From d30fffc2a70871438bedd6c857c08c1303c64f5d Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Sun, 28 Oct 2018 20:49:50 +0100 Subject: [PATCH 0119/5331] STY: pep8 --- easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb index 0b5fb87e213..ca86ca58b68 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb @@ -15,7 +15,7 @@ patches = [ 'WRF_parallel_build_fix.patch', 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', # 'WRF-%(version)s_known_problems.patch', # no known problems as of 2018-10-19 - ] +] checksums = [ 'a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe', # v4.0.1.tar.gz 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch From 132be7b2be46e1347c0a4a49a44b6178cb983dfa Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Wed, 7 Nov 2018 12:17:12 +0100 Subject: [PATCH 0120/5331] STY: fix minor issues --- easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb | 2 +- easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb index 5a74b38bd1f..f4728ca2a06 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb @@ -25,7 +25,7 @@ buildtype = "dmpar" versionsuffix = '-%s' % buildtype dependencies = [ - ('WRF', version, '%s' % versionsuffix), + ('WRF', version, versionsuffix), ('JasPer', '2.0.14'), ('netCDF', '4.6.1'), ('netCDF-Fortran', '4.4.4'), diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb index ca86ca58b68..1dce8c20568 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb @@ -14,7 +14,6 @@ sources = ['v%(version)s.tar.gz'] patches = [ 'WRF_parallel_build_fix.patch', 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', - # 'WRF-%(version)s_known_problems.patch', # no known problems as of 2018-10-19 ] checksums = [ 'a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe', # v4.0.1.tar.gz From ec41e4b1fbfd61622384e2f69743ce122164cfd7 Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Wed, 21 Nov 2018 17:20:37 +0100 Subject: [PATCH 0121/5331] BUG: fix WRFv4 and WPSv4 build problems on some platforms Using the easyblocks from easybuilders/easybuild-easyblocks#1592, this fixes build problems occurring on some platforms. I can successfully build on Debian/Buster (my laptop) using foss-2018b, and on our HPC using both intel-2018b and foss-2018b. --- .../w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb | 4 +- .../w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb | 36 +++++++++++++++++ .../w/WPS/WPS-4.0.2_find-wrfdir.patch | 24 ++++++++++++ ... WPSv4_netCDF-Fortran_seperate_path.patch} | 20 ++++++++-- .../w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb | 4 +- .../w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb | 39 +++++++++++++++++++ ... WRFv4_netCDF-Fortran_separate_path.patch} | 35 +++++++++-------- 7 files changed, 138 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch rename easybuild/easyconfigs/w/WPS/{WPS-4.0.1_netCDF-Fortran_seperate_path.patch => WPSv4_netCDF-Fortran_seperate_path.patch} (76%) create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb rename easybuild/easyconfigs/w/WRF/{WRF-4.0.1_netCDF-Fortran_separate_path.patch => WRFv4_netCDF-Fortran_separate_path.patch} (90%) diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb index f4728ca2a06..2c7853c159f 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.1-intel-2018b-dmpar.eb @@ -12,12 +12,12 @@ toolchainopts = {'opt': True} source_urls = ['https://github.com/wrf-model/WPS/archive/'] sources = ['v%(version)s.tar.gz'] patches = [ - 'WPS-%(version)s_netCDF-Fortran_seperate_path.patch', + 'WPSv4_netCDF-Fortran_seperate_path.patch', 'WPS-%(version)s_find-wrfdir.patch', ] checksums = [ '1379cee8029818e7a69376a7c425d1a00801284182dd0f56a58a753703d5fb2b', # v4.0.1.tar.gz - 'ca8e931847658b0fe24283dc16a87479c8093571f4bae9a04fa1ab6cad49bcb1', # WPS-4.0.1_netCDF-Fortran_seperate_path.patch + '495341f7ae883ba4eb1fbeb41f336745d55d6b63e79360d35680c3f7f29f01ec', # WPSv4_netCDF-Fortran_seperate_path.patch '279fc79909a3eb0370fea0bdf5690e0d5bfb9c5d04350f10ae0bf48680238111', # WPS-4.0.1_find-wrfdir.patch ] diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb new file mode 100644 index 00000000000..24257a43d60 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.2-foss-2018b-dmpar.eb @@ -0,0 +1,36 @@ +name = 'WPS' +version = '4.0.2' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WPSv4_netCDF-Fortran_seperate_path.patch', + 'WPS-%(version)s_find-wrfdir.patch', +] +checksums = [ + 'e053b3348d942288d04aca642ec700d97ec6895d6ef96ffa6168581c127dac00', # v4.0.2.tar.gz + '495341f7ae883ba4eb1fbeb41f336745d55d6b63e79360d35680c3f7f29f01ec', # WPSv4_netCDF-Fortran_seperate_path.patch + '4c8ac67526c3600a5252f2fe8efbe706a556af1b3f58e206a734f31899fbeee9', # WPS-4.0.2_find-wrfdir.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +dependencies = [ + ('WRF', version, versionsuffix), + ('JasPer', '2.0.14'), + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('zlib', '1.2.11'), + ('libpng', '1.6.34'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch b/easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch new file mode 100644 index 00000000000..fc1a67d5426 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.0.2_find-wrfdir.patch @@ -0,0 +1,24 @@ +diff -uNr WPS-4.0.2.orig/arch/preamble WPS-4.0.2/arch/preamble +--- WPS-4.0.2.orig/arch/preamble 2018-11-10 01:13:04.000000000 +0100 ++++ WPS-4.0.2/arch/preamble 2018-11-21 16:42:38.066848290 +0100 +@@ -39,16 +39,16 @@ + # repository, or an older WRF v3.x tar file. + # To override the path to the compiled WRF code, just set the WRF_DIR variable after the "endif" below + # +-ifneq ($(wildcard $(DEV_TOP)/../WRF-4.0.2), ) # Check for WRF v4.0.2 directory (probably GitHub archive) ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF-4.0.2), ) # Check for WRF v4.0.2 directory (probably GitHub archive) + WRF_DIR = ../WRF-4.0.2 + else +-ifneq ($(wildcard $(DEV_TOP)/../WRF-4.0.1), ) # Check for WRF v4.0.1 directory (probably GitHub archive) ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF-4.0.1), ) # Check for WRF v4.0.1 directory (probably GitHub archive) + WRF_DIR = ../WRF-4.0.1 + else +-ifneq ($(wildcard $(DEV_TOP)/../WRF-4.0), ) # Check for WRF v4.0 directory (probably GitHub archive) ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF-4.0), ) # Check for WRF v4.0 directory (probably GitHub archive) + WRF_DIR = ../WRF-4.0 + else +-ifneq ($(wildcard $(DEV_TOP)/../WRF), ) # Check for clone of the WRF repository ++ifneq ($(wildcard $(WRF_DIR_PRE)/../WRF), ) # Check for clone of the WRF repository + WRF_DIR = ../WRF + else # Check for old WRF v3.x directory + WRF_DIR = ../WRFV3 diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPSv4_netCDF-Fortran_seperate_path.patch similarity index 76% rename from easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch rename to easybuild/easyconfigs/w/WPS/WPSv4_netCDF-Fortran_seperate_path.patch index 432299fbcaf..22d13491dfc 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.0.1_netCDF-Fortran_seperate_path.patch +++ b/easybuild/easyconfigs/w/WPS/WPSv4_netCDF-Fortran_seperate_path.patch @@ -1,7 +1,7 @@ # Allow netCDF library with separate directories for C and Fortran # ============================================================================ # This patch has been around in EasyBuild since 2013; it was committed by -# @boegel then. +# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain diff -uNr WPS.orig/arch/Config.pl WPS/arch/Config.pl --- WPS.orig/arch/Config.pl 2017-07-13 01:16:49.000000000 +0200 @@ -14,9 +14,21 @@ diff -uNr WPS.orig/arch/Config.pl WPS/arch/Config.pl } if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") { -diff -uNr WPS.orig/configure WPS/configure ---- WPS.orig/configure 2017-07-13 01:16:49.000000000 +0200 -+++ WPS/configure 2017-10-05 15:11:12.749218059 +0200 +diff -uNr WPS-4.0.1.orig/arch/preamble WPS-4.0.1.ncff/arch/preamble +--- WPS-4.0.1.orig/arch/preamble 2018-10-02 18:21:14.000000000 +0200 ++++ WPS-4.0.1.ncff/arch/preamble 2018-11-20 17:25:13.005578671 +0100 +@@ -59,7 +59,7 @@ + -I$(WRF_DIR)/external/io_grib1 \ + -I$(WRF_DIR)/external/io_int \ + -I$(WRF_DIR)/inc \ +- -I$(NETCDF)/include ++ -I$(NETCDF)/include -I$(NETCDFF)/include + + WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ + -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ +diff -uNr WPS-4.0.1.orig/configure WPS-4.0.1.ncff/configure +--- WPS-4.0.1.orig/configure 2018-10-02 18:21:14.000000000 +0200 ++++ WPS-4.0.1.ncff/configure 2018-11-20 17:59:14.299417528 +0100 @@ -119,9 +119,14 @@ echo "Will use NETCDF in dir: $NETCDF" # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb index 1dce8c20568..da0969fb160 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb @@ -13,12 +13,12 @@ source_urls = ['https://github.com/wrf-model/WRF/archive/'] sources = ['v%(version)s.tar.gz'] patches = [ 'WRF_parallel_build_fix.patch', - 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', + 'WRFv4_netCDF-Fortran_separate_path.patch', ] checksums = [ 'a14fe10ffe615d4cd1888d6f9d1dfc4aa46478f2ff360399feb8549748aa94fe', # v4.0.1.tar.gz 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch - 'c5287268f0f1f4f8816c3384a59ff10649f68ceee11d24238149ea27620f5ba1', # WRF-4.0.1_netCDF-Fortran_separate_path.patch + '3b9b1334b4611f924961008181d0202d2e3160af67d67b2ab5869d0db968cac9', # WRFv4_netCDF-Fortran_separate_path.patch ] # csh is used by WRF install scripts diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb new file mode 100644 index 00000000000..984cd3a1abe --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb @@ -0,0 +1,39 @@ +name = 'WRF' +version = '4.0.2' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRFv4_netCDF-Fortran_separate_path.patch', +] +checksums = [ + '161637aded4c1b30105cee66d3dee5d0f5bd57a78a4a8704d1dde1734f83a17e', # v4.0.2.tar.gz + 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + '3b9b1334b4611f924961008181d0202d2e3160af67d67b2ab5869d0db968cac9', # WRFv4_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.20.00')] + +dependencies = [ + ('JasPer', '2.0.14'), + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRFv4_netCDF-Fortran_separate_path.patch similarity index 90% rename from easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch rename to easybuild/easyconfigs/w/WRF/WRFv4_netCDF-Fortran_separate_path.patch index 3196108ca09..a7527b42d44 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.0.1_netCDF-Fortran_separate_path.patch +++ b/easybuild/easyconfigs/w/WRF/WRFv4_netCDF-Fortran_separate_path.patch @@ -1,11 +1,11 @@ # Allow netCDF library with separate directories for C and Fortran # ============================================================================ # This patch has been around in EasyBuild since WRF3.5; it was committed by -# @boegel then. +# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain diff -uNr WRF-4.0.1.orig/arch/Config.pl WRF-4.0.1/arch/Config.pl --- WRF-4.0.1.orig/arch/Config.pl 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/arch/Config.pl 2018-10-25 00:03:03.060958813 +0200 ++++ WRF-4.0.1/arch/Config.pl 2018-11-19 14:20:04.776144494 +0100 @@ -8,6 +8,7 @@ select((select(STDOUT), $|=1)[0]); $sw_perl_path = perl ; @@ -46,7 +46,7 @@ diff -uNr WRF-4.0.1.orig/arch/Config.pl WRF-4.0.1/arch/Config.pl $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; } else { - $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; -+ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; } } else @@ -116,8 +116,8 @@ diff -uNr WRF-4.0.1.orig/arch/postamble WRF-4.0.1/arch/postamble wrfio_grib_share : diff -uNr WRF-4.0.1.orig/configure WRF-4.0.1/configure --- WRF-4.0.1.orig/configure 2018-10-03 00:17:21.000000000 +0200 -+++ WRF-4.0.1/configure 2018-10-19 18:39:36.232467326 +0200 -@@ -183,12 +183,20 @@ ++++ WRF-4.0.1/configure 2018-11-20 12:08:49.040926889 +0100 +@@ -183,10 +183,14 @@ if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" ] ; then USENETCDFF="-lnetcdff" else @@ -129,19 +129,22 @@ diff -uNr WRF-4.0.1.orig/configure WRF-4.0.1/configure + fi fi - if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" ] ; then -+ if [ -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then - USENETCDF="-lnetcdf" +- USENETCDF="-lnetcdf" ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then ++ USENETCDF="-lnetcdf" else -- USENETCDF=" " -+ if [ -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then -+ USENETCDF="-L$NETCDF/lib!-L$NETCDF/lib64!-lnetcdf" # ! will be replaced with space -+ else -+ USENETCDF=" " -+ fi + USENETCDF=" " fi - export USENETCDF=$USENETCDF - export USENETCDFF=$USENETCDFF -@@ -629,14 +637,14 @@ +@@ -549,7 +553,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -629,14 +633,14 @@ echo "If you wish to change the default options, edit the file:" echo " arch/configure.defaults" From bfc2a4a21b69bfee4af32ff82aa1798c176dd149 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 22 Nov 2018 16:38:48 +0100 Subject: [PATCH 0122/5331] adding easyconfigs: Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb --- ...b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb new file mode 100644 index 00000000000..5b8b2de2851 --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb @@ -0,0 +1,77 @@ +easyblock = 'CMakeMake' + +name = 'Blender' +version = '2.79b' +cuda_ver = '10.0.130' +versionsuffix = '-Python-%%(pyver)s-CUDA-%s' % cuda_ver + +homepage = 'https://www.blender.org/' +description = """Blender is the free and open source 3D creation suite. It supports + the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, + compositing and motion tracking, even video editing and game creation.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://download.blender.org/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4c944c304a49e68ac687ea06f5758204def049b66dc211e1cffa1857716393bc'] + +# disable SSE detection to give EasyBuild full control over optimization compiler flags being used +configopts = '-DWITH_CPU_SSE=OFF -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG" -DCMAKE_CXX_FLAGS_RELEASE="-DNDEBUG" ' + +# these are needed until extra dependencies are added for them to work +configopts += '-DWITH_INSTALL_PORTABLE=OFF ' +configopts += '-DWITH_BUILDINFO=OFF ' +configopts += '-DWITH_GAMEENGINE=OFF ' +configopts += '-DWITH_SYSTEM_GLEW=OFF ' + +# Python paths +site_packages = '$EBROOTPYTHON/lib/python%(pyshortver)s/site-packages' +configopts += '-DPYTHON_VERSION=%(pyshortver)s ' +configopts += '-DPYTHON_LIBRARY=${EBROOTPYTHON}/lib/libpython%%(pyshortver)sm.%s ' % SHLIB_EXT +configopts += '-DPYTHON_INCLUDE_DIR=${EBROOTPYTHON}/include/python%(pyshortver)sm ' +configopts += '-DPYTHON_NUMPY_PATH=' + site_packages + '/numpy-1.15.0-py%(pyshortver)s-linux-x86_64.egg ' +configopts += '-DPYTHON_REQUESTS_PATH=' + site_packages + '/requests-2.19.1-py%(pyshortver)s.egg ' + +# OpenEXR +configopts += '-DOPENEXR_INCLUDE_DIR=$EBROOTOPENEXR/include ' + +# OpenColorIO +configopts += '-DWITH_OPENCOLORIO=ON ' + +# CUDA +configopts += '-DWITH_CYCLES_CUDA_BINARIES=ON ' +configopts += '-DCYCLES_CUDA_BINARIES_ARCH="sm_30;sm_35;sm_37;sm_50;sm_52;sm_60;sm_61;sm_62;sm_72;sm_75" ' + +dependencies = [ + ('Python', '3.6.6'), + ('Boost', '1.67.0'), + ('libjpeg-turbo', '2.0.0'), + ('zlib', '1.2.11'), + ('X11', '20180604'), + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), + ('OpenColorIO', '1.1.0'), # for advanced color management + ('OpenImageIO', '1.8.16'), # required for cycles render engine + ('CUDA', cuda_ver, '', True), +] + +builddependencies = [('CMake', '3.12.1')] + +separate_build_dir = 'True' + +# remove CUPTI headers, included in CUDA, from CPATH +# the CUPTI directory contains old GL headers, which interfere with Blender +# see: https://github.com/easybuilders/easybuild-easyblocks/issues/1492 +# see: https://github.com/easybuilders/easybuild-easyblocks/pull/1306/files +buildopts = "CPATH=${CPATH/${EBROOTCUDA}'/extras/CUPTI/include:'/}" + +# use Intel software rasterizer by default (no GPU hardware acceleration) +modextravars = {'GALLIUM_DRIVER': 'swr'} + +sanity_check_paths = { + 'files': ['bin/blender'], + 'dirs': [] +} + +moduleclass = 'vis' From bb9c8f397f343ab9ddcb67f8b8c4db19dfdedf79 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 22 Nov 2018 16:42:42 +0100 Subject: [PATCH 0123/5331] add OpenEXR-2.3.0-foss-2018b.eb --- .../o/OpenEXR/OpenEXR-2.3.0-foss-2018b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.3.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.3.0-foss-2018b.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.3.0-foss-2018b.eb new file mode 100644 index 00000000000..a754e84e21c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.3.0-foss-2018b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '2.3.0' + +homepage = 'http://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/openexr/openexr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8243b7de12b52239fe9235a6aeb4e35ead2247833e4fbc41541774b222717933'] + +builddependencies = [('CMake', '3.12.1')] + +configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' + +sanity_check_paths = { + 'files': ['lib/lib%s-%%(version_major)s_%%(version_minor)s.%s' % (x, SHLIB_EXT) for x in + ['Half', 'Iex', 'IexMath', 'IlmImf', 'IlmImfUtil', 'IlmThread', 'Imath']] + + ['bin/exr%s' % x for x in + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr']], + 'dirs': ['include/OpenEXR', 'share'], +} + +moduleclass = 'vis' From 18bf51ebe6f2852f7583bc46e9912e922d9dc6a4 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 23 Nov 2018 09:57:00 +0100 Subject: [PATCH 0124/5331] add OpenImageIO easyconfig --- .../OpenImageIO-1.8.16-foss-2018b.eb | 35 +++++++++++++++++++ .../OpenImageIO-1.8.16-intel-2018b.eb | 2 +- 2 files changed, 36 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.8.16-foss-2018b.eb diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.8.16-foss-2018b.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.8.16-foss-2018b.eb new file mode 100644 index 00000000000..d32832d50f3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.8.16-foss-2018b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'OpenImageIO' +version = '1.8.16' + +homepage = 'http://openimageio.org/' +description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, + and applications.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/OpenImageIO/oiio/archive/'] +sources = ['Release-%(version)s.tar.gz'] +checksums = ['a67bb2800805bce10c055bc3f5ed32ce31498381fc1cf8e42e24d4193f3f935f'] + +dependencies = [ + ('Boost', '1.67.0'), + ('libjpeg-turbo', '2.0.0'), + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), + ('OpenEXR', '2.3.0'), +] +builddependencies = [('CMake', '3.12.1')] + +separate_build_dir = True + +configopts = '-DSTOP_ON_WARNING=OFF -DUSE_PYTHON=OFF ' +configopts += '-DCMAKE_EXE_LINKER_FLAGS="-L$EBROOTZLIB/lib $LDFLAGS" ' + +sanity_check_paths = { + 'files': ['bin/oiiotool', 'lib/libOpenImageIO.%s' % SHLIB_EXT, 'lib/libOpenImageIO_Util.%s' % SHLIB_EXT], + 'dirs': ['include/OpenImageIO', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.8.16-intel-2018b.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.8.16-intel-2018b.eb index 4ceda5f0fcc..c04a4e5a931 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.8.16-intel-2018b.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-1.8.16-intel-2018b.eb @@ -27,7 +27,7 @@ separate_build_dir = True configopts = '-DSTOP_ON_WARNING=OFF -DUSE_PYTHON=OFF' sanity_check_paths = { - 'files': ['bin/oiiotool', 'lib/libOpenImageIO.so', 'lib/libOpenImageIO_Util.so'], + 'files': ['bin/oiiotool', 'lib/libOpenImageIO.%s' % SHLIB_EXT, 'lib/libOpenImageIO_Util.%s' % SHLIB_EXT], 'dirs': ['include/OpenImageIO', 'share'], } From fc78e8296db850fc04f6118da9b0662afbaa9995 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 23 Nov 2018 11:22:07 +0100 Subject: [PATCH 0125/5331] downgrade CUDA version to comply with single variant rule --- ...79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb new file mode 100644 index 00000000000..8434d690e76 --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb @@ -0,0 +1,77 @@ +easyblock = 'CMakeMake' + +name = 'Blender' +version = '2.79b' +cuda_ver = '9.2.88' +versionsuffix = '-Python-%%(pyver)s-CUDA-%s' % cuda_ver + +homepage = 'https://www.blender.org/' +description = """Blender is the free and open source 3D creation suite. It supports + the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, + compositing and motion tracking, even video editing and game creation.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://download.blender.org/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4c944c304a49e68ac687ea06f5758204def049b66dc211e1cffa1857716393bc'] + +# disable SSE detection to give EasyBuild full control over optimization compiler flags being used +configopts = '-DWITH_CPU_SSE=OFF -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG" -DCMAKE_CXX_FLAGS_RELEASE="-DNDEBUG" ' + +# these are needed until extra dependencies are added for them to work +configopts += '-DWITH_INSTALL_PORTABLE=OFF ' +configopts += '-DWITH_BUILDINFO=OFF ' +configopts += '-DWITH_GAMEENGINE=OFF ' +configopts += '-DWITH_SYSTEM_GLEW=OFF ' + +# Python paths +site_packages = '$EBROOTPYTHON/lib/python%(pyshortver)s/site-packages' +configopts += '-DPYTHON_VERSION=%(pyshortver)s ' +configopts += '-DPYTHON_LIBRARY=${EBROOTPYTHON}/lib/libpython%%(pyshortver)sm.%s ' % SHLIB_EXT +configopts += '-DPYTHON_INCLUDE_DIR=${EBROOTPYTHON}/include/python%(pyshortver)sm ' +configopts += '-DPYTHON_NUMPY_PATH=' + site_packages + '/numpy-1.15.0-py%(pyshortver)s-linux-x86_64.egg ' +configopts += '-DPYTHON_REQUESTS_PATH=' + site_packages + '/requests-2.19.1-py%(pyshortver)s.egg ' + +# OpenEXR +configopts += '-DOPENEXR_INCLUDE_DIR=$EBROOTOPENEXR/include ' + +# OpenColorIO +configopts += '-DWITH_OPENCOLORIO=ON ' + +# CUDA +configopts += '-DWITH_CYCLES_CUDA_BINARIES=ON ' +configopts += '-DCYCLES_CUDA_BINARIES_ARCH="sm_30;sm_35;sm_37;sm_50;sm_52;sm_60;sm_61;sm_62;sm_72" ' + +dependencies = [ + ('Python', '3.6.6'), + ('Boost', '1.67.0'), + ('libjpeg-turbo', '2.0.0'), + ('zlib', '1.2.11'), + ('X11', '20180604'), + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), + ('OpenColorIO', '1.1.0'), # for advanced color management + ('OpenImageIO', '1.8.16'), # required for cycles render engine + ('CUDA', cuda_ver, '', True), +] + +builddependencies = [('CMake', '3.12.1')] + +separate_build_dir = 'True' + +# remove CUPTI headers, included in CUDA, from CPATH +# the CUPTI directory contains old GL headers, which interfere with Blender +# see: https://github.com/easybuilders/easybuild-easyblocks/issues/1492 +# see: https://github.com/easybuilders/easybuild-easyblocks/pull/1306/files +buildopts = "CPATH=${CPATH/${EBROOTCUDA}'/extras/CUPTI/include:'/}" + +# use Intel software rasterizer by default (no GPU hardware acceleration) +modextravars = {'GALLIUM_DRIVER': 'swr'} + +sanity_check_paths = { + 'files': ['bin/blender'], + 'dirs': [] +} + +moduleclass = 'vis' From be4d092c78e501ef923cbd6e18ae79a75f3e38d4 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Fri, 23 Nov 2018 12:01:24 +0100 Subject: [PATCH 0126/5331] Delete Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb --- ...b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb | 77 ------------------- 1 file changed, 77 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb deleted file mode 100644 index 5b8b2de2851..00000000000 --- a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-10.0.130.eb +++ /dev/null @@ -1,77 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Blender' -version = '2.79b' -cuda_ver = '10.0.130' -versionsuffix = '-Python-%%(pyver)s-CUDA-%s' % cuda_ver - -homepage = 'https://www.blender.org/' -description = """Blender is the free and open source 3D creation suite. It supports - the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, - compositing and motion tracking, even video editing and game creation.""" - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = ['http://download.blender.org/source/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['4c944c304a49e68ac687ea06f5758204def049b66dc211e1cffa1857716393bc'] - -# disable SSE detection to give EasyBuild full control over optimization compiler flags being used -configopts = '-DWITH_CPU_SSE=OFF -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG" -DCMAKE_CXX_FLAGS_RELEASE="-DNDEBUG" ' - -# these are needed until extra dependencies are added for them to work -configopts += '-DWITH_INSTALL_PORTABLE=OFF ' -configopts += '-DWITH_BUILDINFO=OFF ' -configopts += '-DWITH_GAMEENGINE=OFF ' -configopts += '-DWITH_SYSTEM_GLEW=OFF ' - -# Python paths -site_packages = '$EBROOTPYTHON/lib/python%(pyshortver)s/site-packages' -configopts += '-DPYTHON_VERSION=%(pyshortver)s ' -configopts += '-DPYTHON_LIBRARY=${EBROOTPYTHON}/lib/libpython%%(pyshortver)sm.%s ' % SHLIB_EXT -configopts += '-DPYTHON_INCLUDE_DIR=${EBROOTPYTHON}/include/python%(pyshortver)sm ' -configopts += '-DPYTHON_NUMPY_PATH=' + site_packages + '/numpy-1.15.0-py%(pyshortver)s-linux-x86_64.egg ' -configopts += '-DPYTHON_REQUESTS_PATH=' + site_packages + '/requests-2.19.1-py%(pyshortver)s.egg ' - -# OpenEXR -configopts += '-DOPENEXR_INCLUDE_DIR=$EBROOTOPENEXR/include ' - -# OpenColorIO -configopts += '-DWITH_OPENCOLORIO=ON ' - -# CUDA -configopts += '-DWITH_CYCLES_CUDA_BINARIES=ON ' -configopts += '-DCYCLES_CUDA_BINARIES_ARCH="sm_30;sm_35;sm_37;sm_50;sm_52;sm_60;sm_61;sm_62;sm_72;sm_75" ' - -dependencies = [ - ('Python', '3.6.6'), - ('Boost', '1.67.0'), - ('libjpeg-turbo', '2.0.0'), - ('zlib', '1.2.11'), - ('X11', '20180604'), - ('Mesa', '18.1.1'), - ('libGLU', '9.0.0'), - ('OpenColorIO', '1.1.0'), # for advanced color management - ('OpenImageIO', '1.8.16'), # required for cycles render engine - ('CUDA', cuda_ver, '', True), -] - -builddependencies = [('CMake', '3.12.1')] - -separate_build_dir = 'True' - -# remove CUPTI headers, included in CUDA, from CPATH -# the CUPTI directory contains old GL headers, which interfere with Blender -# see: https://github.com/easybuilders/easybuild-easyblocks/issues/1492 -# see: https://github.com/easybuilders/easybuild-easyblocks/pull/1306/files -buildopts = "CPATH=${CPATH/${EBROOTCUDA}'/extras/CUPTI/include:'/}" - -# use Intel software rasterizer by default (no GPU hardware acceleration) -modextravars = {'GALLIUM_DRIVER': 'swr'} - -sanity_check_paths = { - 'files': ['bin/blender'], - 'dirs': [] -} - -moduleclass = 'vis' From bdeffa22514fbbd73b8cc8e097530267d8dbaceb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Nov 2018 15:37:08 +0100 Subject: [PATCH 0127/5331] adding easyconfigs: LUSCUS-0.8.6-intel-2018a.eb and patches: LUSCUS-0.8.6_fix-X11-link.patch --- .../l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb | 32 +++++++++++++++++++ .../l/LUSCUS/LUSCUS-0.8.6_fix-X11-link.patch | 14 ++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb create mode 100644 easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6_fix-X11-link.patch diff --git a/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb new file mode 100644 index 00000000000..55d6a0f1f2d --- /dev/null +++ b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'LUSCUS' +version = '0.8.6' + +homepage = 'https://sourceforge.net/projects/luscus/' +description = "Luscus is the program for graphical display and editing of molecular systems." + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['luscus_%(version)s.tar.gz'] +patches = ['LUSCUS-%(version)s_fix-X11-link.patch'] +checksums = [ + 'e1bf08de586b6e1c88c22b3d1d9b00a49c227fded7d6dc17023d3e9a84c573a3', # luscus_0.8.6.tar.gz + 'b4831c00ecb2311738ed236bbbe5307522d9fca90544967186cab342065b8fc7', # LUSCUS-0.8.6_fix-X11-link.patch +] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('GTK+', '2.24.32'), + ('Mesa', '17.3.6'), + ('libGLU', '9.0.0'), +] + +sanity_check_paths = { + 'files': ['bin/luscus'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6_fix-X11-link.patch b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6_fix-X11-link.patch new file mode 100644 index 00000000000..93d92c6e168 --- /dev/null +++ b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6_fix-X11-link.patch @@ -0,0 +1,14 @@ +fix linking issue with libX11: +error adding symbols: DSO missing from command line +author: Kenneth Hoste (HPC-UGent) +--- luscus_0.8.6/CMakeLists.txt.orig 2018-11-23 15:01:47.737809689 +0100 ++++ luscus_0.8.6/CMakeLists.txt 2018-11-23 15:01:54.027747459 +0100 +@@ -124,7 +124,7 @@ + target_link_libraries(luscus ${GTKGLEXT_LDFLAGS} -lm) + else(USE_GTK3) + add_definitions(-DGTK2 -D_GNU_SOURCE ${GTK2_CFLAGS}) +- target_link_libraries(luscus ${GTK2_LDFLAGS} -lm) ++ target_link_libraries(luscus ${GTK2_LDFLAGS} -lm -lX11) + endif(USE_GTK3) + + include_directories("${PROJECT_BINARY_DIR}") From fe8af4edf1494718cf89e50de738161fdc898af2 Mon Sep 17 00:00:00 2001 From: Andreas Hilboll Date: Fri, 23 Nov 2018 21:39:54 +0100 Subject: [PATCH 0128/5331] UPD: new version 1.10.0 of PnetCDF see easybuilders/easybuild-easyblocks/pull/1592 --- .../p/PnetCDF/PnetCDF-1.10.0-foss-2018b.eb | 22 +++++++++++++++++++ .../p/PnetCDF/PnetCDF-1.10.0-intel-2018b.eb | 22 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.10.0-foss-2018b.eb create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.10.0-intel-2018b.eb diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.10.0-foss-2018b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.10.0-foss-2018b.eb new file mode 100644 index 00000000000..57aa8b99620 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.10.0-foss-2018b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = '1.10.0' + +homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' +description = """Parallel netCDF: A Parallel I/O Library for NetCDF File Access""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://parallel-netcdf.github.io/Release/'] +sources = ['parallel-netcdf-%(version)s.tar.gz'] +checksums = ['ed189228b933cfeac3b7b4f8944eb00e4ff2b72cf143365b1a77890980663a09'] + +sanity_check_paths = { + 'files': ['bin/pnetcdf_version'], + 'dirs': ['include', 'lib'], +} + +modextravars = {'PNETCDF': '%(installdir)s'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.10.0-intel-2018b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.10.0-intel-2018b.eb new file mode 100644 index 00000000000..4a518d519bd --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.10.0-intel-2018b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = '1.10.0' + +homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' +description = """Parallel netCDF: A Parallel I/O Library for NetCDF File Access""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://parallel-netcdf.github.io/Release/'] +sources = ['parallel-netcdf-%(version)s.tar.gz'] +checksums = ['ed189228b933cfeac3b7b4f8944eb00e4ff2b72cf143365b1a77890980663a09'] + +sanity_check_paths = { + 'files': ['bin/pnetcdf_version'], + 'dirs': ['include', 'lib'], +} + +modextravars = {'PNETCDF': '%(installdir)s'} + +moduleclass = 'data' From c7a3f37399705774dac5685ff540455165c044c6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 26 Nov 2018 19:00:51 +0200 Subject: [PATCH 0129/5331] Add patch for cpptraj to link with lapack/blas from EB --- .../Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb | 3 +++ .../Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb b/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb index bd8df90856d..5ccaa4411f9 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb @@ -35,6 +35,7 @@ patches = [ 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, 'Amber-%%(version)s-AT-%s_use_easybuild_pythonpath.patch' % ambertools_ver, 'Amber-%%(version)s-AT-%s_use_external_boost_in_packmol_memembed.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_make_cpptraj_link_with_EBs_blas_lapack_fftw.patch' % ambertools_ver, 'Amber-%(version)s_fix_missing_build_target.patch', 'Amber-%(version)s_dont_use_ipo.patch', ] @@ -67,6 +68,8 @@ checksums = [ 'dcfdf064e774b4a55802b660146f1cdebb1226bdd75713de7a783848fc23526e', # Amber-18-AT-18_use_easybuild_pythonpath.patch # Amber-18-AT-18_use_external_boost_in_packmol_memembed.patch '9493a3dfddf62d6aa1bbb0a92a39e766a2b76a9ff8a9006e0fcc9ee3e5d94aac', + # Amber-18-AT-18_make_cpptraj_link_with_EBs_blas_lapack_fftw.patch + 'f916dac2f4c43d00ddc0e0b09ab2c5aae2a98f3f852a4cec47e4911c15666ec4', '6b09a6548fa18127245e05c79bdca143adf31db349349cb39bfdb8c4f60772a7', # Amber-18_fix_missing_build_target.patch 'a4c12ad39088ce6e9e7bad39e8d9a736989e6ae4a380c70535a5451eb3060903', # Amber-18_dont_use_ipo.patch ] diff --git a/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb b/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb index 838e5e5c3ae..0958e6728a2 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb @@ -35,6 +35,7 @@ patches = [ 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, 'Amber-%%(version)s-AT-%s_use_easybuild_pythonpath.patch' % ambertools_ver, 'Amber-%%(version)s-AT-%s_use_external_boost_in_packmol_memembed.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_make_cpptraj_link_with_EBs_blas_lapack_fftw.patch' % ambertools_ver, 'Amber-%(version)s_fix_missing_build_target.patch', 'Amber-%(version)s_dont_use_ipo.patch', ] @@ -67,6 +68,8 @@ checksums = [ 'dcfdf064e774b4a55802b660146f1cdebb1226bdd75713de7a783848fc23526e', # Amber-18-AT-18_use_easybuild_pythonpath.patch # Amber-18-AT-18_use_external_boost_in_packmol_memembed.patch '9493a3dfddf62d6aa1bbb0a92a39e766a2b76a9ff8a9006e0fcc9ee3e5d94aac', + # Amber-18-AT-18_make_cpptraj_link_with_EBs_blas_lapack_fftw.patch + 'f916dac2f4c43d00ddc0e0b09ab2c5aae2a98f3f852a4cec47e4911c15666ec4', '6b09a6548fa18127245e05c79bdca143adf31db349349cb39bfdb8c4f60772a7', # Amber-18_fix_missing_build_target.patch 'a4c12ad39088ce6e9e7bad39e8d9a736989e6ae4a380c70535a5451eb3060903', # Amber-18_dont_use_ipo.patch ] From 4ed765b9ea777733e4fa80ec3b26e9b8c9384295 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 27 Nov 2018 12:26:40 +0100 Subject: [PATCH 0130/5331] use blender easyblock --- ...79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb | 36 +------------------ 1 file changed, 1 insertion(+), 35 deletions(-) diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb index 8434d690e76..b852cffa7b7 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb @@ -1,5 +1,3 @@ -easyblock = 'CMakeMake' - name = 'Blender' version = '2.79b' cuda_ver = '9.2.88' @@ -16,33 +14,6 @@ source_urls = ['http://download.blender.org/source/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['4c944c304a49e68ac687ea06f5758204def049b66dc211e1cffa1857716393bc'] -# disable SSE detection to give EasyBuild full control over optimization compiler flags being used -configopts = '-DWITH_CPU_SSE=OFF -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG" -DCMAKE_CXX_FLAGS_RELEASE="-DNDEBUG" ' - -# these are needed until extra dependencies are added for them to work -configopts += '-DWITH_INSTALL_PORTABLE=OFF ' -configopts += '-DWITH_BUILDINFO=OFF ' -configopts += '-DWITH_GAMEENGINE=OFF ' -configopts += '-DWITH_SYSTEM_GLEW=OFF ' - -# Python paths -site_packages = '$EBROOTPYTHON/lib/python%(pyshortver)s/site-packages' -configopts += '-DPYTHON_VERSION=%(pyshortver)s ' -configopts += '-DPYTHON_LIBRARY=${EBROOTPYTHON}/lib/libpython%%(pyshortver)sm.%s ' % SHLIB_EXT -configopts += '-DPYTHON_INCLUDE_DIR=${EBROOTPYTHON}/include/python%(pyshortver)sm ' -configopts += '-DPYTHON_NUMPY_PATH=' + site_packages + '/numpy-1.15.0-py%(pyshortver)s-linux-x86_64.egg ' -configopts += '-DPYTHON_REQUESTS_PATH=' + site_packages + '/requests-2.19.1-py%(pyshortver)s.egg ' - -# OpenEXR -configopts += '-DOPENEXR_INCLUDE_DIR=$EBROOTOPENEXR/include ' - -# OpenColorIO -configopts += '-DWITH_OPENCOLORIO=ON ' - -# CUDA -configopts += '-DWITH_CYCLES_CUDA_BINARIES=ON ' -configopts += '-DCYCLES_CUDA_BINARIES_ARCH="sm_30;sm_35;sm_37;sm_50;sm_52;sm_60;sm_61;sm_62;sm_72" ' - dependencies = [ ('Python', '3.6.6'), ('Boost', '1.67.0'), @@ -58,7 +29,7 @@ dependencies = [ builddependencies = [('CMake', '3.12.1')] -separate_build_dir = 'True' +configopts = '-DCYCLES_CUDA_BINARIES_ARCH="sm_30;sm_35;sm_37;sm_50;sm_52;sm_60;sm_61;sm_62;sm_72" ' # remove CUPTI headers, included in CUDA, from CPATH # the CUPTI directory contains old GL headers, which interfere with Blender @@ -69,9 +40,4 @@ buildopts = "CPATH=${CPATH/${EBROOTCUDA}'/extras/CUPTI/include:'/}" # use Intel software rasterizer by default (no GPU hardware acceleration) modextravars = {'GALLIUM_DRIVER': 'swr'} -sanity_check_paths = { - 'files': ['bin/blender'], - 'dirs': [] -} - moduleclass = 'vis' From 011c618c0da39d79dd6b476a41120ef5a4dd5abd Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 27 Nov 2018 16:26:14 +0100 Subject: [PATCH 0131/5331] {bio}[foss/2018b] OptiType 1.3.2 w/ Python 3.6.6 (REVIEW) --- .../future-0.16.0-foss-2018b-Python-3.6.6.eb | 23 +++++++++ .../numexpr-2.6.5-foss-2018b-Python-3.6.6.eb | 28 ++++++++++ .../OptiType-1.3.2-foss-2018b-Python-3.6.6.eb | 49 ++++++++++++++++++ .../PyTables-3.4.4-foss-2018b-Python-3.6.6.eb | 42 +++++++++++++++ .../Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb | 51 +++++++++++++++++++ 5 files changed, 193 insertions(+) create mode 100644 easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/o/OptiType/OptiType-1.3.2-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..10ec0dfaaa0 --- /dev/null +++ b/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'future' +version = '0.16.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://python-future.org/' +description = "python-future is the missing compatibility layer between Python 2 and Python 3." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'] + +dependencies = [('Python', '3.6.6')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..1eaabddd008 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'numexpr' +version = '2.6.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/numexpr/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fe78a78e002806e87e012b6105f3b3d52d47fc7a72bafb56341fcec7ce02cfd7'] + +dependencies = [ + ('Python', '3.6.6'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OptiType/OptiType-1.3.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/o/OptiType/OptiType-1.3.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..6b456321c0b --- /dev/null +++ b/easybuild/easyconfigs/o/OptiType/OptiType-1.3.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,49 @@ +easyblock = 'Tarball' + +name = 'OptiType' +version = '1.3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/FRED-2/OptiType' +description = """ OptiType is a novel HLA genotyping algorithm based on integer linear programming, + capable of producing accurate 4-digit HLA genotyping predictions from NGS data + by simultaneously selecting all major and minor HLA Class I alleles. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/FRED-2/OptiType/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7cc74b3a163afcd9f734c56b6753781d7ffe56b8f92874b788088147cf62cd6a'] + +dependencies = [ + ('future', '0.16.0', versionsuffix), + ('GLPK', '4.65'), + ('HDF5', '1.10.2'), + ('matplotlib', '3.0.0', versionsuffix), + ('Python', '3.6.6'), + ('Pyomo', '5.5.0', versionsuffix), + ('Pysam', '0.15.1', versionsuffix), + ('PyTables', '3.4.4', versionsuffix), + ('SAMtools', '1.9'), + ('SeqAn', '2.4.0'), +] + +postinstallcmds = [ + 'cp %(installdir)s/config.ini{.example,}', + 'sed -i -e "s|/path/to/razers3|$EBROOTSEQAN/bin/razers3|" %(installdir)s/config.ini', + 'sed -i -e "1i #!/usr/bin/env python" %(installdir)s/OptiTypePipeline.py', +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['config.ini', 'hlatyper.py', 'model.py', 'OptiTypePipeline.py'], + 'dirs': [], +} + +sanity_check_commands = [( + 'OptiTypePipeline.py -i %(installdir)s/test/exome/NA11995_SRR766010_1_fished.fastq ' + '%(installdir)s/test/exome/NA11995_SRR766010_2_fished.fastq --dna -v -o %(builddir)s/' +)] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..a88d1c4baa2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.4.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['pyTables-3.4.2-fix-libs.patch'] +checksums = [ + 'c9682c0f35d8175e12bbd38d925bdb606d47b7c8e358ba056a9dbf3b1f183114', # v3.4.4.tar.gz + 'f34a05573e7843e67dab011bede8436074362041747c028b409fac9f599231a3', # pyTables-3.4.2-fix-libs.patch +] + +dependencies = [ + ('Python', '3.6.6'), + ('numexpr', '2.6.5', versionsuffix), + ('HDF5', '1.10.2'), + ('LZO', '2.10'), + ('Blosc', '1.14.4'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..72612b05080 --- /dev/null +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'Pyomo' +version = '5.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pyomo.org/' +description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization + capabilities for formulating and analyzing optimization models. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [('Python', '3.6.6')] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('appdirs', '1.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], + 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], + }), + ('ply', '3.11', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ply'], + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('PyUtilib', '5.6.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyutilib'], + 'checksums': ['6a21fccfe691c39566c0bb19b5c9aa11bca8b076aa6f1dbf21c11711f5105191'], + # use setuptools: pip fails due to missing __init__.py files + # see: https://github.com/PyUtilib/pyutilib/issues/39 + 'use_pip': False, + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyomo'], + 'checksums': ['6079a7a24d148b1c725d5364de1e0fa99e2e9c284ba223517e0955ef2b8f3ea1'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'math' From e541b4498e3f40066a37e661db939ce21979fd11 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 28 Nov 2018 11:20:14 +0100 Subject: [PATCH 0132/5331] adding easyconfigs: beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb --- ...beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb new file mode 100644 index 00000000000..d6ef58c46b2 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '3.0.2' +cuda_ver = '9.2.88' +versionsuffix = '-CUDA-%s' % cuda_ver +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['59a7081b61ead0a5738e813c6fcfb614d2c5bb49c29b28609de8e2b51bea3ec0'] + +dependencies = [ + ('Java', '1.8', '', True), + ('CUDA', cuda_ver, '', True), +] + +builddependencies = [('Autotools', '20180311')] + +preconfigopts = "./autogen.sh && " + +configopts = '--with-cuda=$EBROOTCUDA ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.%s" % (libfile, SHLIB_EXT) + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' From 7fa447bce5f8d32daea65d02a7c33391cfea02f1 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 28 Nov 2018 15:04:56 +0100 Subject: [PATCH 0133/5331] {bio}[foss/2018b] NovoCraft w/ R and Perl (REVIEW) --- .../NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb | 58 +++++++++++++++++++ .../n/NovoCraft/NovoCraftV3.09.01.patch | 40 +++++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb create mode 100644 easybuild/easyconfigs/n/NovoCraft/NovoCraftV3.09.01.patch diff --git a/easybuild/easyconfigs/n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb new file mode 100644 index 00000000000..470f8b57990 --- /dev/null +++ b/easybuild/easyconfigs/n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb @@ -0,0 +1,58 @@ +easyblock = 'PackedBinary' + +name = 'NovoCraft' +version = '3.09.01' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.novocraft.com/' +description = """NovoCraft is a software bundle. + NovoAlign: + Market’s leading aligner with fully packed features designed for mapping + of short reads onto a reference genome from Illumina, Ion Torrent, 454, + and Color Spance NGS platforms. + NovoAlignCS: + Leading aligner packed with features designed to fully support reads from + ABI SOLiD Color Space. + NovoSort: + Custom designed multi-threaded sort/merge tools for BAM files. + NovoMethyl: + It can analyse a set of alignments to identify methylated cytosine’s. + WARNING! + You can only ise the sofware without a license (with some features disabled) + if you are a non-profit organisation and use is for your own research or for + use by students as part of their course. A license is required for use where + these programs are part of a service where a third party is billed.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +# You can only use the sofware without a license (with some features disabled) +# if you are a non-profit organisation and use is for your own research or for +# use by students as part of their course. A license is required for use where +# these programs are part of a service where a third party is billed. +# MPI versions need a license, and MPICH or MPICH2 compatible MPI libraries. +# You have to download the sofware manually (see commented source_urls). +# source_urls = ['http://www.novocraft.com/support/download/'] +# Currently you can chose binary compiled on UBUNTU 11.10 (Linux3.10.0) +# or CentOS 5.10 (Linux2.6.32). +sources = ['%(namelower)sV%(version)s.Linux3.10.0.tar.gz'] +#sources = ['%(namelower)sV%(version)s.Linux2.6.32.tar.gz'] +patches = ['%(name)sV%(version)s.patch'] +checksums = [ + '08c9cef29ba9c10f81946e7287912982b009a54fb47a226302d99399c19a5b97', # novocraftV3.09.01.Linux3.10.0.tar.gz + # 'c6c974ca914ae97abb3ad39d86e002227c52b3685dfa0bbc031b5ba7ecfb3ecd', # novocraftV3.09.01.Linux2.6.32.tar.gz + 'c1e16faf273272c51325bbd3d4e7946b343a72b9f6736fe39e3ebe40b38fae2e', # NovoCraftV3.09.01.patch +] + +dependencies = [ + ('R', '3.5.1'), + ('Perl', '5.28.0'), +] + +sanity_check_paths = { + 'files': ['novoalign', 'novoalignCS', 'novosort', 'novomethyl'], + 'dirs': [], +} + +sanity_check_commands = [('novoalign', '--help')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NovoCraft/NovoCraftV3.09.01.patch b/easybuild/easyconfigs/n/NovoCraft/NovoCraftV3.09.01.patch new file mode 100644 index 00000000000..4c3e90d6d41 --- /dev/null +++ b/easybuild/easyconfigs/n/NovoCraft/NovoCraftV3.09.01.patch @@ -0,0 +1,40 @@ +--- novocraft/IONTorrent.R.orig 2018-11-27 10:13:55.000000000 +0100 ++++ novocraft/IONTorrent.R 2018-11-28 12:14:56.360220314 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/Rscript --no-save --no-restore ++#!/usr/bin/env Rscript --no-save --no-restore + ## IONTorrent.R + ## Colin Hercus + ## SYNOPSIS: Plot Run Length error charts +--- novocraft/novo2paf.orig 2018-11-27 10:13:55.000000000 +0100 ++++ novocraft/novo2paf 2018-11-28 12:14:27.959763232 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + use Getopt::Long; + use Data::Dumper; + +--- novocraft/novo2sam.pl.orig 2018-11-27 10:13:55.000000000 +0100 ++++ novocraft/novo2sam.pl 2018-11-28 12:14:47.102071340 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + + # Contact: lh3 + # Version: 0.2.0 +--- novocraft/novorun.pl.orig 2018-11-27 10:13:55.000000000 +0100 ++++ novocraft/novorun.pl 2018-11-28 12:14:40.673967889 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + + use File::Basename; + use Data::Dumper; +--- novocraft/qcalplot.R.orig 2018-11-27 10:13:55.000000000 +0100 ++++ novocraft/qcalplot.R 2018-11-28 12:15:00.823292120 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/Rscript --no-save --no-restore ++#!/usr/bin/env Rscript --no-save --no-restore + ## qcalplot.R + ## Colin Hercus and Zayed Albertyn + ## SYNOPSIS: Plot quality values From d329f6e5a8be46a107483858590d5c9f1b98523c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 28 Nov 2018 21:33:25 +0100 Subject: [PATCH 0134/5331] {data}[intel/iomkl 2018b] CDO 1.9.5 and ncview 2.1.7 w/ deps (REVIEW) --- .../c/CDO/CDO-1.9.5-intel-2018b.eb | 33 ++++++++++++++ .../c/CDO/CDO-1.9.5-iomkl-2018b.eb | 33 ++++++++++++++ .../e/ecCodes/ecCodes-2.9.2-intel-2018b.eb | 34 ++++++++++++++ .../e/ecCodes/ecCodes-2.9.2-iomkl-2018b.eb | 34 ++++++++++++++ .../n/ncview/ncview-2.1.7-intel-2018b.eb | 45 +++++++++++++++++++ .../n/ncview/ncview-2.1.7-iomkl-2018b.eb | 45 +++++++++++++++++++ .../u/UDUNITS/UDUNITS-2.2.26-intel-2018b.eb | 39 ++++++++++++++++ .../u/UDUNITS/UDUNITS-2.2.26-iomkl-2018b.eb | 39 ++++++++++++++++ .../y/YAXT/YAXT-0.6.0-intel-2018b.eb | 23 ++++++++++ .../y/YAXT/YAXT-0.6.0-iomkl-2018b.eb | 23 ++++++++++ 10 files changed, 348 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-1.9.5-intel-2018b.eb create mode 100644 easybuild/easyconfigs/c/CDO/CDO-1.9.5-iomkl-2018b.eb create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.9.2-intel-2018b.eb create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.9.2-iomkl-2018b.eb create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2018b.eb create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.7-iomkl-2018b.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-intel-2018b.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-iomkl-2018b.eb create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.6.0-intel-2018b.eb create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.6.0-iomkl-2018b.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.5-intel-2018b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.5-intel-2018b.eb new file mode 100644 index 00000000000..dda0e92caf1 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.5-intel-2018b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.9.5' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/18264/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48ed65cc5b436753c8e7f9eadd8aa97376698ce230ceafed2a4350a5b1a27148'] + +dependencies = [ + ('HDF5', '1.10.2'), + ('netCDF', '4.6.1'), + ('YAXT', '0.6.0'), + ('ecCodes', '2.9.2'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES" + +# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && " + +sanity_check_paths = { + 'files': ['bin/cdo'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.5-iomkl-2018b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.5-iomkl-2018b.eb new file mode 100644 index 00000000000..82beb92a8e4 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.5-iomkl-2018b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.9.5' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'iomkl', 'version': '2018b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/18264/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48ed65cc5b436753c8e7f9eadd8aa97376698ce230ceafed2a4350a5b1a27148'] + +dependencies = [ + ('HDF5', '1.10.2'), + ('netCDF', '4.6.1'), + ('YAXT', '0.6.0'), + ('ecCodes', '2.9.2'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES" + +# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && " + +sanity_check_paths = { + 'files': ['bin/cdo'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.9.2-intel-2018b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.9.2-intel-2018b.eb new file mode 100644 index 00000000000..7f57a812f28 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.9.2-intel-2018b.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.9.2' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['08f476c94605fb03a405fa83ea8fbd7078b1480e5836a0c8602bce753efcf2a1'] + +builddependencies = [('CMake', '3.12.1')] +dependencies = [ + ('netCDF', '4.6.1'), + ('JasPer', '2.0.14'), +] + +separate_build_dir = True + +configopts = "-DENABLE_NETCDF=ON -DENABLE_JPG=ON -DENABLE_PYTHON=OFF" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bufr_copy', 'bufr_dump', 'bufr_filter', 'bufr_ls', + 'codes_count', 'codes_info', 'codes_split_file', + 'grib_copy', 'grib_dump', 'grib_filter', 'grib_ls']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.9.2-iomkl-2018b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.9.2-iomkl-2018b.eb new file mode 100644 index 00000000000..485c7b67647 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.9.2-iomkl-2018b.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.9.2' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'iomkl', 'version': '2018b'} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['08f476c94605fb03a405fa83ea8fbd7078b1480e5836a0c8602bce753efcf2a1'] + +builddependencies = [('CMake', '3.12.1')] +dependencies = [ + ('netCDF', '4.6.1'), + ('JasPer', '2.0.14'), +] + +separate_build_dir = True + +configopts = "-DENABLE_NETCDF=ON -DENABLE_JPG=ON -DENABLE_PYTHON=OFF" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bufr_copy', 'bufr_dump', 'bufr_filter', 'bufr_ls', + 'codes_count', 'codes_info', 'codes_split_file', + 'grib_copy', 'grib_dump', 'grib_filter', 'grib_ls']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2018b.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2018b.eb new file mode 100644 index 00000000000..80a48370586 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-intel-2018b.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.7' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a14c2dddac0fc78dad9e4e7e35e2119562589738f4ded55ff6e0eca04d682c82'] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(which $CC) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('UDUNITS', '2.2.26'), + ('X11', '20180604'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.7-iomkl-2018b.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-iomkl-2018b.eb new file mode 100644 index 00000000000..81c2d9b5782 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.7-iomkl-2018b.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.7' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'iomkl', 'version': '2018b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a14c2dddac0fc78dad9e4e7e35e2119562589738f4ded55ff6e0eca04d682c82'] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(which $CC) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('UDUNITS', '2.2.26'), + ('X11', '20180604'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-intel-2018b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-intel-2018b.eb new file mode 100644 index 00000000000..e04a4179691 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-intel-2018b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.26' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] + +dependencies = [('expat', '2.2.5')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-iomkl-2018b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-iomkl-2018b.eb new file mode 100644 index 00000000000..7d34ffec9e3 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-iomkl-2018b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.26' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'iomkl', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] + +dependencies = [('expat', '2.2.5')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.6.0-intel-2018b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.6.0-intel-2018b.eb new file mode 100644 index 00000000000..a75aba8c008 --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.6.0-intel-2018b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.6.0' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.dkrz.de/redmine/attachments/download/488/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bc4d8d8a6815fd616c0e119fe4f194dafab56583ea7f38f4431eef12cb192f43'] + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.6.0-iomkl-2018b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.6.0-iomkl-2018b.eb new file mode 100644 index 00000000000..fa0198a7f76 --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.6.0-iomkl-2018b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.6.0' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'iomkl', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.dkrz.de/redmine/attachments/download/488/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bc4d8d8a6815fd616c0e119fe4f194dafab56583ea7f38f4431eef12cb192f43'] + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' From ee99764a1e2998972147b7eceba366faafba1e6e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 29 Nov 2018 09:43:52 +0800 Subject: [PATCH 0135/5331] use amd versionsuffix instead of different software names --- .../BLIS/BLIS-1.2-GCC-7.3.0-2.30-amd.eb} | 3 ++- .../libFLAME/libFLAME-1.0-GCC-7.3.0-2.30-amd.eb} | 5 +++-- 2 files changed, 5 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/{a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb => b/BLIS/BLIS-1.2-GCC-7.3.0-2.30-amd.eb} (95%) rename easybuild/easyconfigs/{a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb => l/libFLAME/libFLAME-1.0-GCC-7.3.0-2.30-amd.eb} (91%) diff --git a/easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/b/BLIS/BLIS-1.2-GCC-7.3.0-2.30-amd.eb similarity index 95% rename from easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb rename to easybuild/easyconfigs/b/BLIS/BLIS-1.2-GCC-7.3.0-2.30-amd.eb index a7295a5fb52..462532ee187 100644 --- a/easybuild/easyconfigs/a/AMD-BLIS/AMD-BLIS-1.2-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-1.2-GCC-7.3.0-2.30-amd.eb @@ -1,7 +1,8 @@ easyblock = 'ConfigureMake' -name = 'AMD-BLIS' +name = 'BLIS' version = '1.2' +versionsuffix = '-amd' homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' description = """AMD fork of BLIS. BLIS is a portable software framework for instantiating high-performance diff --git a/easybuild/easyconfigs/a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/l/libFLAME/libFLAME-1.0-GCC-7.3.0-2.30-amd.eb similarity index 91% rename from easybuild/easyconfigs/a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb rename to easybuild/easyconfigs/l/libFLAME/libFLAME-1.0-GCC-7.3.0-2.30-amd.eb index db6eae93ded..0416fc867a6 100644 --- a/easybuild/easyconfigs/a/AMD-libFLAME/AMD-libFLAME-1.0-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/l/libFLAME/libFLAME-1.0-GCC-7.3.0-2.30-amd.eb @@ -1,7 +1,8 @@ easyblock = 'ConfigureMake' -name = 'AMD-libFLAME' +name = 'libFLAME' version = '1.0' +versionsuffix = '-amd' homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame' description = """AMD fork of libFLAME. libFLAME is a portable library for dense matrix computations, @@ -17,7 +18,7 @@ checksums = ['11e7b21b59849416ac372ef2c2b38beb73e62bead85d0ae3ffd0f4f1f6f760cf'] # '--enable-max-arg-list-hack --enable-dynamic-build' requires 'file' function from GNU Make 4.x builddependencies = [('make', '4.2.1')] -dependencies = [('AMD-BLIS', '1.2')] +dependencies = [('BLIS', '1.2', versionsuffix)] configopts = '--enable-max-arg-list-hack --enable-lapack2flame --enable-cblas-interfaces --enable-dynamic-build' From eb860a98e299bbab3218ab3f74ba0317d668cd1e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 29 Nov 2018 11:19:15 +0100 Subject: [PATCH 0136/5331] commend added in patch and minor style fix --- .../n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb | 4 ++-- easybuild/easyconfigs/n/NovoCraft/NovoCraftV3.09.01.patch | 2 ++ 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb index 470f8b57990..73952107604 100644 --- a/easybuild/easyconfigs/n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb @@ -35,12 +35,12 @@ toolchain = {'name': 'foss', 'version': '2018b'} # Currently you can chose binary compiled on UBUNTU 11.10 (Linux3.10.0) # or CentOS 5.10 (Linux2.6.32). sources = ['%(namelower)sV%(version)s.Linux3.10.0.tar.gz'] -#sources = ['%(namelower)sV%(version)s.Linux2.6.32.tar.gz'] +# sources = ['%(namelower)sV%(version)s.Linux2.6.32.tar.gz'] patches = ['%(name)sV%(version)s.patch'] checksums = [ '08c9cef29ba9c10f81946e7287912982b009a54fb47a226302d99399c19a5b97', # novocraftV3.09.01.Linux3.10.0.tar.gz # 'c6c974ca914ae97abb3ad39d86e002227c52b3685dfa0bbc031b5ba7ecfb3ecd', # novocraftV3.09.01.Linux2.6.32.tar.gz - 'c1e16faf273272c51325bbd3d4e7946b343a72b9f6736fe39e3ebe40b38fae2e', # NovoCraftV3.09.01.patch + 'ba668f69b207e41906d435a9fa2150cc12c0968ee471575ea7f45c06c8b6c130', # NovoCraftV3.09.01.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/n/NovoCraft/NovoCraftV3.09.01.patch b/easybuild/easyconfigs/n/NovoCraft/NovoCraftV3.09.01.patch index 4c3e90d6d41..e1409d3c323 100644 --- a/easybuild/easyconfigs/n/NovoCraft/NovoCraftV3.09.01.patch +++ b/easybuild/easyconfigs/n/NovoCraft/NovoCraftV3.09.01.patch @@ -1,3 +1,5 @@ +# Fix hard-coded R and Python paths +# Novermber 29th 2018 by B. Hajgato (Free University Brussels - VUB) --- novocraft/IONTorrent.R.orig 2018-11-27 10:13:55.000000000 +0100 +++ novocraft/IONTorrent.R 2018-11-28 12:14:56.360220314 +0100 @@ -1,4 +1,4 @@ From 94690a1c5b522b587c2d456bb938c94c05620caa Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 30 Nov 2018 10:24:26 +0100 Subject: [PATCH 0137/5331] change name form NovoCraft to novoalign --- .../novoalign-3.09.01-foss-2018b-R-3.5.1.eb} | 10 +++++----- .../novoalign-3.09.01_fix_hardcoded.patch} | 0 2 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/n/{NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb => novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb} (90%) rename easybuild/easyconfigs/n/{NovoCraft/NovoCraftV3.09.01.patch => novoalign/novoalign-3.09.01_fix_hardcoded.patch} (100%) diff --git a/easybuild/easyconfigs/n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb similarity index 90% rename from easybuild/easyconfigs/n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb rename to easybuild/easyconfigs/n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb index 73952107604..8042e44026e 100644 --- a/easybuild/easyconfigs/n/NovoCraft/NovoCraft-3.09.01-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb @@ -1,6 +1,6 @@ easyblock = 'PackedBinary' -name = 'NovoCraft' +name = 'novoalign' version = '3.09.01' versionsuffix = '-R-%(rver)s' @@ -34,13 +34,13 @@ toolchain = {'name': 'foss', 'version': '2018b'} # source_urls = ['http://www.novocraft.com/support/download/'] # Currently you can chose binary compiled on UBUNTU 11.10 (Linux3.10.0) # or CentOS 5.10 (Linux2.6.32). -sources = ['%(namelower)sV%(version)s.Linux3.10.0.tar.gz'] -# sources = ['%(namelower)sV%(version)s.Linux2.6.32.tar.gz'] -patches = ['%(name)sV%(version)s.patch'] +sources = ['novocraftV%(version)s.Linux3.10.0.tar.gz'] +# sources = ['novocraftV%(version)s.Linux2.6.32.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded.patch'] checksums = [ '08c9cef29ba9c10f81946e7287912982b009a54fb47a226302d99399c19a5b97', # novocraftV3.09.01.Linux3.10.0.tar.gz # 'c6c974ca914ae97abb3ad39d86e002227c52b3685dfa0bbc031b5ba7ecfb3ecd', # novocraftV3.09.01.Linux2.6.32.tar.gz - 'ba668f69b207e41906d435a9fa2150cc12c0968ee471575ea7f45c06c8b6c130', # NovoCraftV3.09.01.patch + 'ba668f69b207e41906d435a9fa2150cc12c0968ee471575ea7f45c06c8b6c130', # novoalign-3.09.01_fix_hardcoded.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/n/NovoCraft/NovoCraftV3.09.01.patch b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01_fix_hardcoded.patch similarity index 100% rename from easybuild/easyconfigs/n/NovoCraft/NovoCraftV3.09.01.patch rename to easybuild/easyconfigs/n/novoalign/novoalign-3.09.01_fix_hardcoded.patch From 28d8fdb2b1639bd172a05bade8a0624a1aad0e92 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 30 Nov 2018 10:27:40 +0100 Subject: [PATCH 0138/5331] in patch change Python->Perl --- .../n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb | 2 +- .../n/novoalign/novoalign-3.09.01_fix_hardcoded.patch | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb index 8042e44026e..e59b9f64c59 100644 --- a/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb @@ -40,7 +40,7 @@ patches = ['%(name)s-%(version)s_fix_hardcoded.patch'] checksums = [ '08c9cef29ba9c10f81946e7287912982b009a54fb47a226302d99399c19a5b97', # novocraftV3.09.01.Linux3.10.0.tar.gz # 'c6c974ca914ae97abb3ad39d86e002227c52b3685dfa0bbc031b5ba7ecfb3ecd', # novocraftV3.09.01.Linux2.6.32.tar.gz - 'ba668f69b207e41906d435a9fa2150cc12c0968ee471575ea7f45c06c8b6c130', # novoalign-3.09.01_fix_hardcoded.patch + '369f0d0654786533f8ee056fd577e492e8269798c8e8611a9e20c6b29a9c96d5', # novoalign-3.09.01_fix_hardcoded.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01_fix_hardcoded.patch b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01_fix_hardcoded.patch index e1409d3c323..a5998d59b7f 100644 --- a/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01_fix_hardcoded.patch +++ b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01_fix_hardcoded.patch @@ -1,4 +1,4 @@ -# Fix hard-coded R and Python paths +# Fix hard-coded R and Perl paths # Novermber 29th 2018 by B. Hajgato (Free University Brussels - VUB) --- novocraft/IONTorrent.R.orig 2018-11-27 10:13:55.000000000 +0100 +++ novocraft/IONTorrent.R 2018-11-28 12:14:56.360220314 +0100 From ac2f62edb948e29a8e3b221cbc5a46992d6007ab Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 30 Nov 2018 19:15:12 +0100 Subject: [PATCH 0139/5331] {bio}[foss/2018b] LOHHLA 2018.11.05 w/ R-3.5.1 (REVIEW) --- .../LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb | 40 +++++++++++++++++++ .../LOHHLA-2018.11.05_add_shebang.patch | 9 +++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb create mode 100644 easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05_add_shebang.patch diff --git a/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb new file mode 100644 index 00000000000..429b1117c43 --- /dev/null +++ b/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb @@ -0,0 +1,40 @@ +easyblock = 'PackedBinary' + +name = 'LOHHLA' +version = '2018.11.05' +commit_id = '61f4675' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bitbucket.org/mcgranahanlab/lohhla' +description = """LOHHLA, Loss Of Heterozygosity in Human Leukocyte Antigen, a computational +tool to evaluate HLA loss using next-generation sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://bitbucket.org/mcgranahanlab/lohhla/get'] +sources = [{'filename': '%(name)s-%(version)s.tar.bz2', 'download_filename': '%s.tar.bz2' % commit_id}] +patches = ['%(name)s-%(version)s_add_shebang.patch'] +checksums = [ + 'a47b4f5bca8237f7fcb55c33b5b8857a89cc7cab765308bea8d0c10c41431855', # LOHHLA-2018.11.05.tar.bz2 + '2c7bdf8012b0e48717e4c6e0f5534502b66f792aafaf82a3760e20b8bdad3369', # LOHHLA-2018.11.05_add_shebang.patch +] + +dependencies = [ + # needs beeswarm, seqinr, zoo + ('R', '3.5.1'), + # needs Biostrings, Rsamtools + ('R-bundle-Bioconductor', '3.7', versionsuffix), + ('GATK', '4.0.8.1', '-Python-3.6.6'), + ('Jellyfish', '2.2.10'), + ('BEDTools', '2.27.1'), + ('SAMtools', '1.9'), + ('novoalign', '3.09.01', versionsuffix), + ('picard', '2.18.17', '-Java-1.8', True), +] + +sanity_check_paths = { + 'files': ['LOHHLAscript.R'], + 'dirs': ['data'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05_add_shebang.patch b/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05_add_shebang.patch new file mode 100644 index 00000000000..497a8b9b02b --- /dev/null +++ b/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05_add_shebang.patch @@ -0,0 +1,9 @@ +# Add shebang for the simple R script so one can run as binary +# November 30th 2018 by B. Hajgato (Free University Brussels - VUB) +--- mcgranahanlab-lohhla-61f4675cdee9/LOHHLAscript.R.orig 2018-11-05 17:55:44.000000000 +0100 ++++ mcgranahanlab-lohhla-61f4675cdee9/LOHHLAscript.R 2018-11-30 13:29:13.148912146 +0100 +@@ -1,3 +1,4 @@ ++#!/usr/bin/env Rscript + # before running + # ml BEDTools/2.26.0-foss-2016b + # ml SAMtools/1.3.1-foss-2016b From 59fc209a63bfedbc88ce573c5adcace8d1874805 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 30 Nov 2018 15:37:36 -0600 Subject: [PATCH 0140/5331] adding easyconfigs: GROMACS-2018.2-foss-2017b.eb, GROMACS-2018.2-intel-2017b.eb --- .../g/GROMACS/GROMACS-2018.2-foss-2017b.eb | 42 +++++++++++++++++++ .../g/GROMACS/GROMACS-2018.2-intel-2017b.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2017b.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intel-2017b.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2017b.eb new file mode 100644 index 00000000000..b4db7222d37 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2017b.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2018.2' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857', # gromacs-2018.2.tar.gz + # GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch + '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06', +] +patches = ['GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch'] + +builddependencies = [ + ('CMake', '3.9.5'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intel-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intel-2017b.eb new file mode 100644 index 00000000000..686667772c1 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intel-2017b.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2018.2' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857', # gromacs-2018.2.tar.gz + # GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch + '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06', +] +patches = ['GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch'] + +builddependencies = [ + ('CMake', '3.9.5'), +] + +moduleclass = 'bio' From 30631b3898d53d9bbcb0f7427ad83bd627198be0 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 30 Nov 2018 15:42:48 -0600 Subject: [PATCH 0141/5331] adding easyconfigs: GROMACS-2018.2-fosscuda-2017b.eb, GROMACS-2018.2-intelcuda-2017b.eb --- .../GROMACS/GROMACS-2018.2-fosscuda-2017b.eb | 50 +++++++++++++++++ .../GROMACS/GROMACS-2018.2-intelcuda-2017b.eb | 53 +++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2017b.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intelcuda-2017b.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2017b.eb new file mode 100644 index 00000000000..7962ab7e415 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2017b.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2018.2' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. +""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857', # gromacs-2018.2.tar.gz + # GROMACS-2018_fix_search_for_nvml_include.patch + '59d59316337ce08134d600b44c6501240f2732826ea5699f4b0ae83bb1ae0bd3', + '769cf8aab2e76bb1b36befa4b60df0b975a35877994218725426bb2c597f321b', # GROMACS-2018_amend_search_for_nvml_lib.patch + # GROMACS-2018_fix_incorrect_cuda_target_single_multiple_compilation_unit.patch + '4dcd0dab3d693cc1c60e1dc9fc3fd1990b42b7480a55b8c658621271aafbc786', +] + +patches = [ + 'GROMACS-2018_fix_search_for_nvml_include.patch', + 'GROMACS-2018_amend_search_for_nvml_lib.patch', + 'GROMACS-2018_fix_incorrect_cuda_target_single_multiple_compilation_unit.patch', +] + +builddependencies = [ + ('CMake', '3.9.5'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intelcuda-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intelcuda-2017b.eb new file mode 100644 index 00000000000..b3d12eea76b --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intelcuda-2017b.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2018.2' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. +""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857', # gromacs-2018.2.tar.gz + # GROMACS-2018_fix_search_for_nvml_include.patch + '59d59316337ce08134d600b44c6501240f2732826ea5699f4b0ae83bb1ae0bd3', + '769cf8aab2e76bb1b36befa4b60df0b975a35877994218725426bb2c597f321b', # GROMACS-2018_amend_search_for_nvml_lib.patch + # GROMACS-2018_fix_incorrect_cuda_target_single_multiple_compilation_unit.patch + '4dcd0dab3d693cc1c60e1dc9fc3fd1990b42b7480a55b8c658621271aafbc786', +] + +patches = [ + 'GROMACS-2018_fix_search_for_nvml_include.patch', + 'GROMACS-2018_amend_search_for_nvml_lib.patch', + 'GROMACS-2018_fix_incorrect_cuda_target_single_multiple_compilation_unit.patch', +] + +builddependencies = [ + ('CMake', '3.9.5'), +] + +configopts = '-DCUDA_HOST_COMPILER=$EBROOTGCCCORE/bin/gcc ' +configopts += '-DCUDA_PROPAGATE_HOST_FLAGS=OFF -DCUDA_NVCC_FLAGS="-std=c++11" ' + +moduleclass = 'bio' From 5a58e235500fdcd01d895b0d8e92e29d53d6aeb3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 3 Dec 2018 09:57:11 +0100 Subject: [PATCH 0142/5331] added novope2bed.pl correct shebang --- .../n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb | 2 +- .../n/novoalign/novoalign-3.09.01_fix_hardcoded.patch | 8 ++++++++ 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb index e59b9f64c59..582b7360185 100644 --- a/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01-foss-2018b-R-3.5.1.eb @@ -40,7 +40,7 @@ patches = ['%(name)s-%(version)s_fix_hardcoded.patch'] checksums = [ '08c9cef29ba9c10f81946e7287912982b009a54fb47a226302d99399c19a5b97', # novocraftV3.09.01.Linux3.10.0.tar.gz # 'c6c974ca914ae97abb3ad39d86e002227c52b3685dfa0bbc031b5ba7ecfb3ecd', # novocraftV3.09.01.Linux2.6.32.tar.gz - '369f0d0654786533f8ee056fd577e492e8269798c8e8611a9e20c6b29a9c96d5', # novoalign-3.09.01_fix_hardcoded.patch + 'ce37027d9ee12ada0404faaa8d674fb166fa802e02805b9ff8683b94ef036393', # novoalign-3.09.01_fix_hardcoded.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01_fix_hardcoded.patch b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01_fix_hardcoded.patch index a5998d59b7f..63a0ce1e2af 100644 --- a/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01_fix_hardcoded.patch +++ b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.01_fix_hardcoded.patch @@ -40,3 +40,11 @@ ## qcalplot.R ## Colin Hercus and Zayed Albertyn ## SYNOPSIS: Plot quality values +--- novocraft/novope2bed.pl.orig 2018-11-27 10:13:55.000000000 +0100 ++++ novocraft/novope2bed.pl 2018-12-03 09:55:07.644779954 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + + use Getopt::Long; + use Data::Dumper; From bc306cd90a70b2c31e06802b21583cb49d694d64 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 4 Dec 2018 10:26:09 +0800 Subject: [PATCH 0143/5331] adding easyconfigs: ELPA-2017.11.001-foss-2018b.eb, ELPA-2017.11.001-intel-2018b.eb, ELPA-2018.05.001-foss-2018b.eb, ELPA-2018.05.001-intel-2018b.eb --- .../e/ELPA/ELPA-2017.11.001-foss-2018b.eb | 43 ++++++++++++++++++ .../e/ELPA/ELPA-2017.11.001-intel-2018b.eb | 44 +++++++++++++++++++ .../e/ELPA/ELPA-2018.05.001-foss-2018b.eb | 43 ++++++++++++++++++ .../e/ELPA/ELPA-2018.05.001-intel-2018b.eb | 44 +++++++++++++++++++ 4 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb new file mode 100644 index 00000000000..5cf6e992e8d --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ELPA' +version = '2017.11.001' + +homepage = 'http://elpa.mpcdf.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['59f99c3abe2190fac0db8a301d0b9581ee134f438669dbc92551a54f6f861820'] + +common_configopts = 'LIBS="$LIBSCALAPACK" ' + +# avx2 is enabled by default... +common_configopts += '--disable-avx2 ' + +configopts = [ + common_configopts + '--enable-openmp ', + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. +] + +buildopts = ' V=1 ' + +sanity_check_paths = { + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', + 'lib/libelpa_openmp.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb new file mode 100644 index 00000000000..d5c6eadd908 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ELPA' +version = '2017.11.001' + +homepage = 'http://elpa.mpcdf.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['59f99c3abe2190fac0db8a301d0b9581ee134f438669dbc92551a54f6f861820'] + +common_configopts = 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +common_configopts += 'LIBS="$LIBSCALAPACK" ' + +# avx2 is enabled by default... +common_configopts += '--disable-avx2 ' + +configopts = [ + common_configopts + '--enable-openmp ', + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. +] + +buildopts = ' V=1 ' + +sanity_check_paths = { + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', + 'lib/libelpa_openmp.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb new file mode 100644 index 00000000000..91ab1053fb5 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ELPA' +version = '2018.05.001' + +homepage = 'http://elpa.mpcdf.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a76c3402eb9d1c19b183aedabde8c20f4cfa4692e73e529384207926aec04985'] + +common_configopts = 'LIBS="$LIBSCALAPACK" ' + +# avx2 is enabled by default... +common_configopts += '--disable-avx2 ' + +configopts = [ + common_configopts + '--enable-openmp ', + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. +] + +buildopts = ' V=1 ' + +sanity_check_paths = { + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', + 'lib/libelpa_openmp.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb new file mode 100644 index 00000000000..88c1f4f3e98 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ELPA' +version = '2018.05.001' + +homepage = 'http://elpa.mpcdf.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a76c3402eb9d1c19b183aedabde8c20f4cfa4692e73e529384207926aec04985'] + +common_configopts = 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +common_configopts += 'LIBS="$LIBSCALAPACK" ' + +# avx2 is enabled by default... +common_configopts += '--disable-avx2 ' + +configopts = [ + common_configopts + '--enable-openmp ', + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. +] + +buildopts = ' V=1 ' + +sanity_check_paths = { + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', + 'lib/libelpa_openmp.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], +} + +moduleclass = 'math' From 88de41a20aca2deee13b5062fdd0375aa5f16ff8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Dec 2018 17:25:31 +0200 Subject: [PATCH 0144/5331] adding easyconfigs: TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb, TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb --- .../h5py-2.8.0-fosscuda-2018b-Python-3.6.6.eb | 33 +++ .../n/NCCL/NCCL-2.3.7-fosscuda-2018b.eb | 28 +++ .../p/Python/Python-3.6.6-fosscuda-2018b.eb | 227 ++++++++++++++++++ ...onfig-1.3.1-fosscuda-2018b-Python-3.6.6.eb | 27 +++ .../protobuf/protobuf-3.6.1-fosscuda-2018b.eb | 24 ++ ...low-1.12.0-fosscuda-2018b-Python-2.7.15.eb | 103 ++++++++ ...Flow-1.12.0-fosscuda-2018b-Python-3.6.6.eb | 102 ++++++++ ...RT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb | 51 ++++ ...heel-0.31.1-fosscuda-2018b-Python-3.6.6.eb | 23 ++ 9 files changed, 618 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.3.7-fosscuda-2018b.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.6.1-fosscuda-2018b.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..769ac039214 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.8.0-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e626c65a8587921ebc7fb8d31a49addfdd0b9a9aa96315ea484c09803337b955'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.6.6'), + ('HDF5', '1.10.2'), + ('pkgconfig', '1.3.1', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.3.7-fosscuda-2018b.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.3.7-fosscuda-2018b.eb new file mode 100644 index 00000000000..278f39a2398 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.3.7-fosscuda-2018b.eb @@ -0,0 +1,28 @@ +easyblock = "MakeCp" + +name = 'NCCL' +version = '2.3.7' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +# fosscuda/2018b uses CUDA 9.2 +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +cuda_version = '9.2' + +# Download from https://developer.nvidia.com/nccl/nccl-download (after log in) +sources = ['%%(namelower)s_%%(version)s-1+cuda%s_x86_64.txz' % cuda_version] +checksums = ['f714ef17ce9616eec1f125c44b6542fdf6f92bd82248064ea60dfe33b3d986d8'] + +skipsteps = ['build'] + +files_to_copy = ['lib', 'include'] + +sanity_check_paths = { + 'files': ['lib/libnccl.%s' % SHLIB_EXT, 'lib/libnccl_static.a', 'include/nccl.h'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb new file mode 100644 index 00000000000..0c32936e61b --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb @@ -0,0 +1,227 @@ +name = 'Python' +version = '3.6.6' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['7d56dadf6c7d92a238702389e80cfe66fbfae73e584189ed6f89c75bbf3eda58'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.1'), + ('SQLite', '3.24.0'), + ('XZ', '5.2.4'), + ('GMP', '6.1.2'), # required for pycrypto + ('libffi', '3.2.1'), # required for cryptography + # OS dependency should be preferred if the OS version is more recent then this version, + # it's nice to have an up to date OpenSSL for security reasons; + # Python 3.7.0 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) + # ('OpenSSL', '1.1.0h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +exts_download_dep_fail = True + +# workaround for "undefined symbol: __stack_chk_guard" +# see also https://software.intel.com/en-us/forums/intel-c-compiler/topic/610514 +buildopts = 'LDFLAGS="$LDFLAGS -lssp"' + +# order is important! +# package versions updated August 15th 2018 +exts_list = [ + ('setuptools', '40.0.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['012adb8e25fbfd64c652e99e7bab58799a3aaf05d39ab38561f69190a909015f'], + }), + ('pip', '18.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + 'checksums': ['a0e11645ee37c90b40c46d607070c4fd583e2cd46231b1c06e389c5e814eed76'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('numpy', '1.15.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + 'checksums': ['f28e73cf18d37a413f7d5de35d024e6b98f14566a10d82100f9dc491a7d449f9'], + }), + ('scipy', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('mpi4py', '3.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + 'checksums': ['1b8be50d938c9bb75d0eaf7eda111eec1bf6dc88a62a6412e33bf077457e0f45'], + }), + ('Cython', '0.28.5', { + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'checksums': ['b64575241f64f6ec005a4d4137339fb0ba5e156e826db2fdb5f458060d9979e0'], + }), + ('six', '1.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], + }), + ('python-dateutil', '2.7.3', { + 'modulename': 'dateutil', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], + }), + ('deap', '1.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], + }), + ('decorator', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], + }), + ('liac-arff', '2.3', { + 'modulename': 'arff', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'checksums': ['21b1b17c082cacd7b554bf9a42f6de61d2bf02feef6eb31ec36b5486c31b2ae9'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], + }), + ('pycparser', '2.18', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], + 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], + }), + ('cffi', '1.11.5', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), + ('asn1crypto', '0.24.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], + 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], + }), + ('idna', '2.7', { + 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], + 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], + }), + ('cryptography', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6'], + }), + ('pyasn1', '0.4.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['f58f2a3d12fd754aa123e9fa74fb7345333000a035f3921dbdaa08597aa53137'], + }), + ('PyNaCl', '1.2.1', { + 'modulename': 'nacl', + 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], + 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], + }), + ('bcrypt', '3.1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], + 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], + }), + ('paramiko', '2.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], + }), + ('netifaces', '0.10.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], + 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], + 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], + 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], + }), + ('pytz', '2018.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + 'checksums': ['ffb9ef1de172603304d9d2819af6f5ece76f2e85ec10692a524dd876e72bf277'], + }), + ('pandas', '0.23.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + 'checksums': ['5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], + 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], + }), + ('virtualenv', '16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], + 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], + }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], + 'checksums': ['e9f04885cf11704669f3a731ea6ac00bbc7dea16137aa4394ef7c272cdb9d008'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('certifi', '2018.8.13', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['4c1d68a1408dd090d2f3a869aa94c3947cc1d967821d1ed303208c9f41f0f2f4'], + }), + ('urllib3', '1.23', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], + }), + ('requests', '2.19.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], + }), + ('xlrd', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], + 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], + }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), + ('mpmath', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], + 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], + }), + ('tabulate', '0.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], + 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..6cd22620ed3 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.3.1-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['0bc77e955a5990b466b7277234a88dc6a62f1f4388ac1e95469051c82a17fd80'] + +dependencies = [ + ('Python', '3.6.6'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1-fosscuda-2018b.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1-fosscuda-2018b.eb new file mode 100644 index 00000000000..b512d29d2a8 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1-fosscuda-2018b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.6.1' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3d4e589d81b2006ca603c1ab712c9715a76227293032d05b26fca603f90b3f5b'] + +builddependencies = [('Autotools', '20180311')] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..79d2272e773 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,103 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '1.12.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'usempi': True} + +builddependencies = [ + # must stick to Bazel 0.18, cfr. https://github.com/tensorflow/tensorflow/issues/23380 + ('Bazel', '0.18.0'), + ('protobuf', '3.6.1'), +] + +dependencies = [ + ('Python', '2.7.15'), + ('wheel', '0.31.1', versionsuffix), + ('h5py', '2.8.0', versionsuffix), + ('cuDNN', '7.1.4.18'), + ('NCCL', '2.3.7'), + ('TensorRT', '4.0.1.6', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('protobuf-python', '3.6.1', { + 'modulename': 'google.protobuf', + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + 'start_dir': 'python', + 'use_pip': False, + 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + }), + ('absl-py', '0.6.1', { + 'modulename': 'absl', + 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], + 'checksums': ['87519e3b91a3d573664c6e2ee33df582bb68dca6642ae3cf3a4361b1c0a4e9d6'], + }), + ('astor', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], + 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], + }), + ('gast', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], + 'checksums': ['7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930'], + }), + ('grpcio', '1.16.0', { + 'modulename': 'grpc', + 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], + 'checksums': ['0cc5f2d3ee21c642d8982f197c83053fd3a8cbcd6a60240d8c87c6c256b10d57'], + }), + ('Markdown', '3.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], + 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], + }), + ('tensorboard', version, { + 'source_tmpl': 'tensorboard-%(version)s-py2-none-any.whl', + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], + 'unpack_sources': False, + 'checksums': ['537603db949e10d2f5f201d88b073f3f8fb4e4c311d5541e1d4518aa59aa8daa'], + }), + ('termcolor', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('Werkzeug', '0.14.1', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], + 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], + }), + ('Keras-Applications', '1.0.6', { + 'modulename': 'keras_applications', + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], + 'checksums': ['a03af60ddc9c5afdae4d5c9a8dd4ca857550e0b793733a5072e0725829b87017'], + }), + ('Keras-Preprocessing', '1.0.5', { + 'modulename': 'keras_preprocessing', + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], + 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], + }), + (name, version, { + 'patches': ['TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.12.0_lrt-flag.patch', 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'checksums': [ + '3c87b81e37d4ed7f3da6200474fa5e656ffd20d8811068572f43610cae97ca92', # v1.12.0.tar.gz + 'aa53c7f6d42b4a9e91e0ba639d79f69a7db3c0a88c3b8e43d332479b6368391a', # TensorFlow-1.11.0_swig-env.patch + # TensorFlow-1.11.0_remove-msse-hardcoding.patch + 'a0f00ee4d03bb4fd3a645ee06045cedaf97d0b85675ec35187e9dd7e479d7bb6', + '164d048c69671f870e306760ee7609564fe02bb6378a06414752f3d6da80a631', # TensorFlow-1.12.0_lrt-flag.patch + # TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch + 'b7cd09694faf8e4427ca9a8a209f26d0837125f61c7b015668ce61d94f719bea', + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..cb0a2bcf323 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,102 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '1.12.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'usempi': True} + +builddependencies = [ + # must stick to Bazel 0.18, cfr. https://github.com/tensorflow/tensorflow/issues/23380 + ('Bazel', '0.18.0'), + ('protobuf', '3.6.1'), +] + +dependencies = [ + ('Python', '3.6.6'), + ('wheel', '0.31.1', versionsuffix), + ('h5py', '2.8.0', versionsuffix), + ('cuDNN', '7.1.4.18'), + ('NCCL', '2.3.7'), +] + +use_pip = True + +exts_list = [ + ('protobuf-python', '3.6.1', { + 'modulename': 'google.protobuf', + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + 'start_dir': 'python', + 'use_pip': False, + 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + }), + ('absl-py', '0.6.1', { + 'modulename': 'absl', + 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], + 'checksums': ['87519e3b91a3d573664c6e2ee33df582bb68dca6642ae3cf3a4361b1c0a4e9d6'], + }), + ('astor', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], + 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], + }), + ('gast', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], + 'checksums': ['7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930'], + }), + ('grpcio', '1.16.0', { + 'modulename': 'grpc', + 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], + 'checksums': ['0cc5f2d3ee21c642d8982f197c83053fd3a8cbcd6a60240d8c87c6c256b10d57'], + }), + ('Markdown', '3.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], + 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], + }), + ('tensorboard', version, { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], + 'unpack_sources': False, + 'checksums': ['ca275a7e39797946930d7d4460999369b73968e8191f2256e23bfb7924004d59'], + }), + ('termcolor', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('Werkzeug', '0.14.1', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], + 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], + }), + ('Keras-Applications', '1.0.6', { + 'modulename': 'keras_applications', + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], + 'checksums': ['a03af60ddc9c5afdae4d5c9a8dd4ca857550e0b793733a5072e0725829b87017'], + }), + ('Keras-Preprocessing', '1.0.5', { + 'modulename': 'keras_preprocessing', + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], + 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], + }), + (name, version, { + 'patches': ['TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.12.0_lrt-flag.patch', 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'checksums': [ + '3c87b81e37d4ed7f3da6200474fa5e656ffd20d8811068572f43610cae97ca92', # v1.12.0.tar.gz + 'aa53c7f6d42b4a9e91e0ba639d79f69a7db3c0a88c3b8e43d332479b6368391a', # TensorFlow-1.11.0_swig-env.patch + # TensorFlow-1.11.0_remove-msse-hardcoding.patch + 'a0f00ee4d03bb4fd3a645ee06045cedaf97d0b85675ec35187e9dd7e479d7bb6', + '164d048c69671f870e306760ee7609564fe02bb6378a06414752f3d6da80a631', # TensorFlow-1.12.0_lrt-flag.patch + # TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch + 'b7cd09694faf8e4427ca9a8a209f26d0837125f61c7b015668ce61d94f719bea', + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..5f5690b3bbf --- /dev/null +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,51 @@ +easyblock = 'Binary' + +name = 'TensorRT' +version = '4.0.1.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://developer.nvidia.com/tensorrt' +description = """NVIDIA TensorRT is a platform for high-performance deep learning inference""" + +sources = ['%(name)s-%(version)s.Ubuntu-16.04.4.x86_64-gnu.cuda-9.2.cudnn7.1.tar.gz'] + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +builddependencies = [ + ('protobuf', '3.6.1'), +] + +dependencies = [ + ('Python', '2.7.15'), + ('cuDNN', '7.1.4.18'), +] + +extract_sources = True +keepsymlinks = True + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('protobuf-python', '3.6.1', { + 'modulename': 'google.protobuf', + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + 'start_dir': 'python', + 'use_pip': False, + 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + }), +] + +postinstallcmds = [ + 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/python/%s ' % 'tensorrt-4.0.1.6-cp27-cp27mu-linux_x86_64.whl', + 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/uff/%s ' % 'uff-0.4.0-py2.py3-none-any.whl', + 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/graphsurgeon/%s ' % 'graphsurgeon-0.2.0-py2.py3-none-any.whl', +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..553e73e0a3f --- /dev/null +++ b/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'wheel' +version = '0.31.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/wheel' +description = """A built-package format for Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['0a2e54558a0628f2145d2fc822137e322412115173e8a2ddbe1c9024338ae83c'] + +dependencies = [('Python', '3.6.6')] + +sanity_check_paths = { + 'files': ['bin/wheel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 60bf26f13148ea8962b37a7d49771dba66913f3c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Dec 2018 16:48:02 +0100 Subject: [PATCH 0145/5331] Add TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch --- ...w-1.12.0_dont_expand_cuda_cudnn_path.patch | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch new file mode 100644 index 00000000000..12274644440 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch @@ -0,0 +1,27 @@ +diff -ru tensorflow-1.12.0.orig/configure.py tensorflow-1.12.0/configure.py +--- tensorflow-1.12.0.orig/configure.py 2018-11-02 02:35:10.000000000 +0100 ++++ tensorflow-1.12.0/configure.py 2018-11-23 19:54:38.521616844 +0100 +@@ -905,8 +905,9 @@ + + # Result returned from "read" will be used unexpanded. That make "~" + # unusable. Going through one more level of expansion to handle that. +- cudnn_install_path = os.path.realpath( +- os.path.expanduser(cudnn_install_path)) ++# Don't expand symlinks ++# cudnn_install_path = os.path.realpath( ++# os.path.expanduser(cudnn_install_path)) + if is_windows() or is_cygwin(): + cudnn_install_path = cygpath(cudnn_install_path) + +diff -ru tensorflow-1.12.0.orig/third_party/gpus/cuda_configure.bzl tensorflow-1.12.0/third_party/gpus/cuda_configure.bzl +--- tensorflow-1.12.0.orig/third_party/gpus/cuda_configure.bzl 2018-11-02 02:35:10.000000000 +0100 ++++ tensorflow-1.12.0/third_party/gpus/cuda_configure.bzl 2018-11-23 19:54:38.525616802 +0100 +@@ -393,7 +393,7 @@ + cuda_toolkit_path = repository_ctx.os.environ[_CUDA_TOOLKIT_PATH].strip() + if not repository_ctx.path(cuda_toolkit_path).exists: + auto_configure_fail("Cannot find cuda toolkit path.") +- return str(repository_ctx.path(cuda_toolkit_path).realpath) ++ return cuda_toolkit_path + + def _cudnn_install_basedir(repository_ctx): + """Finds the cudnn install directory.""" From 2e663c028a7ec2f9552125de1831e768ec32ae66 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Dec 2018 16:49:32 +0100 Subject: [PATCH 0146/5331] Add comment to TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch --- .../TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch index 12274644440..a7ffa9ef34e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch @@ -1,3 +1,7 @@ +# Don't expand path for cuda_toolkit and cudnn. +# We want the EasyBuild created path to be used. +# +# Åke Sandgren, 20180613 diff -ru tensorflow-1.12.0.orig/configure.py tensorflow-1.12.0/configure.py --- tensorflow-1.12.0.orig/configure.py 2018-11-02 02:35:10.000000000 +0100 +++ tensorflow-1.12.0/configure.py 2018-11-23 19:54:38.521616844 +0100 From 1374941cd247c1ea14cd5d501606de6f16baa819 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Dec 2018 17:52:17 +0200 Subject: [PATCH 0147/5331] Update checksum for TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch --- .../TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb | 2 +- .../TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb index 79d2272e773..8e9ae9274a6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb @@ -95,7 +95,7 @@ exts_list = [ 'a0f00ee4d03bb4fd3a645ee06045cedaf97d0b85675ec35187e9dd7e479d7bb6', '164d048c69671f870e306760ee7609564fe02bb6378a06414752f3d6da80a631', # TensorFlow-1.12.0_lrt-flag.patch # TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch - 'b7cd09694faf8e4427ca9a8a209f26d0837125f61c7b015668ce61d94f719bea', + '843acddc197639273cb26e676685a12a1107a3bccca516be1af873df6352bb00', ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb index cb0a2bcf323..d38ebe735e3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb @@ -94,7 +94,7 @@ exts_list = [ 'a0f00ee4d03bb4fd3a645ee06045cedaf97d0b85675ec35187e9dd7e479d7bb6', '164d048c69671f870e306760ee7609564fe02bb6378a06414752f3d6da80a631', # TensorFlow-1.12.0_lrt-flag.patch # TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch - 'b7cd09694faf8e4427ca9a8a209f26d0837125f61c7b015668ce61d94f719bea', + '843acddc197639273cb26e676685a12a1107a3bccca516be1af873df6352bb00', ], }), ] From aa5224db23c1b4772f3ba71c9d3bd1c395eac952 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 7 Dec 2018 09:57:45 +0200 Subject: [PATCH 0148/5331] Add checksum for TensorRT --- .../t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb index 5f5690b3bbf..af969f90fdc 100644 --- a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb @@ -8,6 +8,7 @@ homepage = 'https://developer.nvidia.com/tensorrt' description = """NVIDIA TensorRT is a platform for high-performance deep learning inference""" sources = ['%(name)s-%(version)s.Ubuntu-16.04.4.x86_64-gnu.cuda-9.2.cudnn7.1.tar.gz'] +checksums = ['fc5fd2ba86225ed62e60870cc24896107770a59829363fcb49229c82bb1f4fb5'] toolchain = {'name': 'fosscuda', 'version': '2018b'} From bb2bf1e5d3fb13d1c1a2488695929f129664e710 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 7 Dec 2018 16:38:57 +0100 Subject: [PATCH 0149/5331] {tools}[foss/2018b] ITSTool 2.0.5 w/Python 2.7.15 (REVIEW) --- .../ITSTool-2.0.5-foss-2018b-Python-2.7.15.eb | 27 +++++++++++++ ...2.Python-2.9.8-foss-2018b-Python-2.7.15.eb | 40 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.5-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.5-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.5-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..7d4e0a9a61f --- /dev/null +++ b/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.5-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'ITSTool' +version = '2.0.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://itstool.org/' +description = """ITS Tool allows you to translate your XML documents with PO files, using rules from the + W3C Internationalization Tag Set (ITS) to determine what to translate and how to separate it into PO file messages.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://files.itstool.org/itstool/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['100506f8df62cca6225ec3e631a8237e9c04650c77495af4919ac6a100d4b308'] + +dependencies = [ + ('Python', '2.7.15'), + ('libxml2.Python', '2.9.8', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/itstool'], + 'dirs': ['share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..1c8f0ee88c1 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'libxml2.Python' +version = '2.9.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://xmlsoft.org/' +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). This is the Python binding.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = ['libxml2-%(version)s.tar.gz'] +checksums = ['0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732'] + +dependencies = [ + ('Python', '2.7.15'), + ('libxml2', version), +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'libxml2'} + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages', 'lib64/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From a77ca3f3c3c5892a4b7dd12013d3be75b0133c11 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 7 Dec 2018 16:42:36 +0100 Subject: [PATCH 0150/5331] {vis}[foss/2018b] p4vasp w/Python 2.7.15 (REVIEW) --- .../f/FLTK/FLTK-1.3.4-foss-2018b.eb | 41 ++++++++++++++ .../Glade-3.8.6-foss-2018b-Python-2.7.15.eb | 44 +++++++++++++++ .../k/kbproto/kbproto-1.0.7-GCCcore-7.3.0.eb | 25 +++++++++ .../libpthread-stubs-0.4-GCCcore-7.3.0.eb | 30 ++++++++++ ...OpenGL-3.1.3b2-foss-2018b-Python-2.7.15.eb | 43 +++++++++++++++ .../p4vasp-0.3.30-foss-2018b-Python-2.7.15.eb | 55 +++++++++++++++++++ .../renderproto-0.11-GCCcore-7.3.0.eb | 23 ++++++++ .../xextproto-7.3.0-GCCcore-7.3.0.eb | 30 ++++++++++ .../x/xproto/xproto-7.0.31-GCCcore-7.3.0.eb | 30 ++++++++++ 9 files changed, 321 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-foss-2018b.eb create mode 100644 easybuild/easyconfigs/g/Glade/Glade-3.8.6-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.30-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/r/renderproto/renderproto-0.11-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-foss-2018b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-foss-2018b.eb new file mode 100644 index 00000000000..f99d4a1f999 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-foss-2018b.eb @@ -0,0 +1,41 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.4' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-%(version)s_fix-LDFLAGS.patch'] +checksums = [ + 'c8ab01c4e860d53e11d40dc28f98d2fe9c85aaf6dbb5af50fd6e66afec3dc58f', # fltk-1.3.4-source.tar.gz + 'b9d39f6dce92fdb34a149f686a5d56e72912f94fd09c4958f3bb12770603da7d', # FLTK-1.3.4_fix-LDFLAGS.patch +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '2.0.0'), + ('xprop', '1.2.3'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Glade/Glade-3.8.6-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/Glade/Glade-3.8.6-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..571fdfac624 --- /dev/null +++ b/easybuild/easyconfigs/g/Glade/Glade-3.8.6-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'Glade' +version = '3.8.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://glade.gnome.org/' +description = """Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit + and the GNOME desktop environment.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s%(version_major)s/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version_major)s-%(version)s.tar.xz'] +checksums = ['aaeeebffaeb3068fb23757a2eede46adeb4c7cecc740feed7654e065491f5449'] + +checksums = ['aaeeebffaeb3068fb23757a2eede46adeb4c7cecc740feed7654e065491f5449'] + +builddependencies = [ + ('intltool', '0.51.0', '-Perl-5.28.0'), + ('pkg-config', '0.29.2'), + ('libpthread-stubs', '0.4'), + ('kbproto', '1.0.7'), + ('xproto', '7.0.31'), + ('xextproto', '7.3.0'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('Python', '2.7.15'), + ('GTK+', '2.24.32'), + ('PyGTK', '2.24.0', versionsuffix), + ('gettext', '0.19.8.1'), + ('ITSTool', '2.0.5', versionsuffix), + ('libxml2', '2.9.8'), +] +sanity_check_paths = { + 'files': ['bin/glade-%(version_major)s', 'lib/libgladeui-1.%s' % SHLIB_EXT, 'lib/pkgconfig/gladeui-1.0.pc', + 'lib/glade%%(version_major)s/modules/libgladegtk.%s' % SHLIB_EXT, + 'lib/glade%%(version_major)s/modules/libgladepython.%s' % SHLIB_EXT], + 'dirs': ['include/libgladeui-1.0/gladeui', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-GCCcore-7.3.0.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..8ce277bd0aa --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-GCCcore-7.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['828cb275b91268b1a3ea950d5c0c5eb076c678fdf005d517411f89cc8c3bb416'] + +builddependencies = [ + ('binutils', '2.30'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..d4737c8a564 --- /dev/null +++ b/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.4-GCCcore-7.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libpthread-stubs' +version = '0.4' + +homepage = 'http://xcb.freedesktop.org/' + +description = """ + The X protocol C-language Binding (XCB) is a replacement for Xlib featuring + a small footprint, latency hiding, direct access to the protocol, improved + threading support, and extensibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'] + +builddependencies = [ + ('binutils', '2.30'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/pthread-stubs.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..7da9c1f14a3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.3b2-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,43 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'PyOpenGL' +version = '3.1.3b2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ac73b4c0b433be02d6a55b9ed768acf07003a92a3315ba9d62bc8f8da5f0c291'] + +builddependencies = [ + ('bzip2', '1.0.6'), +] + +dependencies = [ + ('Python', '2.7.15'), + ('Mesa', '18.1.1'), +] + +options = {'modulename': 'OpenGL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.30-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.30-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..9e16f63c78a --- /dev/null +++ b/easybuild/easyconfigs/p/p4vasp/p4vasp-0.3.30-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'p4vasp' +version = '0.3.30' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.p4vasp.at/' +description = """Visualization suite for VASP""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://www.p4vasp.at/files'] +sources = [SOURCE_TGZ] +patches = [ + ('p4vasp-%(version)s_drop_fltk_from_makefile.patch'), + ('p4vasp-%(version)s_fix_compiler_spec.patch'), + ('p4vasp-%(version)s_fix_fltk-config_usage.patch'), + ('p4vasp-%(version)s_dont_preload_libstdc_nor_set_PYTHONPATH_again.patch'), +] +checksums = [ + '7052926f70a799f87c2d3a5d52c86575422113e3f589776b071dfc554969df7d', # p4vasp-0.3.30.tgz + '1a7b4a59d4605bd022af0b90b20922137a0a90b077e512041a0091221daf26a1', # p4vasp-0.3.30_drop_fltk_from_makefile.patch + 'b73f6f99261fa3399b673c27f0d3e2164bf7f5da0018e536a0c5a1349a341aa3', # p4vasp-0.3.30_fix_compiler_spec.patch + 'ca226baeb49abb681beb057b781c059e41d1988d16dae1aca38d1e6b2d425801', # p4vasp-0.3.30_fix_fltk-config_usage.patch + # p4vasp-0.3.30_dont_preload_libstdc_nor_set_PYTHONPATH_again.patch + '94ac59b261789ea197380678703bacdddbcf6722b7fb302408984a2d7e25ce3c', +] + +dependencies = [ + ('Python', '2.7.15'), + ('PyGTK', '2.24.0', versionsuffix), + ('PyOpenGL', '3.1.3b2', versionsuffix), + ('Glade', '3.8.6', versionsuffix), + ('X11', '20180604'), + ('FLTK', '1.3.4'), +] + +skipsteps = ['configure', 'build'] + +# redefine $HOME to specify installation prefix O_o +preinstallopts = "make cleanall && env HOME=%(installdir)s make local && " + +sanity_check_paths = { + 'files': ['p4vasp/bin/p4v', 'p4vasp/lib/libODP.a', 'p4vasp/lib/libp4vasp.a'], + 'dirs': ['p4vasp/data', 'p4vasp/include/ODP', 'p4vasp/include/p4vasp', 'p4vasp/python-packages', 'p4vasp/utils'], +} + +modextrapaths = { + 'CPATH': ['p4vasp/include'], + 'LIBRARY_PATH': ['p4vasp/lib'], + 'PATH': ['p4vasp/bin'], + 'PYTHONPATH': ['p4vasp/python-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-GCCcore-7.3.0.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..fa96d9d0b44 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-GCCcore-7.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'optarch': True} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['256e4af1d3b4007872a276ed9e5c2522f80f5fe69b97268542917635b4dbf758'] + +builddependencies = [('binutils', '2.30')] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..cd2c8fceb92 --- /dev/null +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-GCCcore-7.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'xextproto' +version = '7.3.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """XExtProto protocol headers.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1b1bcdf91221e78c6c33738667a57bd9aaa63d5953174ad8ed9929296741c9f5'] + +builddependencies = [ + ('binutils', '2.30'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in [ + 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', + 'mitmiscproto.h', 'multibufproto.h', 'securproto.h', 'shapeproto.h', 'shm.h', 'shmstr.h', 'syncproto.h', + 'xtestconst.h', 'xtestext1proto.h' + ] + ], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-7.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..b787dbc1e88 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-7.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.30'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' From 98d725580bf08b702022570640ac387a845e1040 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Dec 2018 18:58:15 +0100 Subject: [PATCH 0151/5331] {bio}[foss/2018b] zingeR v20180131 w/ R 3.5.1 --- .../zingeR-20180131-foss-2018b-R-3.5.1.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/z/zingeR/zingeR-20180131-foss-2018b-R-3.5.1.eb diff --git a/easybuild/easyconfigs/z/zingeR/zingeR-20180131-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/z/zingeR/zingeR-20180131-foss-2018b-R-3.5.1.eb new file mode 100644 index 00000000000..832e27bda9a --- /dev/null +++ b/easybuild/easyconfigs/z/zingeR/zingeR-20180131-foss-2018b-R-3.5.1.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'zingeR' +commit = 'c789ae5' +version = '20180131' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/statOmics/zingeR' +description = "Zero-Inflated Negative binomial Gene Expression in R" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ["https://github.com/statOmics/zingeR/archive/"] +sources = [{'download_filename': '%s.tar.gz' % commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['409567dfb823f5d030a86536533ce775f6e409e0914afb08558f2534514332cc'] + +dependencies = [ + ('R', '3.5.1'), + ('R-bundle-Bioconductor', '3.7', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From fb9ee27cdfcd6d8db5e5045344c17155fa87f4cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Dec 2018 22:24:02 +0100 Subject: [PATCH 0152/5331] {tools}[foss/2018b] Spyder v3.3.2 w/ Python 3.6.6 --- .../Spyder-3.3.2-foss-2018b-Python-3.6.6.eb | 133 ++++++++++++++++++ 1 file changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..9d2024f4b17 --- /dev/null +++ b/easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,133 @@ +easyblock = 'PythonBundle' + +name = 'Spyder' +version = '3.3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/spyder-ide/spyder' +description = """Spyder is an interactive Python development environment providing MATLAB-like features in a simple + and light-weighted software.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [ + ('CMake', '3.12.1'), + ('wheel', '0.31.1', versionsuffix), +] +dependencies = [ + ('Python', '3.6.6'), + ('PyQt5', '5.11.3', versionsuffix), + ('ZeroMQ', '4.2.5'), + ('IPython', '7.2.0', versionsuffix), + ('Sphinx', '1.8.1', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('psutil', '5.4.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'checksums': ['6e265c8f3da00b015d24b842bfeb111f856b13d24f2c57036582568dc650d6c3'], + }), + ('cloudpickle', '0.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], + 'checksums': ['f169a8523a40eb0a3452e1878aac31da6759409fbafa51dd50d89d4a6b42bcf1'], + }), + ('spyder-kernels', '1.1.0', { + 'modulename': 'spyder_kernels', + 'source_urls': ['https://pypi.python.org/packages/source/s/spyder-kernels'], + 'checksums': ['7e4d6a55e679757bdbae833f9fcdc4239f0086a8ba38439a252612cd113ac4fa'], + }), + ('QtPy', '1.5.2', { + 'source_urls': ['https://pypi.python.org/packages/source/Q/QtPy'], + 'checksums': ['4c690f90586c82c1210bb6fdf5e9ee4d1228809421dc6a349c5afacc27caabcd'], + }), + ('QtAwesome', '0.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/Q/QtAwesome'], + 'checksums': ['8dfd8bcac56caa6d81639fc43db673b62aeca6129f4c8e9b1da17a32c0d309fd'], + }), + ('lazy-object-proxy', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lazy-object-proxy'], + 'checksums': ['eb91be369f945f10d3a49f5f9be8b3d0b93a4c2be8f8a5b83b0571b8123e0a7a'], + }), + ('typed-ast', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typed-ast'], + 'checksums': ['57fe287f0cdd9ceaf69e7b71a2e94a24b5d268b35df251a88fef5cc241bf73aa'], + }), + ('wrapt', '1.10.11', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt'], + 'checksums': ['d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6'], + }), + ('astroid', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/astroid'], + 'checksums': ['35b032003d6a863f5dcd7ec11abd5cd5893428beaa31ab164982403bcb311f22'], + }), + ('isort', '4.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/i/isort'], + 'checksums': ['b9c40e9750f3d77e6e4d441d8b0266cf555e7cdabdcff33c4fd06366ca761ef8'], + }), + ('mccabe', '0.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mccabe'], + 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], + }), + ('pylint', '2.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pylint'], + 'checksums': ['689de29ae747642ab230c6d37be2b969bf75663176658851f456619aacf27492'], + }), + ('pycodestyle', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycodestyle'], + 'checksums': ['cbfca99bd594a10f674d0cd97a3d802a1fdef635d4361e1a2658de47ed261e3a'], + }), + ('jeepney', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jeepney'], + 'checksums': ['6089412a5de162c04747f0220f6b2223b8ba660acd041e52a76426ca550e3c70'], + }), + ('SecretStorage', '3.1.0', { + 'source_tmpl': 'SecretStorage-%(version)s-py3-none-any.whl', + 'source_urls': ['https://pypi.python.org/packages/source/S/SecretStorage'], + 'unpack_sources': False, + 'checksums': ['20196abd1a9d1310df7573d58ca6e7ed9292218c98ca3638eea07beb16080343'], + }), + ('keyrings.alt', '3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/keyrings.alt'], + 'checksums': ['b59c86b67b9027a86e841a49efc41025bcc3b1b0308629617b66b7011e52db5a'], + }), + ('keyring', '17.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/k/keyring'], + 'checksums': ['d3744d22e398c19405d819d3c2d3bb82dc05a96513f577411c8847bb207dc289'], + }), + ('pyflakes', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyflakes'], + 'checksums': ['9a7662ec724d0120012f6e29d6248ae3727d821bba522a0e6b356eff19126a49'], + }), + ('qtconsole', '4.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/q/qtconsole'], + 'checksums': ['bc1ba15f50c29ed50f1268ad823bb6543be263c18dd093b80495e9df63b003ac'], + }), + ('rope', '0.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/rope'], + 'checksums': ['a108c445e1cd897fe19272ab7877d172e7faf3d4148c80e7d20faba42ea8f7b2'], + }), + ('docutils', '0.14', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], + 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], + }), + ('spyder', version, { + 'source_urls': ['https://pypi.python.org/packages/source/s/spyder'], + 'checksums': ['ab3a30321d3142bf6c98f71cea3a6d65b4b6f67d4b77c4966249e8547bb9bbfa'], + }), +] + +# 'pip check' reports missing pyqt5, even though PyQt5 is included as a dependency +# problem is that PyQt5 was not installed with pip (and it's not trivial to do so) +run_pip_check = False + +sanity_check_paths = { + 'files': ['bin/spyder3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["spyder3 --help"] + +moduleclass = 'tools' From 317acc9842bba3550f04258573235aeae07252f1 Mon Sep 17 00:00:00 2001 From: Ruben Di Battista Date: Thu, 29 Nov 2018 17:38:30 +0100 Subject: [PATCH 0153/5331] Add llvm 7.0 for GCC 7.2.0 toolchain --- .../c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb | 57 +++++++++++++++++++ .../c/cURL/cURL-7.60.0-GCCcore-7.2.0.eb | 49 ++++++++++++++++ .../l/LLVM/LLVM-7.0.0-GCCcore-7.2.0.eb | 45 +++++++++++++++ .../Python-2.7.15-GCCcore-7.2.0-bare.eb | 37 ++++++++++++ .../s/SQLite/SQLite-3.24.0-GCCcore-7.2.0.eb | 45 +++++++++++++++ .../t/Tcl/Tcl-8.6.8-GCCcore-7.2.0.eb | 45 +++++++++++++++ 6 files changed, 278 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.60.0-GCCcore-7.2.0.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-7.0.0-GCCcore-7.2.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-7.2.0-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.24.0-GCCcore-7.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.8-GCCcore-7.2.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb new file mode 100644 index 00000000000..287f3d6348a --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1-GCCcore-7.2.0.eb @@ -0,0 +1,57 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.12.1' + +homepage = 'http://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c53d5c2ce81d7a957ee83e3e635c8cda5dfe20c9d501a4828ee28e1615e57ab2'] + +builddependencies = [ + ('binutils', '2.29'), +] + +dependencies = [ + ('ncurses', '6.1'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('cURL', '7.60.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0h'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +configopts = '-- -DCMAKE_USE_OPENSSL=1 ' +configopts += '-DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include ' +configopts += '-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.%s ' % SHLIB_EXT +configopts += '-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.%s ' % SHLIB_EXT +configopts += '-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.%s ' % SHLIB_EXT +configopts += '-DCMAKE_USE_SYSTEM_BZIP2=1 ' +configopts += '-DBZIP2_INCLUDE_DIR=$EBROOTBZIP2/include ' +configopts += '-DBZIP2_LIBRARY_RELEASE=$EBROOTBZIP2/lib/libbz2.%s ' % SHLIB_EXT +configopts += '-DCMAKE_USE_SYSTEM_ZLIB=1 ' +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DZLIB_LIBRARY_RELEASE=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT +configopts += '-DCMAKE_USE_SYSTEM_CURL=1 ' +configopts += '-DCURL_INCLUDE_DIR=$EBROOTCURL/include ' +configopts += '-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.%s ' % SHLIB_EXT + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.60.0-GCCcore-7.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.60.0-GCCcore-7.2.0.eb new file mode 100644 index 00000000000..b0889589f8f --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.60.0-GCCcore-7.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.60.0' + +homepage = 'http://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e9c37986337743f37fd14fe8737f246e97aec94b39d1b71e8a5973f72a9fc4f5'] + +builddependencies = [ + ('binutils', '2.29'), +] + +dependencies = [ + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0h') +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +configopts = '--with-zlib' +# configopts += '--with-ssl=$EBROOTOPENSSL' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-7.0.0-GCCcore-7.2.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-7.0.0-GCCcore-7.2.0.eb new file mode 100644 index 00000000000..e5020fb2a79 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-7.0.0-GCCcore-7.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '7.0.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] +checksums = ['8bc1f844e6cbde1b652c19c1edebc1864456fd9c78b8c1bea038e51b363fe222'] + +builddependencies = [ + ('binutils', '2.29'), + ('CMake', '3.12.1'), + ('Python', '2.7.15', '-bare'), +] + +dependencies = [ + ('ncurses', '6.1'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-7.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-7.2.0-bare.eb new file mode 100644 index 00000000000..b4a6ef133a6 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-7.2.0-bare.eb @@ -0,0 +1,37 @@ +name = 'Python' +version = '2.7.15' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['18617d1f15a380a919d517630a9cd85ce17ea602f9bbdc58ddc672df4b0239db'] + +# python needs bzip2 to build the bz2 package + +builddependencies = [ + ('binutils', '2.29'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.1'), + ('SQLite', '3.24.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.24.0-GCCcore-7.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.24.0-GCCcore-7.2.0.eb new file mode 100644 index 00000000000..0e34343dc4d --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.24.0-GCCcore-7.2.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.24.0' + +homepage = 'http://www.sqlite.org/' + +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.sqlite.org/2018/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] +checksums = ['d9d14e88c6fb6d68de9ca0d1f9797477d82fc3aed613558f87ffbdbbc5ceb74a'] + +builddependencies = [ + ('binutils', '2.29'), +] + +dependencies = [ + ('libreadline', '7.0'), + ('Tcl', '8.6.8'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.8-GCCcore-7.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.8-GCCcore-7.2.0.eb new file mode 100644 index 00000000000..79ee2a4d15e --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.8-GCCcore-7.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.8' + +homepage = 'http://www.tcl.tk/' + +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['c43cb0c1518ce42b00e7c8f6eaddd5195c53a98f94adc717234a65cbcfd3f96a'] + +builddependencies = [ + ('binutils', '2.29'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = [ + 'ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh' +] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' From 58576bf45eff179d34597a02186517ad2bbe03e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Dec 2018 14:24:42 +0100 Subject: [PATCH 0154/5331] {bio}[foss/2018b] VarDict v1.5.7 w/ Perl 5.28.0 --- .../VarDict-1.5.7-foss-2018b-Perl-5.28.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/v/VarDict/VarDict-1.5.7-foss-2018b-Perl-5.28.0.eb diff --git a/easybuild/easyconfigs/v/VarDict/VarDict-1.5.7-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/v/VarDict/VarDict-1.5.7-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..4db16843340 --- /dev/null +++ b/easybuild/easyconfigs/v/VarDict/VarDict-1.5.7-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,40 @@ +easyblock = 'Tarball' + +name = 'VarDict' +version = '1.5.7' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://github.com/AstraZeneca-NGS/VarDict' +description = """VarDict is an ultra sensitive variant caller for both single + and paired sample variant calling from BAM files.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/AstraZeneca-NGS/VarDict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6cc3fdd4c58d0024a594366da9ca5c31257b2e8f13244c704a636b6fe6061b71'] + +dependencies = [ + ('R', '3.5.1'), + ('Perl', '5.28.0'), + ('SAMtools', '1.9'), +] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ['testsomatic.R', 'teststrandbias.R', 'vardict', 'vardict.pl', 'var2vcf_paired.pl', 'var2vcf_valid.pl'], + 'dirs': ['Stat'], +} + +sanity_check_commands = [ + "vardict -H", + "vardict2mut.pl -H", # requires Stat::Basic Perl module included in VarDict +] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} + +moduleclass = 'bio' From de6150040fed034a34be21ec3f75f7a3cb216ad9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Dec 2018 20:24:48 +0100 Subject: [PATCH 0155/5331] adding easyconfigs: Valgrind-3.14.0-foss-2018b.eb --- .../v/Valgrind/Valgrind-3.14.0-foss-2018b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.14.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.14.0-foss-2018b.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.14.0-foss-2018b.eb new file mode 100644 index 00000000000..42de2086ff0 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.14.0-foss-2018b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.14.0' + +homepage = 'http://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'optarch': False} + +source_urls = [ + 'ftp://sourceware.org/pub/valgrind/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['037c11bfefd477cc6e9ebe8f193bb237fe397f7ce791b4a4ce3fa1c6a520baa5'] + +configopts = ' --with-mpicc="$MPICC"' + +binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'debugger' From cc8bdebb649dbb2ecd4a474fc7b7624207a7c9de Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 12 Dec 2018 08:20:09 +0100 Subject: [PATCH 0156/5331] VTK8: Make sure that Python3 wrapper is used --- easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-3.6.4.eb | 1 + .../easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-3.6.4.eb | 1 + easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-3.6.6.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-3.6.4.eb index f78a49a0cc8..7d6ed26d9a4 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-3.6.4.eb @@ -48,6 +48,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +configopts += "-DVTK_PYTHON_VERSION=3 " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)sm " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)sm.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-3.6.4.eb index 04beed748ab..d8bc3e68897 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-3.6.4.eb @@ -48,6 +48,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +configopts += "-DVTK_PYTHON_VERSION=3 " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)sm " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)sm.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-3.6.6.eb index 11cd15af6f3..b48a78a8aff 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-3.6.6.eb @@ -48,6 +48,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +configopts += "-DVTK_PYTHON_VERSION=3 " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)sm " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)sm.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " From 137b4df31a184e8bda675921111536bd3d5625b1 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 12 Dec 2018 08:34:30 +0100 Subject: [PATCH 0157/5331] VTK8: Make sure that right wrapper is used --- .../easyconfigs/v/VTK/VTK-8.0.1-foss-2017b-Python-2.7.14.eb | 1 + .../easyconfigs/v/VTK/VTK-8.0.1-intel-2017b-Python-2.7.14.eb | 1 + .../easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-2.7.14.eb | 1 + .../easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-3.6.4.eb | 2 +- .../easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-2.7.14.eb | 1 + .../easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-3.6.4.eb | 2 +- .../easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-2.7.15.eb | 1 + .../easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-3.6.6.eb | 2 +- .../easyconfigs/v/VTK/VTK-8.1.1-intel-2018a-Python-2.7.14.eb | 1 + 9 files changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.0.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/v/VTK/VTK-8.0.1-foss-2017b-Python-2.7.14.eb index 7bbc5fe3fb6..78810c4e862 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.0.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.0.1-foss-2017b-Python-2.7.14.eb @@ -47,6 +47,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.0.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/v/VTK/VTK-8.0.1-intel-2017b-Python-2.7.14.eb index 08ae53ba504..e2ca55ce7bb 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.0.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.0.1-intel-2017b-Python-2.7.14.eb @@ -47,6 +47,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-2.7.14.eb index 9b0c23ea3b3..89bb06ad992 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-2.7.14.eb @@ -47,6 +47,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-3.6.4.eb index 7d6ed26d9a4..2f8d3492bf2 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-3.6.4.eb @@ -48,7 +48,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " -configopts += "-DVTK_PYTHON_VERSION=3 " +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)sm " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)sm.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-2.7.14.eb index 4cf124c404e..623388ccfe2 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-2.7.14.eb @@ -47,6 +47,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-3.6.4.eb index d8bc3e68897..4e4b87e32c4 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-3.6.4.eb @@ -48,7 +48,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " -configopts += "-DVTK_PYTHON_VERSION=3 " +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)sm " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)sm.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-2.7.15.eb index d95d4be981e..8e2bbadb919 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-2.7.15.eb @@ -48,6 +48,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-3.6.6.eb index b48a78a8aff..a98a0e952a7 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.1-foss-2018b-Python-3.6.6.eb @@ -48,7 +48,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " -configopts += "-DVTK_PYTHON_VERSION=3 " +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)sm " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)sm.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.1-intel-2018a-Python-2.7.14.eb index c97a75b945d..437280d0e82 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.1-intel-2018a-Python-2.7.14.eb @@ -48,6 +48,7 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " From 551a55c9a1e4fe986d8aa7fe22314ddd4bd3a3f8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 12 Dec 2018 08:37:58 +0100 Subject: [PATCH 0158/5331] fixed configopt order --- .../easyconfigs/v/VTK/VTK-8.0.1-foss-2017b-Python-2.7.14.eb | 2 +- .../easyconfigs/v/VTK/VTK-8.0.1-intel-2017b-Python-2.7.14.eb | 2 +- .../easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-2.7.14.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.0.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/v/VTK/VTK-8.0.1-foss-2017b-Python-2.7.14.eb index 78810c4e862..0e763ce38a2 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.0.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.0.1-foss-2017b-Python-2.7.14.eb @@ -47,8 +47,8 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.0.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/v/VTK/VTK-8.0.1-intel-2017b-Python-2.7.14.eb index e2ca55ce7bb..77b564721fa 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.0.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.0.1-intel-2017b-Python-2.7.14.eb @@ -47,8 +47,8 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-2.7.14.eb index 89bb06ad992..40553f255c8 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-foss-2018a-Python-2.7.14.eb @@ -47,8 +47,8 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-2.7.14.eb index 623388ccfe2..461cbc7defa 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.1.0-intel-2018a-Python-2.7.14.eb @@ -47,8 +47,8 @@ dependencies = [ configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT -configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +configopts += "-DVTK_PYTHON_VERSION=%(pyshortver)s " configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT configopts += "-DVTK_Group_MPI:BOOL=ON " From 6353c8b6bb832d15c148fd172f8bd5b5ff1b81f9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 12 Dec 2018 08:41:25 +0100 Subject: [PATCH 0159/5331] {vis}[foss/2018b] VV 2018.09.19 w/Python 3.6.6 command line interface only (REVIEW) --- .../VV-2018.09.19-foss-2018b-Python-3.6.6.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/v/VV/VV-2018.09.19-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/v/VV/VV-2018.09.19-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/v/VV/VV-2018.09.19-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..3fc923d6c7f --- /dev/null +++ b/easybuild/easyconfigs/v/VV/VV-2018.09.19-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'VV' +version = '2018.09.19' +versionsuffix = '-Python-%(pyver)s' +commit_id = 'aa42479' + +homepage = 'https://www.creatis.insa-lyon.fr/rio/vv' +description = """VV is an open-source and cross platform image viewer, designed for fast and + simple visualization of spatio-temporal images: 2D, 2D+t, 3D and 3D+t (or 4D) + images. Only the command-line (clitk) tools are build.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/open-vv/vv/archive'] +sources = [{'download_filename': '%s.tar.gz' % commit_id, 'filename': SOURCE_TAR_GZ}] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '3.6.6'), + ('VTK', '8.1.1', versionsuffix), + ('ITK', '4.13.1', versionsuffix), +] + +separate_build_dir = True + +configopts = '-DCLITK_BUILD_VV=OFF -DCLITK_BUILD_TOOLS=ON -DCLITK_BUILD_REGISTRATION=ON -DCLITK_BUILD_SEGMENTATION=ON ' + +postinstallcmds = ['cp -a %(builddir)s/easybuild_obj/bin/clitkRegionGrowing %(installdir)s/bin'] + +clitk_bins = [ + '4DImageToNVectorImage', 'AffineRegistration', 'AffineTransform', 'AnisotropicDiffusion', 'AutoCrop', + 'BackProjectImage', 'BinarizeImage', 'BlurImage', 'BLUTDIR', 'CalculateTRE', 'CatImage', 'ChangeDicomTag', + 'ChangeImageInfo', 'ComposeVF', 'ConnectedComponentLabeling', 'ConvertBSplineDeformableTransformToVF', 'CropImage', + 'DecomposeAndReconstruct', 'DemonsDeformableRegistration', 'Dice', 'Dicom2Image', 'DicomInfo', 'DicomRTPlan2Gate', + 'DicomRTStruct2Image', 'DicomWave2Text', 'ElastixTransformToMatrix', 'ExtractBones', 'ExtractLung', + 'ExtractPatient', 'FlipImage', 'GammaIndex', 'GateSimulation2Dicom', 'HistogramImage', 'Image2DicomDose', + 'ImageArithm', 'ImageConvert', 'ImageCreate', 'ImageGradientMagnitude', 'ImageInfo', 'ImageIntensityWindowing', + 'ImageLaplacian', 'ImageMoment', 'ImageStatistics', 'ImageToVectorImage', 'ImageUncertainty', 'InvertVF', + 'JacobianImage', 'MaskLandmarks', 'MaskOfIntegratedIntensity', 'MatrixInverse', 'MatrixMultiply', + 'MatrixToElastixTransform', 'MatrixTransformToVF', 'MedianImageFilter', 'MedianTemporalDimension', + 'MergeAsciiDoseActor', 'MergeSequence', 'MinMaxMask', 'MIP', 'MirrorPadImage', 'MorphoMath', 'MotionMask', + 'NormalizeImageFilter', 'NVectorImageTo4DImage', 'PadImage', 'PartitionEnergyWindowDicom', 'ProfileImage', + 'RegionGrowing', 'SetBackground', 'Spect2Dicom', 'SplitImage', 'Sum', 'TransformLandmarks', 'UnsharpMask', + 'UpdateVRTagDicom', 'VectorArithm', 'VectorImageToImage', 'VFConvert', 'VFInterpolate', 'VFResample', 'WarpImage', + 'WriteDicomSeries', 'ZeroVF', +] + +sanity_check_paths = { + 'files': ['bin/clitk%s' % x for x in clitk_bins], + 'dirs': [] +} + +moduleclass = 'vis' From a4d179ee061f8b00e38cf3891fe992205f4bb59b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 12 Dec 2018 08:42:46 +0100 Subject: [PATCH 0160/5331] add checksum --- .../easyconfigs/v/VV/VV-2018.09.19-foss-2018b-Python-3.6.6.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/VV/VV-2018.09.19-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/v/VV/VV-2018.09.19-foss-2018b-Python-3.6.6.eb index 3fc923d6c7f..9eb0425daae 100644 --- a/easybuild/easyconfigs/v/VV/VV-2018.09.19-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/v/VV/VV-2018.09.19-foss-2018b-Python-3.6.6.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/open-vv/vv/archive'] sources = [{'download_filename': '%s.tar.gz' % commit_id, 'filename': SOURCE_TAR_GZ}] +checksums = ['268d520ab2d7dcf31050566a2dce22c8eac679c497c7ac2a1582a4b5ffef3a2e'] builddependencies = [('CMake', '3.12.1')] From 0e98a8e5b11ce61b697169a67bc1d55f9b7bd780 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Wed, 12 Dec 2018 09:48:00 +0100 Subject: [PATCH 0161/5331] BamM 1.7.3 for foss-2018a --- .../BamM-1.7.3-foss-2018a-Python-2.7.14.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..043995344a0 --- /dev/null +++ b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb @@ -0,0 +1,46 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: GPL-v3.0 +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'BamM' +version = '1.7.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ecogenomics.github.io/BamM/' +description = """ BamM is a c library, wrapped in python, that parses BAM files """ + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Ecogenomics/BamM/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['1a30a5014aa64aea23f12b82c8e474044af126c9e6ddb575530ab14b6ef765b8'] + +builddependencies = [ + ('Automake', '1.15.1'), + ('texinfo', '6.5'), +] + +dependencies = [ + ('Python', '2.7.14'), + ('SAMtools', '1.7'), + ('BWA', '0.7.17'), +] + +prebuildopts = "cd c && ./autogen.sh && cd .. &&" + +sanity_check_paths = { + 'files': ['bin/bamm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 86ec557cddcdfa5671d5f6272d9e45e50291ddb3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 13 Dec 2018 09:24:02 +0100 Subject: [PATCH 0162/5331] Fix hard-coded libxml includes path --- .../l/libiconv/libiconv-1.15-GCCcore-7.3.0.eb | 23 +++++++++++++++++++ .../libxml2-2.9.8_fix-hardcoded-paths.patch | 18 +++++++++++++++ ...2.Python-2.9.8-foss-2018b-Python-2.7.15.eb | 7 +++++- 3 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2.Python/libxml2-2.9.8_fix-hardcoded-paths.patch diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..fcfc4c4d9a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-7.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.15' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.30', '', True)] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2.Python/libxml2-2.9.8_fix-hardcoded-paths.patch b/easybuild/easyconfigs/l/libxml2.Python/libxml2-2.9.8_fix-hardcoded-paths.patch new file mode 100644 index 00000000000..439407e2188 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2.Python/libxml2-2.9.8_fix-hardcoded-paths.patch @@ -0,0 +1,18 @@ +# Add easybuild locations of dependencies +# December 13th 2018 by B. Hajgato (Free University Brussels - VUB) +--- libxml2-2.9.8/python/setup.py.orig 2018-03-05 16:54:29.000000000 +0100 ++++ libxml2-2.9.8/python/setup.py 2018-12-13 09:06:59.345196079 +0100 +@@ -56,11 +56,8 @@ + # - iconv.h + # - libxslt/xsltconfig.h + includes_dir = [ +-"/usr/include", +-"/usr/local/include", +-"/opt/include", +-os.path.join(ROOT,'include'), +-HOME ++os.path.join(os.getenv("EBROOTLIBXML2"),"include"), ++os.path.join(os.getenv("EBROOTLIBICONV"),"include"), + ]; + + xml_includes="" diff --git a/easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb index 1c8f0ee88c1..eaac3c29bf7 100644 --- a/easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb @@ -17,11 +17,16 @@ source_urls = [ 'http://xmlsoft.org/sources/old/' ] sources = ['libxml2-%(version)s.tar.gz'] -checksums = ['0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732'] +patches = ['libxml2-%(version)s_fix-hardcoded-paths.patch'] +checksums = [ + '0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732', # libxml2-2.9.8.tar.gz + '3d5651c015fd375d855421983b7d33ffd4af797b7411f46e05cd8c57b210e542', # libxml2-2.9.8_fix-hardcoded-paths.patch +] dependencies = [ ('Python', '2.7.15'), ('libxml2', version), + ('libiconv', '1.15'), ] start_dir = 'python' From a445a640ce1dca8cdb42981ffe05f6ba6de87bb8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 13 Dec 2018 10:18:12 +0100 Subject: [PATCH 0163/5331] Add Checksum --- easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-7.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-7.3.0.eb index fcfc4c4d9a1..b708daaa5ca 100644 --- a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-7.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['ccf536620a45458d26ba83887a983b96827001e92a13847b45e4925cc8913178'] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.30', '', True)] From 970f3a0c7d5afda20c5e951d0813fe2a32be7496 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 14 Dec 2018 14:34:20 +0200 Subject: [PATCH 0164/5331] Adding patches for Surf and Stride --- .../n/nettle/nettle-3.4-GCCcore-7.3.0.eb | 40 +++++++ .../s/SQLite/SQLite-3.13.0-GCCcore-5.4.0.eb | 44 +++++++ .../t/Tcl/Tcl-8.6.5-GCCcore-5.4.0.eb | 30 +++++ .../VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb | 30 ++++- .../VMD-1.9.3-intel-2016b-Python-2.7.12.eb | 30 ++++- .../VMD-1.9.3-intel-2018a-Python-2.7.14.eb | 30 ++++- .../VMD-1.9.3-intel-2018b-Python-2.7.15.eb | 29 ++++- .../VMD/VMD-1.9.3_stride_MAX_AT_IN_RES.patch | 15 +++ .../v/VMD/VMD-1.9.3_stride_Makefile.patch | 37 ++++++ .../v/VMD/VMD-1.9.3_surf_Makefile.patch | 112 ++++++++++++++++++ .../v/VMD/VMD-1.9.3_surf_bad_printfs.patch | 74 ++++++++++++ 11 files changed, 451 insertions(+), 20 deletions(-) create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-5.4.0.eb create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.3_stride_MAX_AT_IN_RES.patch create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.3_stride_Makefile.patch create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.3_surf_Makefile.patch create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.3_surf_bad_printfs.patch diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..6e7872c651b --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.4' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' + +description = """ + Nettle is a cryptographic library that is designed to fit easily in more or + less any context: In crypto toolkits for object-oriented languages (C++, + Python, Pike, ...), in applications like LSH or GNUPG, or even in + kernel space. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ae7a42df026550b85daca8389b6a60ba6313b0567f374392e54918588a411e94'] + +builddependencies = [ + ('binutils', '2.30'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-5.4.0.eb new file mode 100644 index 00000000000..80e2ae77c58 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-5.4.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.13.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = ['http://www.sqlite.org/2016/'] +version_minor_etc = version.split('.')[1:] +version_minor_etc += '0' * (3 - len(version_minor_etc)) +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +builddependencies = [ + ('binutils', '2.26'), +] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.5'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-5.4.0.eb new file mode 100644 index 00000000000..5da46dbc0b4 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-5.4.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +builddependencies = [ + ('binutils', '2.26'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb index 31d148766f1..e5dd9e0f5b8 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb @@ -12,12 +12,32 @@ description = """VMD is a molecular visualization program for displaying, animat toolchain = {'name': 'foss', 'version': '2017b'} -# downloading requires registration -sources = ['vmd-%(version)s.src.tar.gz'] +unpack_stride_cmd = 'tar -C vmd-%(version)s/lib/stride -xf %s' -patches = ['VMD-%(version)s_configure.patch'] - -checksums = ['5bdc314dc836d620fe510ed4b6c3dbe3cf66525b61680ffec4e2563cf495f128'] +# downloading requires registration, so only stride's URL here +source_urls = [ + 'http://webclu.bio.wzw.tum.de/stride/' +] +sources = [ + 'vmd-%(version)s.src.tar.gz', + {'filename': 'stride.tar.gz', 'extract_cmd': unpack_stride_cmd}, +] +patches = [ + 'VMD-%(version)s_configure.patch', + 'VMD-%(version)s_surf_Makefile.patch', + 'VMD-%(version)s_surf_bad_printfs.patch', + 'VMD-%(version)s_stride_Makefile.patch', + 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', +] +checksums = [ + '0538f35273668df2e38cdeb170293bf3b9178d6033170b38638fec285160e287', # vmd-1.9.3.src.tar.gz + '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz + 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch + 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch + 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch + 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch + 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch +] dependencies = [ ('Tcl', '8.6.7'), diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb index 2f45c3f95b2..cd9946233a7 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb @@ -12,12 +12,32 @@ description = """VMD is a molecular visualization program for displaying, animat toolchain = {'name': 'intel', 'version': '2016b'} -# downloading requires registration -sources = ['vmd-%(version)s.src.tar.gz'] +unpack_stride_cmd = 'tar -C vmd-%(version)s/lib/stride -xf %s' -patches = ['VMD-%(version)s_configure.patch'] - -checksums = ['5706f88b9b77cc5fafda6fef3a82d6fa'] +# downloading requires registration, so only stride's URL here +source_urls = [ + 'http://webclu.bio.wzw.tum.de/stride/' +] +sources = [ + 'vmd-%(version)s.src.tar.gz', + {'filename': 'stride.tar.gz', 'extract_cmd': unpack_stride_cmd}, +] +patches = [ + 'VMD-%(version)s_configure.patch', + 'VMD-%(version)s_surf_Makefile.patch', + 'VMD-%(version)s_surf_bad_printfs.patch', + 'VMD-%(version)s_stride_Makefile.patch', + 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', +] +checksums = [ + '0538f35273668df2e38cdeb170293bf3b9178d6033170b38638fec285160e287', # vmd-1.9.3.src.tar.gz + '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz + 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch + 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch + 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch + 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch + 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch +] dependencies = [ ('Tcl', '8.6.5'), diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb index 0862d6cb3c9..ced6067a4ba 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb @@ -12,12 +12,32 @@ description = """VMD is a molecular visualization program for displaying, animat toolchain = {'name': 'intel', 'version': '2018a'} -# downloading requires registration -sources = ['vmd-%(version)s.src.tar.gz'] +unpack_stride_cmd = 'tar -C vmd-%(version)s/lib/stride -xf %s' -patches = ['VMD-%(version)s_configure.patch'] - -checksums = ['5bdc314dc836d620fe510ed4b6c3dbe3cf66525b61680ffec4e2563cf495f128'] +# downloading requires registration, so only stride's URL here +source_urls = [ + 'http://webclu.bio.wzw.tum.de/stride/' +] +sources = [ + 'vmd-%(version)s.src.tar.gz', + {'filename': 'stride.tar.gz', 'extract_cmd': unpack_stride_cmd}, +] +patches = [ + 'VMD-%(version)s_configure.patch', + 'VMD-%(version)s_surf_Makefile.patch', + 'VMD-%(version)s_surf_bad_printfs.patch', + 'VMD-%(version)s_stride_Makefile.patch', + 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', +] +checksums = [ + '0538f35273668df2e38cdeb170293bf3b9178d6033170b38638fec285160e287', # vmd-1.9.3.src.tar.gz + '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz + 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch + 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch + 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch + 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch + 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch +] dependencies = [ ('Tcl', '8.6.8'), diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb index 7b48156ce1b..d1bd8e4e417 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb @@ -12,12 +12,31 @@ description = """VMD is a molecular visualization program for displaying, animat toolchain = {'name': 'intel', 'version': '2018b'} -# downloading requires registration -sources = ['vmd-%(version)s.src.tar.gz'] -patches = ['VMD-%(version)s_configure.patch'] +unpack_stride_cmd = 'tar -C vmd-%(version)s/lib/stride -xf %s' + +# downloading requires registration, so only stride's URL here +source_urls = [ + 'http://webclu.bio.wzw.tum.de/stride/' +] +sources = [ + 'vmd-%(version)s.src.tar.gz', + {'filename': 'stride.tar.gz', 'extract_cmd': unpack_stride_cmd}, +] +patches = [ + 'VMD-%(version)s_configure.patch', + 'VMD-%(version)s_surf_Makefile.patch', + 'VMD-%(version)s_surf_bad_printfs.patch', + 'VMD-%(version)s_stride_Makefile.patch', + 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', +] checksums = [ - '5bdc314dc836d620fe510ed4b6c3dbe3cf66525b61680ffec4e2563cf495f128', # vmd-1.9.3.src.tar.gz - '74eea72d83a27253a83003b821e9375f8c596da00de838048fd1b4e99156ccaa', # VMD-1.9.3_configure.patch + '0538f35273668df2e38cdeb170293bf3b9178d6033170b38638fec285160e287', # vmd-1.9.3.src.tar.gz + '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz + 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch + 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch + 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch + 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch + 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3_stride_MAX_AT_IN_RES.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_stride_MAX_AT_IN_RES.patch new file mode 100644 index 00000000000..9011384eff5 --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_stride_MAX_AT_IN_RES.patch @@ -0,0 +1,15 @@ +Increase number of atoms allowed per residues as per stride README from VMD + +Åke Sandgren, 2017-05-02 +diff -ru vmd-1.9.3.orig/lib/stride/stride.h vmd-1.9.3/lib/stride/stride.h +--- vmd-1.9.3.orig/lib/stride/stride.h 2017-05-02 13:47:26.484463970 +0200 ++++ vmd-1.9.3/lib/stride/stride.h 2017-05-02 13:47:43.748279797 +0200 +@@ -40,7 +40,7 @@ + #define MAX_BOND 100 + #define MAX_ASSIGN 500 + #define MAX_INFO 1000 +-#define MAX_AT_IN_RES 75 ++#define MAX_AT_IN_RES 100 + #define MAX_AT_IN_HETERORES 200 + #define MAXRESDNR 6 + #define MAXRESACC 6 diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3_stride_Makefile.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_stride_Makefile.patch new file mode 100644 index 00000000000..036430db8ff --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_stride_Makefile.patch @@ -0,0 +1,37 @@ +Make stride use CC, CFLAGS and LDFLAGS from EB. + +Åke Sandgren, 2017-05-02 +diff -ru vmd-1.9.3.orig/lib/stride/Makefile vmd-1.9.3/lib/stride/Makefile +--- vmd-1.9.3.orig/lib/stride/Makefile 2003-04-08 14:03:14.000000000 +0200 ++++ vmd-1.9.3/lib/stride/Makefile 2017-05-02 13:46:01.973365383 +0200 +@@ -1,13 +1,14 @@ + #FLAGS = -lm -L/usr/pub/lib -lefence -o + #CC = cc -O2 -fullwarn -TENV:large_GOT + #CC = cc -g -Wall +-CC = gcc -O2 # at least for SunOS ++#CC = gcc -O2 # at least for SunOS + #CC = cc -g + + #CC = cc -O2 -fullwarn + + #CC = cc -O2 +-FLAGS = -lm -o ++#FLAGS = -lm -o ++LIBS = -lm + + SOURCE = stride.c splitstr.c rdpdb.c initchn.c geometry.c thr2one.c one2thr.c filename.c tolostr.c strutil.c place_h.c hbenergy.c memory.c helix.c sheet.c rdmap.c phipsi.c command.c molscr.c die.c hydrbond.c mergepat.c fillasn.c escape.c p_jrnl.c p_rem.c p_atom.c p_helix.c p_sheet.c p_turn.c p_ssbond.c p_expdta.c p_model.c p_compnd.c report.c nsc.c area.c ssbond.c chk_res.c chk_atom.c turn.c pdbasn.c dssp.c outseq.c chkchain.c elem.c measure.c asngener.c p_endmdl.c stred.c contact_order.c contact_map.c + +@@ -15,12 +16,9 @@ + + BINDIR = . + +-.c.o: +- $(CC) -c $< -o $@ +- + + stride : $(OBJECT) +- $(CC) $(OBJECT) $(FLAGS) $(BINDIR)/stride${ARCH} ++ $(CC) $(LDFLAGS) $(OBJECT) $(LIBS) -o stride + + $(OBJECT) : stride.h protot.h + diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3_surf_Makefile.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_surf_Makefile.patch new file mode 100644 index 00000000000..93f430a64a1 --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_surf_Makefile.patch @@ -0,0 +1,112 @@ +Fix surf Makefile. +Use CC, CFLAGS, etc from EB. +Drop bad make depend lines. + +Åke Sandgren, 2017-05-02 +diff -ru vmd-1.9.3.orig/lib/surf/Makefile vmd-1.9.3/lib/surf/Makefile +--- vmd-1.9.3.orig/lib/surf/Makefile 1994-03-22 16:44:20.000000000 +0100 ++++ vmd-1.9.3/lib/surf/Makefile 2017-05-02 13:41:51.911991381 +0200 +@@ -1,12 +1,7 @@ + # Compilation flags +-#CC = cc +-CC = cc + INCLUDE = -I. +-#LINCLUDE = -lcurses -ltermcap -lm +-LINCLUDE = -lm +-OPT_CFLAGS = -O2 $(FLAGS) $(INCLUDE) +-#CFLAGS = -g $(FLAGS) $(INCLUDE) +-CFLAGS = -O2 $(FLAGS) $(INCLUDE) ++LIBS = -lm ++CFLAGS = $(OPT) $(INCLUDE) + + # These are the user object files in the application + SRCS = surf.c io.c compute.c dual.c utils.c lp.c chull.c tessel_cases.c \ +@@ -18,7 +13,7 @@ + + # make objects + surf: $(OBJS) Makefile +- $(CC) $(CFLAGS) $(OBJS) -o surf $(LINCLUDE) ++ $(CC) $(LDFLAGS) $(OBJS) -o surf $(LIBS) + + lint: + lint $(INCLUDE) $(SRCS) +@@ -30,9 +25,6 @@ + tar -cvf surf.tar README *.[hc] Makefile + compress surf.tar + +-.c.o: +- $(CC) $(CFLAGS) -c $*.c +- + + # make depend makes the proper include file dependencies. You _could_ run + # it on a sun4, but there's a bug in the SunOS version of sed that causes +@@ -61,48 +53,3 @@ + @ echo ' ' >> Makefile + + # DO NOT DELETE THIS LINE -- make depend depends on it. +- +- +-# DO NOT DELETE THIS LINE -- make depend depends on it. +- +-surf.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h +-surf.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h +-surf.o: linalg.h +-io.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h +-io.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h +-io.o: linalg.h +-compute.o: surf.h /usr/include/stdio.h /usr/include/math.h +-compute.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h +-compute.o: /usr/include/sys/time.h linalg.h chull.h dual.h +-dual.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h +-dual.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h +-dual.o: linalg.h dual.h chull.h +-utils.o: surf.h /usr/include/stdio.h /usr/include/math.h +-utils.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h +-utils.o: /usr/include/sys/time.h linalg.h +-lp.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h +-lp.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h +-lp.o: linalg.h +-chull.o: surf.h /usr/include/stdio.h /usr/include/math.h +-chull.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h +-chull.o: /usr/include/sys/time.h linalg.h chull.h +-tessel_cases.o: surf.h /usr/include/stdio.h /usr/include/math.h +-tessel_cases.o: /usr/include/stdlib.h /usr/include/sgidefs.h +-tessel_cases.o: /usr/include/string.h /usr/include/sys/time.h linalg.h dual.h +-tessel_patches.o: surf.h /usr/include/stdio.h /usr/include/math.h +-tessel_patches.o: /usr/include/stdlib.h /usr/include/sgidefs.h +-tessel_patches.o: /usr/include/string.h /usr/include/sys/time.h linalg.h +-tessel_convex.o: surf.h /usr/include/stdio.h /usr/include/math.h +-tessel_convex.o: /usr/include/stdlib.h /usr/include/sgidefs.h +-tessel_convex.o: /usr/include/string.h /usr/include/sys/time.h linalg.h +-tessel_concave.o: surf.h /usr/include/stdio.h /usr/include/math.h +-tessel_concave.o: /usr/include/stdlib.h /usr/include/sgidefs.h +-tessel_concave.o: /usr/include/string.h /usr/include/sys/time.h linalg.h +-tessel_torus.o: surf.h /usr/include/stdio.h /usr/include/math.h +-tessel_torus.o: /usr/include/stdlib.h /usr/include/sgidefs.h +-tessel_torus.o: /usr/include/string.h /usr/include/sys/time.h linalg.h +- +-# DEPENDENCIES MUST END AT END OF FILE +-# IF YOU PUT STUFF HERE IT WILL GO AWAY +-# see make depend above +- +diff -ru vmd-1.9.3.orig/lib/surf/surf.c vmd-1.9.3/lib/surf/surf.c +--- vmd-1.9.3.orig/lib/surf/surf.c 1994-03-21 10:33:00.000000000 +0100 ++++ vmd-1.9.3/lib/surf/surf.c 2017-05-02 13:41:51.911991381 +0200 +@@ -7,7 +7,7 @@ + #define EXTERN + #include "surf.h" + +-void ++int + main(ac,av) + int ac; + char* av[]; +@@ -56,6 +56,8 @@ + if (Write_Option == 2) output_dataset(); + + if (Write_Option) end_output_dataset(); ++ ++ return(0); + } + + diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3_surf_bad_printfs.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_surf_bad_printfs.patch new file mode 100644 index 00000000000..9b9db3889bf --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3_surf_bad_printfs.patch @@ -0,0 +1,74 @@ +Fix some bad printfs in surf. + +Åke Sandgren, 2017-05-02 +diff -ru vmd-1.9.3.orig/lib/surf/chull.c vmd-1.9.3/lib/surf/chull.c +--- vmd-1.9.3.orig/lib/surf/chull.c 1994-03-19 06:50:54.000000000 +0100 ++++ vmd-1.9.3/lib/surf/chull.c 2017-05-02 13:44:07.046582827 +0200 +@@ -378,7 +378,7 @@ + print_out( v ) + struct tvertex *v; + { +- fprintf( stderr, "\nAdding vertex %6x :\n", v ); ++ fprintf( stderr, "\nAdding vertex %6p :\n", v ); + print_verts(); + print_edges(); + print_fs(); +@@ -398,11 +398,11 @@ + temp = vertices; + fprintf (stderr, "Vertex List\n"); + if (vertices) do { +- fprintf(stderr," addr %6x\t", vertices ); ++ fprintf(stderr," addr %6p\t", vertices ); + fprintf(stderr,"(%g,%g,%g)",vertices->v[X], + vertices->v[Y], vertices->v[Z] ); + fprintf(stderr," active:%3d", vertices->active ); +- fprintf(stderr," duplicate:%5x", vertices->duplicate ); ++ fprintf(stderr," duplicate:%5p", vertices->duplicate ); + fprintf(stderr," mark:%2d\n", vertices->mark ); + vertices = vertices->next; + } while ( vertices != temp ); +@@ -424,13 +424,13 @@ + temp = edges; + fprintf (stderr, "Edge List\n"); + if (edges) do { +- fprintf( stderr, " addr: %6x\t", edges ); ++ fprintf( stderr, " addr: %6p\t", edges ); + fprintf( stderr, "adj: "); + for (i=0; i<3; ++i) +- fprintf( stderr, "%6x", edges->adjface[i] ); ++ fprintf( stderr, "%6p", edges->adjface[i] ); + fprintf( stderr, " endpts:"); + for (i=0; i<2; ++i) +- fprintf( stderr, "%8x", edges->endpts[i]); ++ fprintf( stderr, "%8p", edges->endpts[i]); + fprintf( stderr, " del:%3d\n", edges->deleted ); + edges = edges->next; + } while (edges != temp ); +@@ -452,13 +452,13 @@ + temp = faces; + fprintf (stderr, "Face List\n"); + if (faces) do { +- fprintf(stderr, " addr: %6x\t", faces ); ++ fprintf(stderr, " addr: %6p\t", faces ); + fprintf(stderr, " edges:"); + for( i=0; i<3; ++i ) +- fprintf(stderr, "%6x", faces->edg[i] ); ++ fprintf(stderr, "%6p", faces->edg[i] ); + fprintf(stderr, " vert:"); + for ( i=0; i<3; ++i) +- fprintf(stderr, "%6x", faces->vert[i] ); ++ fprintf(stderr, "%6p", faces->vert[i] ); + fprintf(stderr, " vis: %d\n", faces->visible ); + faces= faces->next; + } while ( faces != temp ); +@@ -552,8 +552,8 @@ + temp_v = temp_v->next; + } while ( temp_v != vertices ); + do { +- printf("3%5d%6d%6d\n", temp_f->vert[0]->vnum, +- temp_f->vert[1]->vnum, temp_f->vert[2]->vnum ); ++ printf("3%5d%6d%6d\n", temp_f->vert[0]->vnum[0], ++ temp_f->vert[1]->vnum[0], temp_f->vert[2]->vnum[0] ); + temp_f = temp_f->next; + } while ( temp_f != faces ); + } From 0cd578d157edc6776ecedc9fe12d7a8a7f004497 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 16 Dec 2018 10:21:29 +0200 Subject: [PATCH 0165/5331] Fix cpptraj linking of blas, lapack, zlib, bzip2 to use EBs libs. --- ...link_with_EBs_blas_lapack_zlib_bzip2.patch | 36 +++++++++++++++++++ ...ss-2018b-AmberTools-17-patchlevel-10-15.eb | 3 ++ ...da-2018b-AmberTools-17-patchlevel-10-15.eb | 3 ++ ...el-2018b-AmberTools-17-patchlevel-10-15.eb | 3 ++ 4 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch new file mode 100644 index 00000000000..55eb98b058a --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch @@ -0,0 +1,36 @@ +diff -ru amber16.orig/AmberTools/src/cpptraj/configure amber16/AmberTools/src/cpptraj/configure +--- amber16.orig/AmberTools/src/cpptraj/configure 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/cpptraj/configure 2018-12-16 09:13:28.413318032 +0100 +@@ -523,10 +523,10 @@ + XDRFILE=$XDRFILE_TARGET + NETCDFLIB="-lnetcdf" + PNETCDFLIB="" +-BZLIB="-lbz2" +-ZLIB="-lz" +-BLAS="-lblas" +-LAPACK="-llapack" ++BZLIB="-L$EBROOTBZIP2/lib -lbz2" ++ZLIB="-L$EBROOTZLIB/lib -lz" ++BLAS="$LIBBLAS" ++LAPACK="$LIBLAPACK" + ARPACK="-larpack" + FFT_LIB="pub_fft.o" + FFT_LIBDIR="" +@@ -960,13 +960,13 @@ + if [[ $STATIC -eq 2 ]] ; then + # Static linking for specified libraries + if [[ ! -z $BLAS_HOME && ! -z $BLAS ]] ; then +- BLAS="$BLAS_HOME/lib/libblas.a" ++ BLAS="$LIBBLAS" + fi + if [[ ! -z $ARPACK_HOME && ! -z $ARPACK ]] ; then + ARPACK="$ARPACK_HOME/lib/libarpack.a" + fi + if [[ ! -z $LAPACK_HOME && ! -z $LAPACK ]] ; then +- LAPACK="$LAPACK_HOME/lib/liblapack.a" ++ LAPACK="$LIBLAPACK" + fi + if [[ ! -z $NETCDF_HOME && ! -z $NETCDFLIB ]] ; then + NETCDFLIB="$NETCDF_HOME/lib/libnetcdf.a" +Only in amber16/AmberTools/src/cpptraj: configure.orig +Only in amber16/AmberTools/src/cpptraj: configure.rej diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb index 777748a7e36..d8b343dae7e 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb @@ -34,6 +34,7 @@ patches = [ 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, 'Amber-%%(version)s-AT-%s_fix_fixed_size_cmd_in_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch' % ambertools_ver, 'Amber-%(version)s-fix_missing_build_target.patch', 'Amber-%(version)s-dont_use_ipo.patch', 'Amber-%%(version)s-AT-%s_use_FFTW_FFT_instead_of_PUBFFT_part2.patch' % ambertools_ver, @@ -66,6 +67,8 @@ checksums = [ '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch + 'e6011e2a59877fb824a74b6c5fd250a2a98d363b5087d880328ba87c8e09dfb9', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch # Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb index e1369411f00..ca8dba8cc0e 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb @@ -34,6 +34,7 @@ patches = [ 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, 'Amber-%%(version)s-AT-%s_fix_fixed_size_cmd_in_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch' % ambertools_ver, 'Amber-%(version)s-fix_missing_build_target.patch', 'Amber-%(version)s-dont_use_ipo.patch', 'Amber-%%(version)s-AT-%s_use_FFTW_FFT_instead_of_PUBFFT_part2.patch' % ambertools_ver, @@ -68,6 +69,8 @@ checksums = [ '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch + 'e6011e2a59877fb824a74b6c5fd250a2a98d363b5087d880328ba87c8e09dfb9', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch # Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb index 4a20d0a047b..6fd181aa434 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb @@ -34,6 +34,7 @@ patches = [ 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, 'Amber-%%(version)s-AT-%s_fix_fixed_size_cmd_in_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch' % ambertools_ver, 'Amber-%(version)s-fix_missing_build_target.patch', 'Amber-%(version)s-dont_use_ipo.patch', ] @@ -65,6 +66,8 @@ checksums = [ '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch + 'e6011e2a59877fb824a74b6c5fd250a2a98d363b5087d880328ba87c8e09dfb9', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch ] From 7c6781cade3b439ffc1747dbcb45ea67be91ec59 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 16 Dec 2018 10:27:51 +0200 Subject: [PATCH 0166/5331] Fix missing comment in cpptraj patch for blas/lapack etc. --- ...-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch | 3 +++ .../Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb | 2 +- .../Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb | 2 +- .../Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb | 2 +- 4 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch index 55eb98b058a..b1e33cff72a 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch +++ b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch @@ -1,3 +1,6 @@ +Make cpptraj link with the BLAS/LAPACK/Zlib/Bzip2 from EasyBuild. + +Åke Sandgren, 20181126 diff -ru amber16.orig/AmberTools/src/cpptraj/configure amber16/AmberTools/src/cpptraj/configure --- amber16.orig/AmberTools/src/cpptraj/configure 2017-04-13 15:00:53.000000000 +0200 +++ amber16/AmberTools/src/cpptraj/configure 2018-12-16 09:13:28.413318032 +0100 diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb index d8b343dae7e..e0689c75ae1 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb @@ -68,7 +68,7 @@ checksums = [ # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch - 'e6011e2a59877fb824a74b6c5fd250a2a98d363b5087d880328ba87c8e09dfb9', + 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch # Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb index ca8dba8cc0e..04ec2b956a5 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb @@ -70,7 +70,7 @@ checksums = [ # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch - 'e6011e2a59877fb824a74b6c5fd250a2a98d363b5087d880328ba87c8e09dfb9', + 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch # Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb index 6fd181aa434..c5e5edbd333 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb @@ -67,7 +67,7 @@ checksums = [ # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch - 'e6011e2a59877fb824a74b6c5fd250a2a98d363b5087d880328ba87c8e09dfb9', + 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch ] From 8fe44ee32259deaba014d86c9d9533d9ac9ad021 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 16 Dec 2018 10:36:34 +0200 Subject: [PATCH 0167/5331] Update checksums to match updated cpptraj link blas/lapack etc patch. --- .../Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb | 2 +- .../Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb b/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb index 5ccaa4411f9..aea05e0eae2 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb @@ -69,7 +69,7 @@ checksums = [ # Amber-18-AT-18_use_external_boost_in_packmol_memembed.patch '9493a3dfddf62d6aa1bbb0a92a39e766a2b76a9ff8a9006e0fcc9ee3e5d94aac', # Amber-18-AT-18_make_cpptraj_link_with_EBs_blas_lapack_fftw.patch - 'f916dac2f4c43d00ddc0e0b09ab2c5aae2a98f3f852a4cec47e4911c15666ec4', + '349c24cc4bc161c96535ad924cff4228d6513082cdcd2758876b9798e27ee1bf', '6b09a6548fa18127245e05c79bdca143adf31db349349cb39bfdb8c4f60772a7', # Amber-18_fix_missing_build_target.patch 'a4c12ad39088ce6e9e7bad39e8d9a736989e6ae4a380c70535a5451eb3060903', # Amber-18_dont_use_ipo.patch ] diff --git a/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb b/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb index 0958e6728a2..1cc60600503 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb @@ -69,7 +69,7 @@ checksums = [ # Amber-18-AT-18_use_external_boost_in_packmol_memembed.patch '9493a3dfddf62d6aa1bbb0a92a39e766a2b76a9ff8a9006e0fcc9ee3e5d94aac', # Amber-18-AT-18_make_cpptraj_link_with_EBs_blas_lapack_fftw.patch - 'f916dac2f4c43d00ddc0e0b09ab2c5aae2a98f3f852a4cec47e4911c15666ec4', + '349c24cc4bc161c96535ad924cff4228d6513082cdcd2758876b9798e27ee1bf', '6b09a6548fa18127245e05c79bdca143adf31db349349cb39bfdb8c4f60772a7', # Amber-18_fix_missing_build_target.patch 'a4c12ad39088ce6e9e7bad39e8d9a736989e6ae4a380c70535a5451eb3060903', # Amber-18_dont_use_ipo.patch ] From 869177d467029cc89698d5ad1c915935bc2abeb9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 16 Dec 2018 14:54:21 +0200 Subject: [PATCH 0168/5331] Drop easyconfig that got pulled in due to minimal-toolchain and do not belong in this PR. --- .../n/nettle/nettle-3.4-GCCcore-7.3.0.eb | 40 ----------------- .../s/SQLite/SQLite-3.13.0-GCCcore-5.4.0.eb | 44 ------------------- .../t/Tcl/Tcl-8.6.5-GCCcore-5.4.0.eb | 30 ------------- 3 files changed, 114 deletions(-) delete mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb delete mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-5.4.0.eb delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-5.4.0.eb diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb deleted file mode 100644 index 6e7872c651b..00000000000 --- a/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'nettle' -version = '3.4' - -homepage = 'http://www.lysator.liu.se/~nisse/nettle/' - -description = """ - Nettle is a cryptographic library that is designed to fit easily in more or - less any context: In crypto toolkits for object-oriented languages (C++, - Python, Pike, ...), in applications like LSH or GNUPG, or even in - kernel space. -""" - -toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['ae7a42df026550b85daca8389b6a60ba6313b0567f374392e54918588a411e94'] - -builddependencies = [ - ('binutils', '2.30'), - ('M4', '1.4.18'), -] - -dependencies = [ - ('GMP', '6.1.2'), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + - [('lib/libhogweed.a', 'lib64/libhogweed.a'), - ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), - ('lib/libnettle.a', 'lib64/libnettle.a'), - ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], - 'dirs': ['include/nettle'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-5.4.0.eb deleted file mode 100644 index 80e2ae77c58..00000000000 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCCcore-5.4.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ -## - -easyblock = 'ConfigureMake' - -name = 'SQLite' -version = '3.13.0' - -homepage = 'http://www.sqlite.org/' -description = 'SQLite: SQL Database Engine in a C Library' - -toolchain = {'name': 'GCCcore', 'version': '5.4.0'} - -source_urls = ['http://www.sqlite.org/2016/'] -version_minor_etc = version.split('.')[1:] -version_minor_etc += '0' * (3 - len(version_minor_etc)) -version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) -sources = ['sqlite-autoconf-%s.tar.gz' % version_str] - -builddependencies = [ - ('binutils', '2.26'), -] - -dependencies = [ - ('libreadline', '6.3'), - ('Tcl', '8.6.5'), -] - -sanity_check_paths = { - 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', - 'lib/libsqlite3.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-5.4.0.eb deleted file mode 100644 index 5da46dbc0b4..00000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCCcore-5.4.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.5' - -homepage = 'http://www.tcl.tk/' -description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, -suitable for a very wide range of uses, including web and desktop applications, networking, administration, -testing and many more.""" - -toolchain = {'name': 'GCCcore', 'version': '5.4.0'} - -source_urls = ["http://prdownloads.sourceforge.net/tcl"] -sources = ['%(namelower)s%(version)s-src.tar.gz'] - -builddependencies = [ - ('binutils', '2.26'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -moduleclass = 'lang' From a3cc1a274c4f93059864b3394ea8dd0503ac24a6 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 24 Dec 2018 18:48:34 +0100 Subject: [PATCH 0169/5331] SuiteSparse builds with intel compiler if icc is found in the path, unless AUTOCC=no is set --- ...eSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb new file mode 100644 index 00000000000..99315f6807e --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb @@ -0,0 +1,21 @@ +name = 'SuiteSparse' +version = '4.5.5' +parmetis_ver = '4.0.3' +versionsuffix = '-ParMETIS-%s' % parmetis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('ParMETIS', parmetis_ver)] + +prebuildopts = 'AUTOCC=no' + +maxparallel = 1 + +moduleclass = 'numlib' From 0fb20b6bef7c435401e4b0efaedc66a871537a1b Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 31 Dec 2018 11:22:43 -0800 Subject: [PATCH 0170/5331] ImageMagick-7.0.8-22-GCCcore-7.3.0 --- .../ImageMagick-7.0.8-22-GCCcore-7.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.8-22-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.8-22-GCCcore-7.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.8-22-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..3c5f600f374 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.8-22-GCCcore-7.3.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.8-22' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://www.imagemagick.org/download/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('X11', '20180604'), + ('Ghostscript', '9.23'), + ('JasPer', '2.0.14'), + ('libjpeg-turbo', '2.0.0'), + ('LibTIFF', '4.0.9'), + ('LittleCMS', '2.9'), +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.30'), + ('pkg-config', '0.29.2'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' From 620c433569a2f271c756c53376ef855523440a89 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Wed, 2 Jan 2019 11:27:45 +0100 Subject: [PATCH 0171/5331] Added checksums --- .../SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb index 99315f6807e..ca26cc5e681 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb @@ -12,6 +12,8 @@ toolchainopts = {'unroll': True, 'pic': True} source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] +checksums = ['b9a98de0ddafe7659adffad8a58ca3911c1afa8b509355e7aa58b02feb35d9b6'] + dependencies = [('ParMETIS', parmetis_ver)] prebuildopts = 'AUTOCC=no' From dde48e7844db38cceb66b3913a5c0133b0346541 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 3 Jan 2019 12:48:15 -0800 Subject: [PATCH 0172/5331] FastANI foss-2018b, with patch --- .../f/FastANI/FastANI-1.1-foss-2018b.eb | 37 +++++++++++++++++++ .../f/FastANI/FastANI-1.1-memcpy.patch | 12 ++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb new file mode 100644 index 00000000000..a96fc173362 --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb @@ -0,0 +1,37 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org + +easyblock = 'ConfigureMake' + +name = 'FastANI' +version = '1.1' + +homepage = "http://www.iodbc.org/" +description = """FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean + nucleotide identity of orthologous gene pairs shared between two microbial + genomes. FastANI supports pairwise comparison of both complete and draft + genome assemblies.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] +sources = ['v%(version)s.zip'] +patches = ['FastANI-1.1-memcpy.patch'] + +preconfigopts = 'autoconf && ' + +builddependencies = [('Autoconf', '2.69')] + +dependencies = [ + ('GSL', '2.5'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fastANI'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch new file mode 100644 index 00000000000..353af7c926e --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch @@ -0,0 +1,12 @@ +diff -ruN FastANI-1.1.orig/Makefile.in FastANI-1.1/Makefile.in +--- FastANI-1.1.orig/Makefile.in 2018-08-01 09:29:53.000000000 -0700 ++++ FastANI-1.1/Makefile.in 2018-12-07 16:00:29.231658000 -0800 +@@ -6,7 +6,7 @@ + ifeq ($(UNAME_S),Darwin) + CXXFLAGS += -mmacosx-version-min=10.7 -stdlib=libc++ + else +- CXXFLAGS += -include src/common/memcpyLink.h -Wl,--wrap=memcpy ++ CXXFLAGS += -include src/common/memcpyLink.h + CFLAGS += -include src/common/memcpyLink.h + endif + From ec3a63d2e0b21fd022863efa6d10a2f70d1065fc Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 3 Jan 2019 14:51:01 -0800 Subject: [PATCH 0173/5331] FastANI foss-2018b, checksums --- easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb index a96fc173362..7cf57a88109 100644 --- a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb @@ -19,6 +19,10 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] sources = ['v%(version)s.zip'] patches = ['FastANI-1.1-memcpy.patch'] +checksums = [ + 'ffb776ddfa2595bba5611b0b017aad5089f9a19ea020c7d708d09c628bb926b3', # v1.1.zip + '12a5ab7514f1c04f6f814ba7b2c11a02640d82d494c53f63a51483f6987da9b6', # FastANI-1.1-memcpy.patch +] preconfigopts = 'autoconf && ' From 0a191a57d60d8ef7026a3b6dba9c034956ac9a8b Mon Sep 17 00:00:00 2001 From: fizwit Date: Sun, 6 Jan 2019 11:06:45 -0800 Subject: [PATCH 0174/5331] resolve version, patch-comment, sanity-check --- easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb | 6 +++--- easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch | 1 + 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb index 7cf57a88109..ad53f8b43b5 100644 --- a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb @@ -18,10 +18,10 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] sources = ['v%(version)s.zip'] -patches = ['FastANI-1.1-memcpy.patch'] +patches = ['%(name)s-%(version)s-memcpy.patch'] checksums = [ 'ffb776ddfa2595bba5611b0b017aad5089f9a19ea020c7d708d09c628bb926b3', # v1.1.zip - '12a5ab7514f1c04f6f814ba7b2c11a02640d82d494c53f63a51483f6987da9b6', # FastANI-1.1-memcpy.patch + 'c2d751b1003ef9501fa54596a23a0083908e7590b1065ddb544484467572be58', # FastANI-1.1-memcpy.patch ] preconfigopts = 'autoconf && ' @@ -35,7 +35,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/fastANI'], - 'dirs': ['bin'], + 'dirs': [] } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch index 353af7c926e..ca0b7d3b682 100644 --- a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch @@ -1,3 +1,4 @@ +remove memcpy wrapper diff -ruN FastANI-1.1.orig/Makefile.in FastANI-1.1/Makefile.in --- FastANI-1.1.orig/Makefile.in 2018-08-01 09:29:53.000000000 -0700 +++ FastANI-1.1/Makefile.in 2018-12-07 16:00:29.231658000 -0800 From 30abbbe183e0c470af8aa9b6eb0252af0b4fdc75 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 7 Jan 2019 13:51:37 -0800 Subject: [PATCH 0175/5331] EMBOSS 6.6.0 for foss-2018b with updated patch, libharu-GCCcore --- .../e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb | 42 +++++++++++++++++++ .../EMBOSS-6.6.0_disable-embossupdate.patch | 22 ++++++++++ .../l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb | 40 ++++++++++++++++++ 3 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb create mode 100644 easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0_disable-embossupdate.patch create mode 100644 easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb new file mode 100644 index 00000000000..f518fe65d32 --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb @@ -0,0 +1,42 @@ +# authors: Kenneth Hoste (Ghent University) +# George Tsouloupas +# Fotis Georgatos +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute +easyblock = 'ConfigureMake' + +name = 'EMBOSS' +version = '6.6.0' + +homepage = 'http://emboss.sourceforge.net/' +description = """EMBOSS is 'The European Molecular Biology Open Software Suite'. + EMBOSS is a free Open Source software analysis package specially developed for + the needs of the molecular biology (e.g. EMBnet) user community.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [ + 'ftp://emboss.open-bio.org/pub/EMBOSS/', + 'ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0', +] +sources = [SOURCE_TAR_GZ] +patches = ['EMBOSS-6.6.0_disable-embossupdate.patch'] +checksums = [ + '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', # EMBOSS-6.6.0.tar.gz + 'b9beee4340a05289f938b4cf6b041459209cdf922c6295aa01cff1998bfb6d9c', # EMBOSS-6.6.0_disable-embossupdate.patch +] + +dependencies = [ + ('X11', '20180604'), + ('libharu', '2.3.0'), + ('Java', '1.8', '', True), +] + +configopts = " --with-hpdf=$EBROOTLIBHARU " + +# jemboss.jar does not build in a parallel build +parallel = 1 diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0_disable-embossupdate.patch b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0_disable-embossupdate.patch new file mode 100644 index 00000000000..eb875023028 --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0_disable-embossupdate.patch @@ -0,0 +1,22 @@ +remove build target embossupdate from Makefile +diff -ruN EMBOSS-6.6.0.orig/Makefile.am EMBOSS-6.6.0/Makefile.am +--- EMBOSS-6.6.0.orig/Makefile.am 2012-07-22 04:16:46.000000000 -0700 ++++ EMBOSS-6.6.0/Makefile.am 2019-01-07 13:11:47.876782000 -0800 +@@ -34,4 +34,4 @@ + tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) + + install-exec-hook: +- $(bindir)/embossupdate ++ echo "Skipping $(bindir)/embossupdate" +diff -ruN EMBOSS-6.6.0.orig/Makefile.in EMBOSS-6.6.0/Makefile.in +--- EMBOSS-6.6.0.orig/Makefile.in 2013-07-15 14:27:28.000000000 -0700 ++++ EMBOSS-6.6.0/Makefile.in 2019-01-07 13:08:27.796667000 -0800 +@@ -833,7 +833,7 @@ + tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) + + install-exec-hook: +- $(bindir)/embossupdate ++ echo "Skipping $(bindir)/embossupdate" + + # Tell versions [3.59,3.63) of GNU make to not export all variables. + # Otherwise a system limit (for SysV at least) may be exceeded. diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..830ae9a9c2f --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Modified for foss-2016b by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'http://libharu.org/' +description = """libHaru is a free, cross platform, open source library for generating PDF files.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [' https://github.com/libharu/libharu/archive/'] +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] + +dependencies = [('libpng', '1.6.34')] + +builddependencies = [('CMake', '3.9.6')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': ['if', 'include', 'lib'] +} + +moduleclass = 'lib' From 3b1267686509671db52af154d5f2cda03e19fc80 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Thu, 10 Jan 2019 14:17:57 +0100 Subject: [PATCH 0176/5331] adding easyconfigs: RDP-Classifier-2.12-Java-1.8.eb --- .../RDP-Classifier-2.12-Java-1.8.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb diff --git a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb new file mode 100644 index 00000000000..763c2f99741 --- /dev/null +++ b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb @@ -0,0 +1,32 @@ +easyblock = 'Tarball' + +name = 'RDP-Classifier' +version = '2.12' + +homepage = 'http://sourceforge.net/projects/rdp-classifier' +description = """The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic + assignments from domain to genus, with confidence estimates for each assignment.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['rdp_classifier_%(version)s.zip'] +checksums = ['977896248189a1ce2146dd3a61d203c3c6bc9aa3982c60332d463832922f7d0a'] + +java = 'Java' +javaver = '1.8' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +modextrapaths = { + 'CLASSPATH': 'dist/classifier.jar', + 'RDP_JAR_PATH': 'dist/classifier.jar', +} + +sanity_check_paths = { + 'files': ['dist/classifier.jar'], + 'dirs': [], +} + +moduleclass = 'bio' From 1aa68dc533adf4848c15cfff39f3677385942f47 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 11 Jan 2019 09:35:38 -0800 Subject: [PATCH 0177/5331] fix dependencies --- easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb index 830ae9a9c2f..f42cd8ef545 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb @@ -28,7 +28,7 @@ checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] dependencies = [('libpng', '1.6.34')] -builddependencies = [('CMake', '3.9.6')] +builddependencies = [('CMake', '3.11.4')] parallel = 1 From bbb992f670d43a015e8418651ce288736796d933 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Fri, 18 Jan 2019 16:44:05 -0300 Subject: [PATCH 0178/5331] Configs for horton-2.1.1 and dependencies --- .../horton-2.1.1-foss-2018b-Python-2.7.15.eb | 50 +++++++++++++++++++ .../horton-2.1.1-intel-2018b-Python-2.7.15.eb | 50 +++++++++++++++++++ .../l/Libint/Libint-2.0.3-foss-2018b.eb | 14 ++++++ .../l/Libint/Libint-2.0.3-intel-2018b.eb | 14 ++++++ .../l/libxc/libxc-2.2.3-foss-2018b.eb | 27 ++++++++++ .../l/libxc/libxc-2.2.3-intel-2018b.eb | 30 +++++++++++ 6 files changed, 185 insertions(+) create mode 100644 easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..9ca0c72698a --- /dev/null +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonPackage' + +name = 'horton' +version = '2.1.1' + +homepage = 'http://theochem.github.io/horton' +description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written + primarily in the Python programming language. (HORTON is named after the helpful + pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON + is to provide a platform for testing new ideas on the quantum many-body problem + at a reasonable computational cost. Although HORTON is primarily designed to be + a quantum-chemistry program, it can perform computations involving model + Hamiltonians, and could be extended for computations in nuclear physics.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.15' +pyversuffix = '-Python-%s' % pyver +dependencies = [ + ('Python', pyver), + ('h5py', '2.8.0', pyversuffix), + ('matplotlib', '2.2.3', pyversuffix), + ('Libint', '2.0.3'), + ('libxc', '2.2.3'), +] + +prebuildopts = ' '.join([ + 'BLAS_EXTRA_COMPILE_ARGS=-DMKL_ILP64:-I${MKLROOT}/include', + 'BLAS_LIBRARY_DIRS=${MKLROOT}/lib/intel64', + 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', +]) + +# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc +#runtest = ' '.join([ +# 'export MATPLOTLIBRC=$PWD;', +# 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', +# '%s python setup.py build_ext -i; ' % prebuildopts, +# 'nosetests -v', +#]) + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/horton' % pyshortver], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..f45e9bb1eef --- /dev/null +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonPackage' + +name = 'horton' +version = '2.1.1' + +homepage = 'http://theochem.github.io/horton' +description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written + primarily in the Python programming language. (HORTON is named after the helpful + pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON + is to provide a platform for testing new ideas on the quantum many-body problem + at a reasonable computational cost. Although HORTON is primarily designed to be + a quantum-chemistry program, it can perform computations involving model + Hamiltonians, and could be extended for computations in nuclear physics.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] +sources = [SOURCE_TAR_GZ] + +pyver = '2.7.15' +pyversuffix = '-Python-%s' % pyver +dependencies = [ + ('Python', pyver), + ('h5py', '2.8.0', pyversuffix), + ('matplotlib', '2.2.3', pyversuffix), + ('Libint', '2.0.3'), + ('libxc', '2.2.3'), +] + +prebuildopts = ' '.join([ + 'BLAS_EXTRA_COMPILE_ARGS=-DMKL_ILP64:-I${MKLROOT}/include', + 'BLAS_LIBRARY_DIRS=${MKLROOT}/lib/intel64', + 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', +]) + +# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc +#runtest = ' '.join([ +# 'export MATPLOTLIBRC=$PWD;', +# 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', +# '%s python setup.py build_ext -i; ' % prebuildopts, +# 'nosetests -v', +#]) + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/horton' % pyshortver], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb new file mode 100644 index 00000000000..456e6b3c095 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -0,0 +1,14 @@ +name = 'Libint' +version = '2.0.3' + +homepage = 'https://sourceforge.net/p/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +sources = ['libint-%(version)s-stable.tgz'] +source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb new file mode 100644 index 00000000000..329f8d37121 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb @@ -0,0 +1,14 @@ +name = 'Libint' +version = '2.0.3' + +homepage = 'https://sourceforge.net/p/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +sources = ['libint-%(version)s-stable.tgz'] +source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb new file mode 100644 index 00000000000..561661417d2 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb new file mode 100644 index 00000000000..85d607baacc --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +# Tests also fail with Intel Compilers on Haswell when optarch is enabled. +toolchainopts = {'lowopt': True, 'optarch': False} + +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' From 782a2560ff6f1b86f5516669b88de5b378f82ab0 Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Mon, 21 Jan 2019 16:35:47 +0000 Subject: [PATCH 0179/5331] adding easyconfigs: Salmon-0.12.0-foss-2018b-Python-2.7.15.eb --- .../Salmon-0.12.0-foss-2018b-Python-2.7.15.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..2aa22463ec7 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '0.12.0' +versionsuffix = '-Python-2.7.15' + +homepage = 'https://github.com/COMBINE-lab/%(namelower)s' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/COMBINE-lab/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91ebd1efc5b0b4c12ec6babecf3c0b79f7102e42b8895ca07c8c8fea869fefa3'] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Boost', '1.68.0', versionsuffix), + ('tbb', '2018_U5'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' From 23f48183775a0d8e1b2a8895d6bebee78da13677 Mon Sep 17 00:00:00 2001 From: "easybuild@GMI" Date: Mon, 21 Jan 2019 20:07:00 +0000 Subject: [PATCH 0180/5331] Fix dependency issue --- .../s/Salmon/Salmon-0.12.0-foss-2018b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb new file mode 100644 index 00000000000..b03cfa35f1d --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '0.12.0' + +homepage = 'https://github.com/COMBINE-lab/%(namelower)s' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/COMBINE-lab/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91ebd1efc5b0b4c12ec6babecf3c0b79f7102e42b8895ca07c8c8fea869fefa3'] + +builddependencies = [('CMake', '3.12.1')] + +runtest = 'test' + +dependencies = [ + ('Boost', '1.67.0'), + ('tbb', '2018_U5'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' From 6f959881f48fa5e8287674b509f9a159b088ffa6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=9Cmit=20Seren?= Date: Mon, 21 Jan 2019 21:55:50 +0100 Subject: [PATCH 0181/5331] Delete Salmon-0.12.0-foss-2018b-Python-2.7.15.eb --- .../Salmon-0.12.0-foss-2018b-Python-2.7.15.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b-Python-2.7.15.eb deleted file mode 100644 index 2aa22463ec7..00000000000 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b-Python-2.7.15.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Salmon' -version = '0.12.0' -versionsuffix = '-Python-2.7.15' - -homepage = 'https://github.com/COMBINE-lab/%(namelower)s' -description = """Salmon is a wicked-fast program to produce a highly-accurate, - transcript-level quantification estimates from RNA-seq data.""" - -toolchain = {'name': 'foss', 'version': '2018b'} -toolchainopts = {'pic': True, 'openmp': True} - -source_urls = ['https://github.com/COMBINE-lab/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['91ebd1efc5b0b4c12ec6babecf3c0b79f7102e42b8895ca07c8c8fea869fefa3'] - -builddependencies = [('CMake', '3.12.1')] - -dependencies = [ - ('Boost', '1.68.0', versionsuffix), - ('tbb', '2018_U5'), -] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [] -} - -moduleclass = 'bio' From ec5e82d18aaecc83ca5cade1f3db019d54e9d007 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 22 Jan 2019 09:18:26 +0100 Subject: [PATCH 0182/5331] adding easyconfigs: FASTX-Toolkit-0.0.14-foss-2018b.eb, libgtextutils-0.7-foss-2018b.eb and patches: FASTX-Toolkit-0.0.14_fix-gcc7.patch --- .../FASTX-Toolkit-0.0.14-foss-2018b.eb | 53 +++++++++++++++++++ .../FASTX-Toolkit-0.0.14_fix-gcc7.patch | 12 +++++ .../libgtextutils-0.7-foss-2018b.eb | 40 ++++++++++++++ 3 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2018b.eb create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14_fix-gcc7.patch create mode 100644 easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2018b.eb diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2018b.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2018b.eb new file mode 100644 index 00000000000..e3dcda045d1 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2018b.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] +sources = ['fastx_toolkit-%(version)s.tar.bz2'] +patches = ['%(name)s-%(version)s_fix-gcc7.patch'] +checksums = [ + '9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806', # fastx_toolkit-0.0.14.tar.bz2 + '10dfca10f8e4678d1034a522535fa85c7273d2c5c04dd007d191f7a484ee42b5', # FASTX-Toolkit-0.0.14_fix-gcc7.patch +] + +builddependencies = [('pkg-config', '0.29.2')] +dependencies = [('libgtextutils', '0.7')] + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']], + 'dirs': ['.'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14_fix-gcc7.patch b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14_fix-gcc7.patch new file mode 100644 index 00000000000..dfc823fd5bd --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14_fix-gcc7.patch @@ -0,0 +1,12 @@ +exit after usage to make sure gcc-7 will not assume that code falls through case statement +author: Paul Jähne +--- a/src/fasta_formatter/fasta_formatter.cpp ++++ b/src/fasta_formatter/fasta_formatter.cpp +@@ -103,6 +103,7 @@ void parse_command_line(int argc, char* + switch(opt) { + case 'h': + usage(); ++ exit(0); + + case 'i': + input_filename = optarg; diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2018b.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2018b.eb new file mode 100644 index 00000000000..bc2bdf152d4 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2018b.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'libgtextutils' +version = '0.7' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = "ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/agordon/%(name)s/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_fix-bool.patch'] +checksums = [ + '792e0ea3c96ffe3ad65617a104b7dc50684932bc96d2adab501c952fd65c3e4a', # libgtextutils-0.7.tar.gz + 'bb16a4fd86c2eb12215d8780b09f0898771a73e53889a015e2351f2d737c9a00', # libgtextutils-0.7_fix-bool.patch +] + +sanity_check_paths = { + 'files': ['lib/%(name)s.so', 'lib/%(name)s.a'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'lib' From 41767405b71f94f34f2e8c25d89ad6fe20a58f71 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 22 Jan 2019 10:02:31 +0100 Subject: [PATCH 0183/5331] adding easyconfigs: HISAT2-2.1.0-foss-2018b.eb --- .../h/HISAT2/HISAT2-2.1.0-foss-2018b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-foss-2018b.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-foss-2018b.eb new file mode 100644 index 00000000000..40d81d2810f --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-foss-2018b.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.1.0' + +homepage = 'https://ccb.jhu.edu/software/%(namelower)s/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['89a276eed1fc07414b1601947bc9466bdeb50e8f148ad42074186fe39a1ee781'] + +dependencies = [ + ('NGS', '2.9.3', '-Java-1.8'), + ('ncbi-vdb', '2.9.3'), +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in executables], + 'dirs': [], +} + +moduleclass = 'bio' From cce68c576616942f87b0b0c91f5c8fa15bd41391 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 22 Jan 2019 14:55:53 +0100 Subject: [PATCH 0184/5331] adding easyconfigs: cuDNN-7.4.2.24-CUDA-10.0.130.eb --- .../c/cuDNN/cuDNN-7.4.2.24-CUDA-10.0.130.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-CUDA-10.0.130.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-CUDA-10.0.130.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-CUDA-10.0.130.eb new file mode 100644 index 00000000000..6048ccf2d21 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-CUDA-10.0.130.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '7.4.2.24' +cuda_version = '10.0.130' + +cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) + +versionsuffix = '-CUDA-%s' % cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +# Download as cudnn-10.0-linux-x64-v7.4.2.24.tgz +sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] +checksums = ['2edfc86a02b50d17e88c478955a332e6a1e8174e7e53a3458b4ea51faf02daa3'] + +dependencies = [('CUDA', cuda_version)] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From 4e73f42dd8ba0f6c0ed2cae5a09c14d549403dc9 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 22 Jan 2019 16:18:04 +0200 Subject: [PATCH 0185/5331] adding easyconfigs: ispc-1.10.0.eb --- easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb | 26 +++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb new file mode 100644 index 00000000000..f1a2bd793b1 --- /dev/null +++ b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'ispc' +version = '1.10.0' + +homepage = 'http://ispc.github.io/ , https://github.com/ispc/ispc/' +description = """Intel SPMD Program Compilers; An open-source compiler for high-performance + SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, + with extensions for 'single program, multiple data' (SPMD) programming. + Under the SPMD model, the programmer writes a program that generally appears + to be a regular serial program, though the execution model is actually that + a number of program instances execute in parallel on the hardware.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['ispc-v%(version)s-linux.tar.gz'] +source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] + +sanity_check_paths = { + 'files': ["bin/ispc"], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'compiler' From fa07e5cdcbd9f83bc08cf7fbb09cc0185efe36e9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 23 Jan 2019 07:11:09 +0100 Subject: [PATCH 0186/5331] adding easyconfigs: PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb, PyCogent-1.9-foss-2018b-Python-2.7.15.eb --- .../PyCogent-1.9-foss-2018b-Python-2.7.15.eb | 36 +++++++++++++++++ .../PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb | 39 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCogent/PyCogent-1.9-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/p/PyCogent/PyCogent-1.9-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyCogent/PyCogent-1.9-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..4284206a75d --- /dev/null +++ b/easybuild/easyconfigs/p/PyCogent/PyCogent-1.9-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonPackage' + +name = 'PyCogent' +version = '1.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://%(namelower)s.org' +description = """PyCogent is a software library for genomic biology. It is a fully + integrated and thoroughly tested framework for: controlling third-party applications; + devising workflows; querying databases; conducting novel probabilistic analyses of + biological sequence evolution; and generating publication quality graphics.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] + +checksums = ['c9f56d21d764aa62e3e8a9df5a300eb7fb59e502572bec41894d21df19aeceb5'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), +] + +options = {'modulename': 'cogent'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..679f2ad31ec --- /dev/null +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonPackage' + +name = 'PyNAST' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://biocore.github.io/%(namelower)s' +description = """PyNAST is a reimplementation of the NAST sequence aligner, which has + become a popular tool for adding new 16s rRNA sequences to existing 16s rRNA alignments. + This reimplementation is more flexible, faster, and easier to install and maintain than + the original NAST implementation.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +github_account = 'biocore' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] + +checksums = ['0799e6c3021d6e163ef7250853922fc365c3fb94246c2cb0984381741b83ea98'] + +dependencies = [ + ('Python', '2.7.15'), + ('PyCogent', '1.9', versionsuffix), + ('UCLUST', '1.2.22q', '-i86linux64', True), +] + +options = {'modulename': '%(namelower)s'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [('%(namelower)s -h')] + +moduleclass = 'bio' From 24140420cd998ba8c3f30060985a879fbcf5c517 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 23 Jan 2019 08:43:55 +0100 Subject: [PATCH 0187/5331] adding easyconfigs: FastQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb --- ...tQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb diff --git a/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..67b9a91d129 --- /dev/null +++ b/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'Tarball' + +name = 'FastQ_Screen' +version = '0.13.0' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s/' +description = """FastQ Screen allows you to screen a library of sequences in FastQ + format against a set of sequence databases so you can see if the composition of the + library matches with what you expect.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] + +checksums = ['972e4dd99a9bedd3023e5ae9cbf98594c1608e43f6c10e44a6ab63fed4fdecbc'] + +dependencies = [ + ('Bowtie', '1.2.2'), + ('Bowtie2', '2.3.4.2'), + ('BWA', '0.7.17'), + ('GD', '2.69', versionsuffix), + ('Perl', '5.28.0'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s -v')] + +moduleclass = 'bio' From 61cc1ac3b2d4494745b2d06b4ca80cbb4932e2da Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 23 Jan 2019 10:51:19 +0100 Subject: [PATCH 0188/5331] Sphinx v1.8.3 for intel/2018a and Python/3.6.4 --- .../Sphinx-1.8.3-intel-2018a-Python-3.6.4.eb | 94 +++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.3-intel-2018a-Python-3.6.4.eb diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.3-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.3-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..a9564d630b7 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.3-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,94 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx' +version = '1.8.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sphinx.pocoo.org/' +description = """Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. + It was originally created for the new Python documentation, and it has excellent facilities for the + documentation of Python projects, but C/C++ is already supported as well, and it is planned to add + special support for other languages as well.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +dependencies = [('Python', '3.6.4')] + +use_pip = True + +exts_list = [ + ('packaging', '19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + 'checksums': ['0c98a5d0be38ed775798ece1b9727178c4469d9c3b4ada66e8e6b7849f8732af'], + }), + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('sphinxcontrib-websupport', '1.1.0', { + 'modulename': 'sphinxcontrib.websupport', + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], + 'use_pip': False, + 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], + }), + ('Pygments', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], + 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], + }), + ('imagesize', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], + }), + ('Docutils', '0.14', { + 'source_tmpl': 'docutils-%(version)s.tar.gz', + 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], + 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], + }), + ('Babel', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], + }), + ('alabaster', '0.7.12', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], + 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + 'checksums': ['c4cb17ba44acffae3d3209646b6baec1e215cad3065e852c68cc569d4df1b9f8'], + }), + ('sphinx_rtd_theme', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], + 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], + }), + ('numpydoc', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], + 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], + }), + ('sphinx-bootstrap-theme', '0.6.5', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx-bootstrap-theme'], + 'checksums': ['82936109a05b84029052e7efb1756161c3b4c27ae18512a90234d50fe608cba7'], + }), + ('sphinx-gallery', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/sphinx-gallery'], + 'checksums': ['b49356b5516cc7dab67b1b378f6bf8146fe2372ee73d5e1ea2c483a2e3f4f182'], + }), +] + +sanity_check_paths = { + 'files': ['bin/sphinx-%s' % x for x in ['apidoc', 'autogen', 'build', 'quickstart']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' From 432144ad54a650892c81f92fe65e14496c23b43c Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 23 Jan 2019 14:22:50 +0100 Subject: [PATCH 0189/5331] EasyConfigs for PLUMED 2.5.0 in foss-2018b and fosscuda-2018b --- .../PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb | 51 +++++++++++++++++++ ...UMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb | 51 +++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..da556116bef --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,51 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['f782d1eafffb919f27fcafc1b317c08b498ff51727ae20d15491f26ed332bbff'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.5'), + ('libmatheval', '1.1.11'), + ('Python', '2.7.15'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python' +prebuildopts = 'source sourceme.sh && ' +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT, + 'lib/plumed/python/plumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..58b9a0fbd3c --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,51 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['f782d1eafffb919f27fcafc1b317c08b498ff51727ae20d15491f26ed332bbff'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.5'), + ('libmatheval', '1.1.11'), + ('Python', '2.7.15'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python' +prebuildopts = 'source sourceme.sh && ' +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT, + 'lib/plumed/python/plumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From 8263f8f38772fe390a5d273bd4036327bfb88a5c Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 23 Jan 2019 15:18:48 +0100 Subject: [PATCH 0190/5331] GROMACS easyconfig for v 2018.4 patched with PLUMED 2.5.0 --- .../GROMACS-2018.4-foss-2018b-PLUMED.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED.eb new file mode 100644 index 00000000000..6604dc0b50c --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED.eb @@ -0,0 +1,47 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2018.4' +versionsuffix = '-PLUMED' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch'] +checksums = [ + '6f2ee458c730994a8549d6b4f601ecfc9432731462f8bd4ffa35d330d9aaa891', # gromacs-2018.4.tar.gz + # GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch + '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06', +] + +builddependencies = [ + ('CMake', '3.11.4'), +] + +dependencies = [ + ('PLUMED', '2.5.0', '-Python-2.7.15'), +] + +moduleclass = 'bio' From 06f31b0559370be9a1bf2ca5b2a28727c1dd6855 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 23 Jan 2019 15:48:02 +0100 Subject: [PATCH 0191/5331] Easyconfig for GPU version of Gromacs patched with PLUMED 2.5.0 --- .../GROMACS-2018.4-fosscuda-2018b-PLUMED.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED.eb new file mode 100644 index 00000000000..93d0e8a25a5 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED.eb @@ -0,0 +1,51 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2018.4' +versionsuffix = '-PLUMED' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. +""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2018_fix_search_for_nvml_include.patch', + 'GROMACS-2018_amend_search_for_nvml_lib.patch', +] +checksums = [ + '6f2ee458c730994a8549d6b4f601ecfc9432731462f8bd4ffa35d330d9aaa891', # gromacs-2018.4.tar.gz + # GROMACS-2018_fix_search_for_nvml_include.patch + '59d59316337ce08134d600b44c6501240f2732826ea5699f4b0ae83bb1ae0bd3', + '769cf8aab2e76bb1b36befa4b60df0b975a35877994218725426bb2c597f321b', # GROMACS-2018_amend_search_for_nvml_lib.patch +] + +builddependencies = [ + ('CMake', '3.11.4'), +] + +dependencies = [ + ('PLUMED', '2.5.0', '-Python-2.7.15'), +] + +moduleclass = 'bio' From 8e7d8e778290399c5040a5a598b21d09b1b7fa1b Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 23 Jan 2019 14:59:57 -0600 Subject: [PATCH 0192/5331] adding easyconfigs: cuDNN-7.0.5.15-fosscuda-2017b.eb, cuDNN-7.0.5.15-intelcuda-2017b.eb --- .../c/cuDNN/cuDNN-7.0.5.15-fosscuda-2017b.eb | 36 +++++++++++++++++++ .../c/cuDNN/cuDNN-7.0.5.15-intelcuda-2017b.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-fosscuda-2017b.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-intelcuda-2017b.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-fosscuda-2017b.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-fosscuda-2017b.eb new file mode 100644 index 00000000000..0eb2d89486c --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-fosscuda-2017b.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# OriginalAuthor: Stephane Thiell +# Author: Ake Sandgren +## +easyblock = 'Tarball' + +# The full version of the library can be found using +# strings -a cuda/lib64/libcudnn_static.a | grep cudnn_version_ +# Download and rename. +name = 'cuDNN' +version = '7.0.5.15' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +# fosscuda 2017b uses CUDA 9.0 +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +# Nvidia developer registration required. +# Download link: +# https://developer.nvidia.com/compute/machine-learning/cudnn/secure/v7.0.5/prod/9.1_20171129/cudnn-9.0-linux-x64-v7 +# Complete version number is taken from the corresponding .deb files from the same URL base +# The downloaded file must be renamed to match the following sources +# line. +sources = ['%(namelower)s-9.0-linux-x64-v%(version)s.tgz'] +checksums = ['1a3e076447d5b9860c73d9bebe7087ffcb7b0c8814fd1e506096435a2ad9ab0e'] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-intelcuda-2017b.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-intelcuda-2017b.eb new file mode 100644 index 00000000000..4ce202a361b --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-intelcuda-2017b.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# OriginalAuthor: Stephane Thiell +# Author: Ake Sandgren +## +easyblock = 'Tarball' + +# The full version of the library can be found using +# strings -a cuda/lib64/libcudnn_static.a | grep cudnn_version_ +# Download and rename. +name = 'cuDNN' +version = '7.0.5.15' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +# intelcuda 2017b uses CUDA 9.0 +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +# Nvidia developer registration required. +# Download link: +# https://developer.nvidia.com/compute/machine-learning/cudnn/secure/v7.0.5/prod/9.1_20171129/cudnn-9.0-linux-x64-v7 +# Complete version number is taken from the corresponding .deb files from the same URL base +# The downloaded file must be renamed to match the following sources +# line. +sources = ['%(namelower)s-9.0-linux-x64-v%(version)s.tgz'] +checksums = ['1a3e076447d5b9860c73d9bebe7087ffcb7b0c8814fd1e506096435a2ad9ab0e'] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From b19d960f2c81120602e1e40605a9d82645329f7e Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 24 Jan 2019 10:38:27 +0200 Subject: [PATCH 0193/5331] added checksum --- easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb index f1a2bd793b1..82c7a63390c 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['ispc-v%(version)s-linux.tar.gz'] source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] +checksums = ['453211ade91c33826f4facb1336114831adbd35196d016e09d589a6ad8699aa3'] sanity_check_paths = { 'files': ["bin/ispc"], From f7fe4c8fba31216499e1cb901bbda67fceeabeae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 24 Jan 2019 10:14:08 +0100 Subject: [PATCH 0194/5331] Update easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb Co-Authored-By: timeu --- easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb index b03cfa35f1d..51714ffceb4 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb @@ -3,7 +3,8 @@ easyblock = 'CMakeMake' name = 'Salmon' version = '0.12.0' -homepage = 'https://github.com/COMBINE-lab/%(namelower)s' +github_account = 'COMBINE-lab' +homepage = 'https://github.com/%(github_account)s/%(namelower)s' description = """Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.""" From 6bc7f0b013608a6510e55c51bf8b3edba36e0517 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 24 Jan 2019 10:14:15 +0100 Subject: [PATCH 0195/5331] Update easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb Co-Authored-By: timeu --- easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb index 51714ffceb4..ba1d6149389 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb @@ -11,7 +11,7 @@ description = """Salmon is a wicked-fast program to produce a highly-accurate, toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'pic': True, 'openmp': True} -source_urls = ['https://github.com/COMBINE-lab/%(namelower)s/archive/'] +source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['91ebd1efc5b0b4c12ec6babecf3c0b79f7102e42b8895ca07c8c8fea869fefa3'] From 7cadd535bd4d0bf898ed1a7063403ec57a4efb81 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 24 Jan 2019 18:47:34 +0800 Subject: [PATCH 0196/5331] use new elpa easyblock --- .../e/ELPA/ELPA-2017.11.001-foss-2018b.eb | 20 ------------------ .../e/ELPA/ELPA-2017.11.001-intel-2018b.eb | 21 ------------------- .../e/ELPA/ELPA-2018.05.001-foss-2018b.eb | 20 ------------------ .../e/ELPA/ELPA-2018.05.001-intel-2018b.eb | 21 ------------------- 4 files changed, 82 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb index 5cf6e992e8d..a76d437222d 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb @@ -7,8 +7,6 @@ # ## -easyblock = 'ConfigureMake' - name = 'ELPA' version = '2017.11.001' @@ -22,22 +20,4 @@ source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['59f99c3abe2190fac0db8a301d0b9581ee134f438669dbc92551a54f6f861820'] -common_configopts = 'LIBS="$LIBSCALAPACK" ' - -# avx2 is enabled by default... -common_configopts += '--disable-avx2 ' - -configopts = [ - common_configopts + '--enable-openmp ', - common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. -] - -buildopts = ' V=1 ' - -sanity_check_paths = { - 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', - 'lib/libelpa_openmp.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb index d5c6eadd908..c627fe2d009 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb @@ -7,8 +7,6 @@ # ## -easyblock = 'ConfigureMake' - name = 'ELPA' version = '2017.11.001' @@ -22,23 +20,4 @@ source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['59f99c3abe2190fac0db8a301d0b9581ee134f438669dbc92551a54f6f861820'] -common_configopts = 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' -common_configopts += 'LIBS="$LIBSCALAPACK" ' - -# avx2 is enabled by default... -common_configopts += '--disable-avx2 ' - -configopts = [ - common_configopts + '--enable-openmp ', - common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. -] - -buildopts = ' V=1 ' - -sanity_check_paths = { - 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', - 'lib/libelpa_openmp.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb index 91ab1053fb5..c04ef1b2663 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb @@ -7,8 +7,6 @@ # ## -easyblock = 'ConfigureMake' - name = 'ELPA' version = '2018.05.001' @@ -22,22 +20,4 @@ source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['a76c3402eb9d1c19b183aedabde8c20f4cfa4692e73e529384207926aec04985'] -common_configopts = 'LIBS="$LIBSCALAPACK" ' - -# avx2 is enabled by default... -common_configopts += '--disable-avx2 ' - -configopts = [ - common_configopts + '--enable-openmp ', - common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. -] - -buildopts = ' V=1 ' - -sanity_check_paths = { - 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', - 'lib/libelpa_openmp.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb index 88c1f4f3e98..026c6c45625 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb @@ -7,8 +7,6 @@ # ## -easyblock = 'ConfigureMake' - name = 'ELPA' version = '2018.05.001' @@ -22,23 +20,4 @@ source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['a76c3402eb9d1c19b183aedabde8c20f4cfa4692e73e529384207926aec04985'] -common_configopts = 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' -common_configopts += 'LIBS="$LIBSCALAPACK" ' - -# avx2 is enabled by default... -common_configopts += '--disable-avx2 ' - -configopts = [ - common_configopts + '--enable-openmp ', - common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. -] - -buildopts = ' V=1 ' - -sanity_check_paths = { - 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', - 'lib/libelpa_openmp.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], -} - moduleclass = 'math' From 951f1ca0d5434f836cd8b0d9eb6fdb8d429fc28e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Jan 2019 12:01:16 +0100 Subject: [PATCH 0197/5331] {math}[binary] MCR R2018b (REVIEW) --- easybuild/easyconfigs/m/MCR/MCR-R2018b.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2018b.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2018b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2018b.eb new file mode 100644 index 00000000000..c6347f89101 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2018b.eb @@ -0,0 +1,19 @@ +name = 'MCR' +version = 'R2018b' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] +checksums = ['cc7f6e042c1b2edd5ae384c77d0b2c860e8dcfd7c5e23dbe07bf04d3a921e459'] + +dependencies = [('Java', '1.8')] + +moduleclass = 'math' From 816b77c2137df36ae8eb3d1e712141a90204e85f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Jan 2019 13:18:32 +0100 Subject: [PATCH 0198/5331] {devel}[intel/2018b] Spark 2.4.0 w/ Python 2.7.15 & 3.6.6 + Hadoop 2.9.2 (+ deps) --- .../Hadoop-2.9.2-GCCcore-7.3.0-native.eb | 42 +++++++++++++++ easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb | 23 ++++++++ .../Spark-2.4.0-intel-2018b-Python-2.7.15.eb | 53 +++++++++++++++++++ .../Spark-2.4.0-intel-2018b-Python-3.6.6.eb | 53 +++++++++++++++++++ .../s/snappy/snappy-1.1.7-GCCcore-7.3.0.eb | 33 ++++++++++++ 5 files changed, 204 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb create mode 100644 easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb create mode 100644 easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.7-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb new file mode 100644 index 00000000000..c5d51bfc141 --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb @@ -0,0 +1,42 @@ +name = 'Hadoop' +version = '2.9.2' +versionsuffix = '-native' + +homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' +description = """Hadoop MapReduce by Cloudera""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [ + 'http://www.eu.apache.org/dist/%(namelower)s/common/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/common/%(namelower)s-%(version)s/', +] +sources = ['hadoop-%(version)s-src.tar.gz'] +patches = ['Hadoop-TeraSort-on-local-filesystem.patch'] +checksums = [ + '590ac3fb05a7f2053bad0de4bfaec31bb5f17c2bf578abbb79ffddd015d52eda', # hadoop-2.9.2-src.tar.gz + 'd0a69a6936b4a01505ba2a20911d0cec4f79440dbc8da52b9ddbd7f3a205468b', # Hadoop-TeraSort-on-local-filesystem.patch +] + +builddependencies = [ + ('binutils', '2.30'), + ('Maven', '3.6.0', '', True), + ('protobuf', '2.5.0', '', True), # *must* be this version + ('CMake', '3.12.1'), + ('snappy', '1.1.7'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), +] + +dependencies = [('Java', '1.8', '', True)] + +build_native_libs = True + +extra_native_libs = [ + ('snappy', 'lib*/libsnappy.%s*' % SHLIB_EXT), + ('zlib', 'lib*/libz.%s*' % SHLIB_EXT), +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb b/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb new file mode 100644 index 00000000000..d30ba048576 --- /dev/null +++ b/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PackedBinary' + +name = 'Maven' +version = '3.6.0' + +homepage = 'http://maven.apache.org/index.html' +description = """Binary maven install, Apache Maven is a software project management and comprehension tool. Based on +the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a +central piece of information. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] +sources = ['apache-maven-%(version)s-bin.tar.gz'] +checksums = ['6a1b346af36a1f1a491c1c1a141667c5de69b42e6611d3687df26868bc0f4637'] + +sanity_check_paths = { + 'files': ['bin/mvn'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..1a783d16948 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,53 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '2.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [ + 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', +] +sources = ['spark-%(version)s-bin-hadoop2.7.tgz'] +checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] + +dependencies = [ + ('Python', '2.7.15'), + ('Java', '1.8', '', True), + ('Hadoop', '2.9.2', '-native'), + ('Arrow', '0.12.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('py4j', '0.10.8.1', { + 'source_tmpl': 'py4j-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/p/py4j'], + 'checksums': ['8329bb156a0cf37be9642a2a060dbdb627b5fcb827919be65d95102daccca274'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyspark', 'bin/spark-shell'], + 'dirs': ['python'] +} + +sanity_check_commands = [ + "pyspark -h", + "python -c 'import pyspark'", +] + +modextrapaths = {'PYTHONPATH': ['python', 'lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..241b40a2ca2 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,53 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '2.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [ + 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', +] +sources = ['spark-%(version)s-bin-hadoop2.7.tgz'] +checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] + +dependencies = [ + ('Python', '3.6.6'), + ('Java', '1.8', '', True), + ('Hadoop', '2.9.2', '-native'), + ('Arrow', '0.12.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('py4j', '0.10.8.1', { + 'source_tmpl': 'py4j-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/p/py4j'], + 'checksums': ['8329bb156a0cf37be9642a2a060dbdb627b5fcb827919be65d95102daccca274'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyspark', 'bin/spark-shell'], + 'dirs': ['python'] +} + +sanity_check_commands = [ + "pyspark -h", + "python -c 'import pyspark'", +] + +modextrapaths = {'PYTHONPATH': ['python', 'lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.7-GCCcore-7.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.7-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..aef2528ccec --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.7-GCCcore-7.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.7' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['3dfa02e873ff51a11ee02b9ca391807f0c8ea0529a4924afa645fbf97163f9d4'] + +builddependencies = [ + ('binutils', '2.30'), + ('CMake', '3.12.1'), +] + +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'lib' From c32e10ea58b1517175fc64a7a2c7cf5b972b1ddc Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Thu, 24 Jan 2019 14:07:11 +0100 Subject: [PATCH 0199/5331] Added PLUMED to the exception list for dependency checking --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c0129534add..657dbe0004a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -197,7 +197,7 @@ def check_dep_vars(dep, dep_vars): # for some dependencies, we allow exceptions for software that depends on a particular version, # as long as that's indicated by the versionsuffix - elif dep in ['Boost', 'R'] and len(dep_vars) > 1: + elif dep in ['Boost', 'R', 'PLUMED'] and len(dep_vars) > 1: for key in dep_vars.keys(): dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') # filter out dep version if all easyconfig filenames using it include specific dep version From f6a519f406d9b22d77928b23d30551b744ab98e3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 24 Jan 2019 15:45:58 +0100 Subject: [PATCH 0200/5331] Fix some overly long lines. --- .../TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb | 7 ++++++- .../TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb | 7 ++++++- .../TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb | 6 ++++-- 3 files changed, 16 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb index 8e9ae9274a6..419be2a2767 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb @@ -85,7 +85,12 @@ exts_list = [ 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], }), (name, version, { - 'patches': ['TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.12.0_lrt-flag.patch', 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch'], + 'patches': [ + 'TensorFlow-1.11.0_swig-env.patch', + 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', + 'TensorFlow-1.12.0_lrt-flag.patch', + 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch' + ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'checksums': [ diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb index d38ebe735e3..8d8a8598e4a 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb @@ -84,7 +84,12 @@ exts_list = [ 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], }), (name, version, { - 'patches': ['TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.12.0_lrt-flag.patch', 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch'], + 'patches': [ + 'TensorFlow-1.11.0_swig-env.patch', + 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', + 'TensorFlow-1.12.0_lrt-flag.patch', + 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch' + ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'checksums': [ diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb index af969f90fdc..b1d6e8f2fbe 100644 --- a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb @@ -42,9 +42,11 @@ exts_list = [ ] postinstallcmds = [ - 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/python/%s ' % 'tensorrt-4.0.1.6-cp27-cp27mu-linux_x86_64.whl', + 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/python/%s ' % + 'tensorrt-4.0.1.6-cp27-cp27mu-linux_x86_64.whl', 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/uff/%s ' % 'uff-0.4.0-py2.py3-none-any.whl', - 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/graphsurgeon/%s ' % 'graphsurgeon-0.2.0-py2.py3-none-any.whl', + 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/graphsurgeon/%s ' % + 'graphsurgeon-0.2.0-py2.py3-none-any.whl', ] modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} From 4c89497badc6bfc2ca8a04b86fe1195d089164e7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Jan 2019 16:02:50 +0100 Subject: [PATCH 0201/5331] {geo}[foss/2017b] GRASS 7.6.0 (REVIEW) --- .../dbus-glib-0.110-GCCcore-7.3.0.eb | 28 ++++++ .../f/FreeXL/FreeXL-1.0.5-GCCcore-7.3.0.eb | 30 ++++++ .../g/GConf/GConf-3.2.6-foss-2018b.eb | 40 ++++++++ .../GRASS-7.6.0-foss-2018b-Python-2.7.15.eb | 96 +++++++++++++++++++ .../g/GRASS/GRASS-7.6.0_GCC_ldlibs.patch | 13 +++ .../GST-plugins-base-0.10.36-foss-2018b.eb | 38 ++++++++ .../GStreamer/GStreamer-0.10.36-foss-2018b.eb | 42 ++++++++ .../libspatialite-4.3.0a-foss-2018b.eb | 35 +++++++ ...Python-3.0.2.0-foss-2018b-Python-2.7.15.eb | 37 +++++++ 9 files changed, 359 insertions(+) create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.5-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb create mode 100644 easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/g/GRASS/GRASS-7.6.0_GCC_ldlibs.patch create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-7.3.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..0314e8dc7f9 --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-7.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.110' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] +checksums = ['7ce4760cf66c69148f6bd6c92feaabb8812dee30846b24cd0f7395c436d7e825'] + +builddependencies = [('binutils', '2.30')] + +dependencies = [ + ('GLib', '2.54.3'), + ('DBus', '1.13.6'), + ('expat', '2.2.5'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.5-GCCcore-7.3.0.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.5-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..4713eaff800 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.5-GCCcore-7.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FreeXL' +version = '1.0.5' + +homepage = 'https://www.gaia-gis.it/fossil/freexl/index' + +description = """ + FreeXL is an open source library to extract valid data from within an + Excel (.xls) spreadsheet. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/freexl-sources/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dc9b150d218b0e280a3d6a41d93c1e45f4d7155829d75f1e5bf3e0b0de6750d'] + +builddependencies = [ + ('binutils', '2.30'), + ('CMake', '3.12.1'), +] + +sanity_check_paths = { + 'files': ['lib/libfreexl.a'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb new file mode 100644 index 00000000000..e4ab476be13 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-foss-2018b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +homepage = 'https://projects.gnome.org/gconf/' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c'] + +dependencies = [ + ('dbus-glib', '0.110'), + ('GLib', '2.54.3'), + ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), + ('libxml2', '2.9.8'), + ('GTK+', '2.24.32'), + ('intltool', '0.51.0', '-Perl-5.28.0'), +] + +configopts = '--disable-orbit ' + +sanity_check_paths = { + 'files': ['bin/gconf%s' % x for x in['-merge-tree', 'tool-2']] + + ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] + + ['lib/libgconf-2.%s' % x for x in['a', 'so']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..6cb57dbfaf0 --- /dev/null +++ b/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,96 @@ +easyblock = 'ConfigureMake' + +name = 'GRASS' +version = '7.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "http://grass.osgeo.org" +description = """The Geographic Resources Analysis Support System - used + for geospatial data management and analysis, image processing, + graphics and maps production, spatial modeling, and visualization""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://grass.osgeo.org/grass%s/source' % ''.join(version.split('.')[:2])] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_GCC_ldlibs.patch'] +checksums = [ + '07628f83ad59ba6d9d097cdc91c490efaf5b1d57bc7ee1fc2709183162741b6a', # grass-7.6.0.tar.gz + '1927578fc81cb8f9d930874b0fd3453f446720b50eb95b9bd1fb2c940ca02e6e', # GRASS-7.6.0_GCC_ldlibs.patch +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('Autotools', '20180311'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('gettext', '0.19.8.1'), + ('Python', '2.7.15'), + ('libxml2', '2.9.8'), + ('libpng', '1.6.34'), + ('libreadline', '7.0'), + ('ncurses', '6.1'), + ('netCDF', '4.6.1'), + ('GDAL', '2.2.3', versionsuffix), + ('libspatialite', '4.3.0a'), + ('GEOS', '3.6.2', versionsuffix), + ('PROJ', '5.0.0'), + ('SQLite', '3.24.0'), + ('freetype', '2.9.1'), + ('FFmpeg', '4.1'), + ('LibTIFF', '4.0.9'), + ('cairo', '1.14.12'), + ('X11', '20180604'), + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), + ('wxPython', '3.0.2.0', versionsuffix), +] + +preconfigopts = "sed -e 's/-lblas/\$LIBBLAS/g' -e 's/-llapack/\$LIBLAPACK/g' -i configure &&" +configopts = '--enable-64bit ' +configopts += '--enable-largefile=yes ' +configopts += '--with-cairo=yes ' +configopts += '--with-cxx ' +configopts += '--with-ffmpeg --with-ffmpeg-libs=$EBROOTFFMPEG/lib --with-ffmpeg-includes=$EBROOTFFMPEG/include/* ' +configopts += '--with-fftw --with-fftw-libs=$EBROOTFFTW/lib --with-fftw-includes=$EBROOTFFTW/include ' +configopts += '--with-freetype ' +configopts += '--with-freetype-libs=$EBROOTFREETYPE/lib --with-freetype-includes=$EBROOTFREETYPE/include ' +configopts += '--with-geos=$EBROOTGEOS/bin/geos-config ' +configopts += '--without-glw ' +configopts += '--with-lapack ' +configopts += '--with-lapack-lib=$LAPACK_LIB_DIR ' +configopts += '--with-lapack-includes=$LAPACK_INC_DIR ' +configopts += '--with-blas ' +configopts += '--with-blas-lib=$BLAS_LIB_DIR ' +configopts += '--with-blas-includes=$BLAS_INC_DIR ' +configopts += '--with-netcdf=$EBROOTNETCDF/bin/nc-config ' +configopts += '--without-odbc ' +configopts += '--with-opengl ' +configopts += '--with-openmp ' +configopts += '--with-png ' +configopts += '--with-png-libs="$EBROOTLIBPNG/lib $EBROOTZLIB/lib" --with-png-includes=$EBROOTLIBPNG/include ' +configopts += '--without-postgres ' +configopts += '--with-proj --with-proj-libs=$EBROOTPROJ/lib ' +configopts += '--with-proj-includes=$EBROOTPROJ/include --with-proj-share=$EBROOTPROJ/share/proj ' +configopts += '--with-pthread ' +configopts += '--with-python ' +configopts += '--with-readline ' +configopts += '--with-readline-libs=$EBROOTLIBREADLINE/lib --with-readline-includes=$EBROOTLIBREADLINE/include ' +configopts += '--with-spatialite ' +configopts += '--with-sqlite ' +configopts += '--with-tiff-libs=$EBROOTLIBTIFF/lib --with-tiff-includes=$EBROOTLIBTIFF/include ' +configopts += '--with-wxwidgets=$EBROOTWXPYTHON/bin/wx-config ' +configopts += '--with-x ' +configopts += '--with-zlib --with-zlib-libs=$EBROOTZLIB/lib --with-zlib-includes=$EBROOTZLIB/include ' +configopts += '--with-bzlib --with-bzlib-libs=$EBROOTBZIP2/lib --with-ibzlib-includes=$EBROOTBZIP2/include ' + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0_GCC_ldlibs.patch b/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0_GCC_ldlibs.patch new file mode 100644 index 00000000000..68c9e1dc3a9 --- /dev/null +++ b/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0_GCC_ldlibs.patch @@ -0,0 +1,13 @@ +# Use mathlib and threads in the LDFALGS +# January 24th 2019 by B. Hajgato (Free University Brussels - VUB) +--- configure.orig 2018-06-06 23:28:35.000000000 +0200 ++++ configure 2019-01-24 14:27:36.985828861 +0100 +@@ -1510,7 +1510,7 @@ + SHLIB_LD_FLAGS="-Wl,-soname,\$(notdir \$@)" + SHLIB_SUFFIX=".so" + SHLIB_LD="${CC} -shared" +- LDFLAGS="-Wl,--export-dynamic" ++ LDFLAGS="-pthread -lm -Wl,--export-dynamic" + LD_SEARCH_FLAGS='-Wl,-rpath-link,${LIB_RUNTIME_DIR}' + LD_LIBRARY_PATH_VAR="LD_LIBRARY_PATH" + ;; diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb new file mode 100644 index 00000000000..d3a8d057e59 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['1fe45c3894903001d4d008b0713dab089f53726dcb5842d5b40c2595a984e64a'] + +dependencies = [ + ('GStreamer', '0.10.36'), +] + +# does not work with Bison 3.x +builddependencies = [ + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['discoverer', 'visualise']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb new file mode 100644 index 00000000000..8be833db619 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '0.10.36' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9151aa108c177054387885763fa0e433e76780f7c5655c70a5390f2a6c6871da'] + +dependencies = [ + ('GLib', '2.54.3'), + ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), + ('zlib', '1.2.11'), +] + +# does not work with Bison 3.x +builddependencies = [ + ('flex', '2.6.4', '', True), + ('Bison', '2.7', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-%%(version_major_minor)s' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-%%(version_major_minor)s.%s' % (x, SHLIB_EXT) for x in ['reamer', 'base', + 'controller', 'check']], + 'dirs': ['include', 'share', 'libexec'], +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb new file mode 100644 index 00000000000..a38bd23cbba --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '4.3.0a' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = """SpatiaLite is an open source library intended to extend the SQLite core to support + fully fledged Spatial SQL capabilities.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.gaia-gis.it/gaia-sins/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('CMake', '3.12.1'), + ('binutils', '2.30'), +] + +dependencies = [ + ('FreeXL', '1.0.5'), + ('GEOS', '3.6.2', '-Python-2.7.15'), + ('SQLite', '3.24.0'), + ('PROJ', '5.0.0'), +] + +configopts = '--disable-geosadvanced' + +sanity_check_paths = { + 'files': ['include/spatialite.h', 'lib/libspatialite.a', 'lib/libspatialite.%s' % SHLIB_EXT], + 'dirs': ['include/spatialite'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..d4cfe66b9a6 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,37 @@ +name = 'wxPython' +version = '3.0.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.wxpython.org' +description = """wxPython is a GUI toolkit for the Python programming language. + It allows Python programmers to create programs with a robust, + highly functional graphical user interface, simply and easily. + It is implemented as a Python extension module (native code) + that wraps the popular wxWidgets cross platform GUI library, + which is written in C++.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tar.bz2'] +patches = ['wxPython-%(version)s_fix-abs-overload.patch'] +checksums = [ + 'd54129e5fbea4fb8091c87b2980760b72c22a386cb3b9dd2eebc928ef5e8df61', # wxPython-src-3.0.2.0.tar.bz2 + '7bc2d671af6cd79930275c9e59c42a7c79ee6d66329190ac13df690f5def4d94', # wxPython-3.0.2.0_fix-abs-overload.patch +] + +dependencies = [ + ('Python', '2.7.15'), + ('libpng', '1.6.34'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.0'), + ('LibTIFF', '4.0.9'), + ('expat', '2.2.5'), + ('GTK+', '2.24.32'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '0.10.36'), + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'vis' From f01b89b3da62d24246b2ad621f337814b6cad19a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Jan 2019 16:37:36 +0100 Subject: [PATCH 0202/5331] add checksum to libspatialite --- .../l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb index a38bd23cbba..e80b3063ea7 100644 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb @@ -12,6 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['http://www.gaia-gis.it/gaia-sins/'] sources = [SOURCE_TAR_GZ] +checksums = ['88900030a4762904a7880273f292e5e8ca6b15b7c6c3fb88ffa9e67ee8a5a499'] builddependencies = [ ('CMake', '3.12.1'), From 0a82e71d22a48452313466a4952aad22a134fc26 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 24 Jan 2019 16:51:21 +0100 Subject: [PATCH 0203/5331] Try to fix hanging indent warning from travis. --- .../TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb index b1d6e8f2fbe..df6d7547ff3 100644 --- a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb @@ -42,11 +42,11 @@ exts_list = [ ] postinstallcmds = [ - 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/python/%s ' % - 'tensorrt-4.0.1.6-cp27-cp27mu-linux_x86_64.whl', + 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/python/%s ' + % 'tensorrt-4.0.1.6-cp27-cp27mu-linux_x86_64.whl', 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/uff/%s ' % 'uff-0.4.0-py2.py3-none-any.whl', - 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/graphsurgeon/%s ' % - 'graphsurgeon-0.2.0-py2.py3-none-any.whl', + 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/graphsurgeon/%s ' + % 'graphsurgeon-0.2.0-py2.py3-none-any.whl', ] modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} From f38cb365a33d817ab9c37367b9ce41ffe03bffc7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 24 Jan 2019 17:41:11 +0100 Subject: [PATCH 0204/5331] Add ulimit_unlimited to python easyconfig --- easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb index 0c32936e61b..95742102c11 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb @@ -30,6 +30,9 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +# Try to make sure stack limit is set to unlimited, to avoid compilation errors for hashlib with Intel compilers +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/6484 +ulimit_unlimited = True exts_download_dep_fail = True # workaround for "undefined symbol: __stack_chk_guard" From 02eafff2cf7114c866361dd2383627cf028d6811 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 24 Jan 2019 17:42:25 +0100 Subject: [PATCH 0205/5331] Move comment about fosscuda's CUDA version closer to cuda_version setting. --- easybuild/easyconfigs/n/NCCL/NCCL-2.3.7-fosscuda-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.3.7-fosscuda-2018b.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.3.7-fosscuda-2018b.eb index 278f39a2398..22ec1b636fe 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.3.7-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.3.7-fosscuda-2018b.eb @@ -7,9 +7,9 @@ homepage = 'https://developer.nvidia.com/nccl' description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.""" -# fosscuda/2018b uses CUDA 9.2 toolchain = {'name': 'fosscuda', 'version': '2018b'} +# fosscuda/2018b uses CUDA 9.2 cuda_version = '9.2' # Download from https://developer.nvidia.com/nccl/nccl-download (after log in) From ad846cab33d5b8b67538db122af1aff68f171590 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 24 Jan 2019 17:46:15 +0100 Subject: [PATCH 0206/5331] Add missing patch to paycheck for Python. --- .../easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb index 95742102c11..8331c2b7550 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb @@ -73,8 +73,13 @@ exts_list = [ 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], }), ('paycheck', '1.0.2', { + 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + 'checksums': [ + '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz + # paycheck-1.0.2_setup-open-README-utf8.patch + 'ceb7f08aebf016cdcd94ae41c1c76c8c120907f85cbfce240d3a112afb264d79', + ], }), ('pbr', '4.2.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], From e210c550e4303fb5e7fee35409a85d2b747ae8a7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 24 Jan 2019 17:47:04 +0100 Subject: [PATCH 0207/5331] Aremove fosscuda build of protobuf-3.6.1, GCCcore build already exists. --- .../protobuf/protobuf-3.6.1-fosscuda-2018b.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.6.1-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1-fosscuda-2018b.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1-fosscuda-2018b.eb deleted file mode 100644 index b512d29d2a8..00000000000 --- a/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1-fosscuda-2018b.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'protobuf' -version = '3.6.1' - -homepage = 'https://github.com/google/protobuf/' -description = """Google Protocol Buffers""" - -toolchain = {'name': 'fosscuda', 'version': '2018b'} - -source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['3d4e589d81b2006ca603c1ab712c9715a76227293032d05b26fca603f90b3f5b'] - -builddependencies = [('Autotools', '20180311')] - -preconfigopts = "./autogen.sh && " - -sanity_check_paths = { - 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'devel' From 3fa8c7d6f91f81cd70a746c580e91b39cae1086a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 24 Jan 2019 18:09:20 +0100 Subject: [PATCH 0208/5331] Order source_urls, source_tmpl, patches, checksums, modulename consistently. --- ...low-1.12.0-fosscuda-2018b-Python-2.7.15.eb | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb index 419be2a2767..abe1d57b79c 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb @@ -29,17 +29,17 @@ use_pip = True exts_list = [ ('protobuf-python', '3.6.1', { - 'modulename': 'google.protobuf', - 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', + 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], 'start_dir': 'python', 'use_pip': False, - 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + 'modulename': 'google.protobuf', }), ('absl-py', '0.6.1', { - 'modulename': 'absl', 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], 'checksums': ['87519e3b91a3d573664c6e2ee33df582bb68dca6642ae3cf3a4361b1c0a4e9d6'], + 'modulename': 'absl', }), ('astor', '0.7.1', { 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], @@ -50,17 +50,17 @@ exts_list = [ 'checksums': ['7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930'], }), ('grpcio', '1.16.0', { - 'modulename': 'grpc', 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], 'checksums': ['0cc5f2d3ee21c642d8982f197c83053fd3a8cbcd6a60240d8c87c6c256b10d57'], + 'modulename': 'grpc', }), ('Markdown', '3.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('tensorboard', version, { - 'source_tmpl': 'tensorboard-%(version)s-py2-none-any.whl', 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], + 'source_tmpl': 'tensorboard-%(version)s-py2-none-any.whl', 'unpack_sources': False, 'checksums': ['537603db949e10d2f5f201d88b073f3f8fb4e4c311d5541e1d4518aa59aa8daa'], }), @@ -73,26 +73,26 @@ exts_list = [ 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Keras-Applications', '1.0.6', { - 'modulename': 'keras_applications', - 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['a03af60ddc9c5afdae4d5c9a8dd4ca857550e0b793733a5072e0725829b87017'], + 'modulename': 'keras_applications', }), ('Keras-Preprocessing', '1.0.5', { - 'modulename': 'keras_preprocessing', - 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], + 'modulename': 'keras_preprocessing', }), (name, version, { + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', 'patches': [ 'TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.12.0_lrt-flag.patch', 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch' ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'checksums': [ '3c87b81e37d4ed7f3da6200474fa5e656ffd20d8811068572f43610cae97ca92', # v1.12.0.tar.gz 'aa53c7f6d42b4a9e91e0ba639d79f69a7db3c0a88c3b8e43d332479b6368391a', # TensorFlow-1.11.0_swig-env.patch From d55f47d1e3ccdd2deedc7abca142b69e2aba856b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 24 Jan 2019 18:10:41 +0100 Subject: [PATCH 0209/5331] Add missing download_dep_fail and use_pip --- .../w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb index 553e73e0a3f..331611679eb 100644 --- a/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/w/wheel/wheel-0.31.1-fosscuda-2018b-Python-3.6.6.eb @@ -15,6 +15,9 @@ checksums = ['0a2e54558a0628f2145d2fc822137e322412115173e8a2ddbe1c9024338ae83c'] dependencies = [('Python', '3.6.6')] +download_dep_fail = True +use_pip = True + sanity_check_paths = { 'files': ['bin/wheel'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From b51bf345bfc382f88d41dcd87bfdbb86e1c4c0ad Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 24 Jan 2019 18:11:43 +0100 Subject: [PATCH 0210/5331] Order source_urls, source_tmpl, patches, checksums, modulename consistently. --- .../TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb index df6d7547ff3..12c69a81e81 100644 --- a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb @@ -32,12 +32,12 @@ exts_default_options = { exts_list = [ ('protobuf-python', '3.6.1', { - 'modulename': 'google.protobuf', - 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', + 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], 'start_dir': 'python', 'use_pip': False, - 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + 'modulename': 'google.protobuf', }), ] From ed4cb309eebd503b445475d16ccb7c3189a1de22 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Jan 2019 18:56:54 +0100 Subject: [PATCH 0211/5331] udocker v1.1.3 for Python/2.7.14 on intel/2018a --- ...udocker-1.1.3-intel-2018a-Python-2.7.14.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/u/udocker/udocker-1.1.3-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/u/udocker/udocker-1.1.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/u/udocker/udocker-1.1.3-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..bf5a345a5a6 --- /dev/null +++ b/easybuild/easyconfigs/u/udocker/udocker-1.1.3-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'udocker' +version = '1.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/indigo-dc/udocker' +description = """A basic user tool to execute simple docker containers in batch + or interactive systems without root privileges.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/indigo-dc/udocker/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5276f3d467f9533234239a022b094d37639b7090acd5e116304a488c57307995'] + +dependencies = [('Python', '2.7.14')] + +# use_pip = True + +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/udocker'], + 'dirs': [], +} + +options = {'modulename': False} + +moduleclass = 'tools' From 8264af196c2753ebee287691368f98a6e8cd16d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Jan 2019 19:53:38 +0100 Subject: [PATCH 0212/5331] avoid depending on protobuf built with dummy toolchain for Hadoop installed with GCCcore/7.3.0 --- .../Hadoop-2.9.2-GCCcore-7.3.0-native.eb | 2 +- .../protobuf/protobuf-2.5.0-GCCcore-7.3.0.eb | 27 +++++++++++++++++++ 2 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb index c5d51bfc141..1f5b16e1284 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb @@ -21,7 +21,7 @@ checksums = [ builddependencies = [ ('binutils', '2.30'), ('Maven', '3.6.0', '', True), - ('protobuf', '2.5.0', '', True), # *must* be this version + ('protobuf', '2.5.0'), # *must* be this version ('CMake', '3.12.1'), ('snappy', '1.1.7'), ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..b036e95fd01 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-7.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '2.5.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c55aa3dc538e6fd5eaf732f4eb6b98bdcb7cedb5b91d3b5bdcf29c98c293f58e'] + +builddependencies = [ + ('binutils', '2.30'), + ('Autotools', '20180311'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From dac576294593dd93ac834bbae046cd8889851263 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Jan 2019 20:55:44 +0100 Subject: [PATCH 0213/5331] use correct source_urls in protobuf-2.5.0-GCCcore-7.3.0.eb --- .../easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-7.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-7.3.0.eb index b036e95fd01..3a0ecc2772c 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-GCCcore-7.3.0.eb @@ -8,7 +8,7 @@ description = """Google Protocol Buffers""" toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +source_urls = ['https://github.com/google/%(namelower)s/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['c55aa3dc538e6fd5eaf732f4eb6b98bdcb7cedb5b91d3b5bdcf29c98c293f58e'] From db30310a26e99caf868cf0535933a7d0c4a12dc4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 25 Jan 2019 07:36:13 +0100 Subject: [PATCH 0214/5331] Update checksum for Amber-18-AT-18_use_fftw_from_mkl_or_external.patch --- .../Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb | 2 +- .../Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb b/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb index aea05e0eae2..bf6faf5990a 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-18-foss-2018b-AmberTools-18-patchlevel-10-8.eb @@ -47,7 +47,7 @@ checksums = [ 'f25d0353b045bc769d3938aa698aea40e9e7bd152a2acca4b7fa1d790cf96297', 'c95db1c296c3512b818a1b34a65c2ea4cbce46acf70689919c5f42c3bb0799d3', # Amber-18-AT-18_fix_mkl_include_path.patch # Amber-18-AT-18_use_fftw_from_mkl_or_external.patch - '10e18ddd1218e73cb10531d8426c3568d8bdc255da92e682fffd2ee2a4ad1867', + 'cd93b4946538195f9ecadcd52ed2a30d377239a7442be6dc97d68ca0af087548', # Amber-18-AT-18_use_FFTW_FFT_instead_of_PUBFFT.patch 'ebe85219f22869ec22e531592b785d68c15337171acd479660ab4e3ecd07655f', # Amber-18-AT-18_fix_sander_link_with_external_fftw.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb b/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb index 1cc60600503..60b981ffbeb 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-18-intel-2017b-AmberTools-18-patchlevel-10-8.eb @@ -47,7 +47,7 @@ checksums = [ 'f25d0353b045bc769d3938aa698aea40e9e7bd152a2acca4b7fa1d790cf96297', 'c95db1c296c3512b818a1b34a65c2ea4cbce46acf70689919c5f42c3bb0799d3', # Amber-18-AT-18_fix_mkl_include_path.patch # Amber-18-AT-18_use_fftw_from_mkl_or_external.patch - '10e18ddd1218e73cb10531d8426c3568d8bdc255da92e682fffd2ee2a4ad1867', + 'cd93b4946538195f9ecadcd52ed2a30d377239a7442be6dc97d68ca0af087548', # Amber-18-AT-18_use_FFTW_FFT_instead_of_PUBFFT.patch 'ebe85219f22869ec22e531592b785d68c15337171acd479660ab4e3ecd07655f', # Amber-18-AT-18_fix_sander_link_with_external_fftw.patch From 006b5b6215bf46c579d56cfb47e637ea070eb599 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Fri, 25 Jan 2019 13:16:42 +0200 Subject: [PATCH 0215/5331] adding easyconfigs: FUSE-3.4.1-foss-2018a.eb --- .../f/FUSE/FUSE-3.4.1-foss-2018a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/f/FUSE/FUSE-3.4.1-foss-2018a.eb diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.4.1-foss-2018a.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.4.1-foss-2018a.eb new file mode 100644 index 00000000000..6b04d4be168 --- /dev/null +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.4.1-foss-2018a.eb @@ -0,0 +1,29 @@ +easyblock = 'MesonNinja' + +name = 'FUSE' +version = '3.4.1' + +homepage = 'https://github.com/libfuse/libfuse' +description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://github.com/libfuse/libfuse/releases/download/fuse-%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = [ + '88302a8fa56e7871066652495b05faf14b36dca9f1b740e9fb00da0785e60485', # fuse-3.4.1.tar.xz +] + +builddependencies = [ + ('Meson', '0.48.1', '-Python-3.6.4'), + ('Ninja', '1.8.2'), +] + +configopts = '-Dutils=false' + +sanity_check_paths = { + 'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT, 'lib64/pkgconfig/fuse%(version_major)s.pc'], + 'dirs': ['include/fuse%(version_major)s'], +} + +moduleclass = 'lib' From 6b204866c8371cd2cfd22f091fb2591659143b0d Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Fri, 25 Jan 2019 14:19:42 +0200 Subject: [PATCH 0216/5331] added missing Meson --- .../Meson-0.48.1-foss-2018a-Python-3.6.4.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..1c0c6a24f86 --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = "0.48.1" +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = [] +dependencies = [ + ('Python', '3.6.4'), + ('Ninja', '1.8.2'), +] + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' \ No newline at end of file From 508041ad47f91a6b61832b066ef487fff927106d Mon Sep 17 00:00:00 2001 From: sassmaj Date: Fri, 25 Jan 2019 17:10:01 +0100 Subject: [PATCH 0217/5331] adding easyconfigs: pubtcrs-master-intel-2019.01.eb --- .../p/pubtcrs/pubtcrs-master-intel-2019.01.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/pubtcrs/pubtcrs-master-intel-2019.01.eb diff --git a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-master-intel-2019.01.eb b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-master-intel-2019.01.eb new file mode 100644 index 00000000000..cc743a81172 --- /dev/null +++ b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-master-intel-2019.01.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'pubtcrs' +version = 'master' + +homepage = 'https://github.com/phbradley/pubtcrs' +description = """This repository contains C++ source code for the TCR clustering and correlation analyses described in the manuscript "Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity" by William S DeWitt III, Anajane Smith, Gary Schoch, John A Hansen, Frederick A Matsen IV and Philip Bradley, available on bioRxiv.""" + +toolchain = {'name': 'intel', 'version': '2019.01'} + +source_urls = ['https://github.com/phbradley/pubtcrs/archive/'] +sources = ['master.zip'] +checksums = ['5d38807bfaec60b1fc8765669dad18c2825f6b614a349f4dcc61e4f99add1ae3'] + +dependencies = [ + ('Boost', '1.69.0'), +] + + +buildopts = "BOOSTDIR=$EBROOTBOOST" + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/correlations', 'bin/neighbors', 'bin/pgen', 'bin/tcrdists'], + 'dirs': ['bin'], +} + From 5007773daef36a79a1a7e0f8e659c542f8fcac46 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Fri, 25 Jan 2019 18:19:18 +0100 Subject: [PATCH 0218/5331] version changed from master to number --- .../pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb diff --git a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb new file mode 100644 index 00000000000..ee39316f240 --- /dev/null +++ b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'pubtcrs' +version = 'f30b96a' + +homepage = 'https://github.com/phbradley/pubtcrs' +description = """This repository contains C++ source code for the TCR clustering and correlation analyses described in the manuscript "Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity" by William S DeWitt III, Anajane Smith, Gary Schoch, John A Hansen, Frederick A Matsen IV and Philip Bradley, available on bioRxiv.""" + +toolchain = {'name': 'intel', 'version': '2019.01'} + +source_urls = ['https://github.com/phbradley/pubtcrs/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['077707390aef4cb617f3b9a0d077a3511205530ac523dbb486af5c832379226e'] + +dependencies = [ + ('Boost', '1.69.0'), +] + + +buildopts = "BOOSTDIR=$EBROOTBOOST" + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/correlations', 'bin/neighbors', 'bin/pgen', 'bin/tcrdists'], + 'dirs': ['bin'], +} + From 73f19609c8ef52a76c56b47c363a7efdcc203c73 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 27 Jan 2019 12:19:04 +0100 Subject: [PATCH 0219/5331] Use pip for udocker v1.1.3 --- .../u/udocker/udocker-1.1.3-intel-2018a-Python-2.7.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/udocker/udocker-1.1.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/u/udocker/udocker-1.1.3-intel-2018a-Python-2.7.14.eb index bf5a345a5a6..a18a3f65e64 100644 --- a/easybuild/easyconfigs/u/udocker/udocker-1.1.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/u/udocker/udocker-1.1.3-intel-2018a-Python-2.7.14.eb @@ -16,7 +16,7 @@ checksums = ['5276f3d467f9533234239a022b094d37639b7090acd5e116304a488c57307995'] dependencies = [('Python', '2.7.14')] -# use_pip = True +use_pip = True download_dep_fail = True From 4f670e0d2f4ad673863407d99c1cb1293b155cc4 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 28 Jan 2019 09:36:03 +0100 Subject: [PATCH 0220/5331] Removed autocc prebuildopt because it is now in EasyBlock of SuiteSparse --- .../SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb index ca26cc5e681..37e9e63d1ae 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.5-foss-2017b-ParMETIS-4.0.3.eb @@ -16,8 +16,6 @@ checksums = ['b9a98de0ddafe7659adffad8a58ca3911c1afa8b509355e7aa58b02feb35d9b6'] dependencies = [('ParMETIS', parmetis_ver)] -prebuildopts = 'AUTOCC=no' - maxparallel = 1 moduleclass = 'numlib' From 7eec56703bd61bed1de26df6c767de57c9901fb1 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Mon, 28 Jan 2019 14:09:44 +0100 Subject: [PATCH 0221/5331] adding easyconfigs: STREAM-5.10-GCCcore-7.3.0.eb, STREAM-5.10-GCCcore-8.2.0.eb --- .../s/STREAM/STREAM-5.10-GCCcore-7.3.0.eb | 45 ++++++++++++++++++ .../s/STREAM/STREAM-5.10-GCCcore-8.2.0.eb | 46 +++++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-7.3.0.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..30e90ce66bb --- /dev/null +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-7.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CmdCp' + +name = 'STREAM' +version = '5.10' + +homepage = 'https://www.cs.virginia.edu/stream/' +description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable + memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] +sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c'}] +checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] + +builddependencies = [ + ('binutils', '2.30'), +] + +skipsteps = ['source'] + +# 10 million array elements (1000 runs): requires ~224MB of memory +cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " +# 100 million array elements (1000 runs): requires ~2.2GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " +# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " +# 5 billion array elements (1000 runs): requires ~111 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " + +cmds_map = [('stream-%(version)s.c', cmds_str)] + +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'dirs': [], +} + +tests = ['%(installdir)s/bin/stream_1Kx10M'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..fc2c9d2bff7 --- /dev/null +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-8.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'CmdCp' + +name = 'STREAM' +version = '5.10' + +homepage = 'https://www.cs.virginia.edu/stream/' +description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable + memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] +sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c'}] +checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + + +skipsteps = ['source'] + +# 10 million array elements (1000 runs): requires ~224MB of memory +cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " +# 100 million array elements (1000 runs): requires ~2.2GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " +# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " +# 5 billion array elements (1000 runs): requires ~111 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " + +cmds_map = [('stream-%(version)s.c', cmds_str)] + +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'dirs': [], +} + +tests = ['%(installdir)s/bin/stream_1Kx10M'] + +moduleclass = 'perf' From 70b1b51a37b773dcae3c45cabaab3d83407e0191 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 28 Jan 2019 14:52:17 +0100 Subject: [PATCH 0222/5331] adding easyconfigs: mosdepth-0.2.4-foss-2018b.eb, Nim-0.19.2-GCCcore-7.3.0.eb --- .../m/mosdepth/mosdepth-0.2.4-foss-2018b.eb | 42 +++++++++++++++++++ .../n/Nim/Nim-0.19.2-GCCcore-7.3.0.eb | 16 +++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb create mode 100644 easybuild/easyconfigs/n/Nim/Nim-0.19.2-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb new file mode 100644 index 00000000000..b0eff3ac8f8 --- /dev/null +++ b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb @@ -0,0 +1,42 @@ +easyblock = 'Binary' + +name = 'mosdepth' +version = '0.2.4' +hts_nim_ver = '0.2.7' + +homepage = 'https://github.com/brentp/mosdepth' +description = "Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [ + 'https://github.com/brentp/hts-nim/archive/', + 'https://github.com/brentp/mosdepth/archive/', +] +sources = [ + {'download_filename': 'v%s.tar.gz' % hts_nim_ver, 'filename': 'hts-nim-%s.tar.gz' % hts_nim_ver}, + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, +] +checksums = [ + '3c9a81eaedb898642c04a14104ccff108104c328b361f7032778194ea9c99f33', # hts-nim-0.2.7.tar.gz + 'e49f1e2973f0016aa1f93fffa2b050a2f320faf552f790f6edd60c9e86edfe18', # mosdepth-0.2.4.tar.gz +] + +dependencies = [ + ('Nim', '0.19.2'), + ('HTSlib', '1.9'), + ('PCRE', '8.41'), +] + +extract_sources = True + +install_cmd = "cd %(builddir)s/hts-nim-*/ && nimble install --nimbleDir:%(installdir)s --verbose -y && " +install_cmd += "cd ../mosdepth-*/ && sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " +install_cmd += "nimble install --nimbleDir:%(installdir)s --verbose -y" + +sanity_check_paths = { + 'files': ['bin/mosdepth'], + 'dirs': ['pkgs/hts-%s' % hts_nim_ver, 'pkgs/mosdepth-%(version)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/Nim/Nim-0.19.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/Nim/Nim-0.19.2-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..142e06efb88 --- /dev/null +++ b/easybuild/easyconfigs/n/Nim/Nim-0.19.2-GCCcore-7.3.0.eb @@ -0,0 +1,16 @@ +name = 'Nim' +version = '0.19.2' + +homepage = 'https://nim-lang.org/' +description = "Nim is a systems and applications programming language." + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://nim-lang.org/download/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['44c3f579c75cc799fc0bff5163b3cc649a200758aa1d6485ab939fc28295238a'] + +builddependencies = [('binutils', '2.30')] +dependencies = [('libreadline', '7.0')] + +moduleclass = 'lang' From e8686dbd34b73aa63f1bff1b77d5124334789b93 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 28 Jan 2019 14:42:37 +0100 Subject: [PATCH 0223/5331] adding easyconfigs: ncdu-1.13-foss-2018b.eb and patches: ncdu-1.13_large-file-counts.patch --- .../n/ncdu/ncdu-1.13-foss-2018b.eb | 31 +++++++++++++++ .../n/ncdu/ncdu-1.13_large-file-counts.patch | 39 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdu/ncdu-1.13-foss-2018b.eb create mode 100644 easybuild/easyconfigs/n/ncdu/ncdu-1.13_large-file-counts.patch diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.13-foss-2018b.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.13-foss-2018b.eb new file mode 100644 index 00000000000..90807c35030 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.13-foss-2018b.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'ncdu' +version = '1.13' + +homepage = 'https://dev.yorhel.nl/%(name)s' +description = """Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a + remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular + desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like + environment with ncurses installed.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://dev.yorhel.nl/download/'] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_large-file-counts.patch'] +checksums = [ + 'f4d9285c38292c2de05e444d0ba271cbfe1a705eee37c2b23ea7c448ab37255a', # ncdu-1.13.tar.gz + '70a75350f362bf54e3738de5c198da8fa1b5d2ce59c54419668a5143eb6aa424', # ncdu-1.13_large-file-counts.patch +] + +dependencies = [('ncurses', '6.1')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.13_large-file-counts.patch b/easybuild/easyconfigs/n/ncdu/ncdu-1.13_large-file-counts.patch new file mode 100644 index 00000000000..c41d2c58f7f --- /dev/null +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.13_large-file-counts.patch @@ -0,0 +1,39 @@ +display larger file counts in browser UI +author: Paul Jähne +--- a/src/browser.c ++++ b/src/browser.c +@@ -169,18 +169,29 @@ static void browse_draw_graph(struct dir *n, int *x) { + + static void browse_draw_items(struct dir *n, int *x) { + enum ui_coltype c = n->flags & FF_BSEL ? UIC_SEL : UIC_DEFAULT; ++ enum ui_coltype cn = c == UIC_SEL ? UIC_NUM_SEL : UIC_NUM; + + if(!show_items) + return; + *x += 7; + +- if(n->items > 99999) { +- addstrc(c, "> "); +- addstrc(c == UIC_SEL ? UIC_NUM_SEL : UIC_NUM, "100"); +- addchc(c, 'k'); +- } else if(n->items) { +- uic_set(c == UIC_SEL ? UIC_NUM_SEL : UIC_NUM); ++ if(!n->items) ++ return; ++ else if(n->items < 100*1000) { ++ uic_set(cn); + printw("%6s", fullsize(n->items)); ++ } else if(n->items < 1000*1000) { ++ uic_set(cn); ++ printw("%5.1f", n->items / 1000.0); ++ addstrc(c, "k"); ++ } else if(n->items < 1000*1000*1000) { ++ uic_set(cn); ++ printw("%5.1f", n->items / 1e6); ++ addstrc(c, "M"); ++ } else { ++ addstrc(c, " > "); ++ addstrc(cn, "1"); ++ addchc(c, 'B'); + } + } From 82bf2994d6eed971ad3a544735c215cbbf382236 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Mon, 28 Jan 2019 16:11:06 +0100 Subject: [PATCH 0224/5331] Adding db directory which is needed as well --- .../easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb index ee39316f240..750118bc4eb 100644 --- a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb +++ b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb @@ -19,10 +19,10 @@ dependencies = [ buildopts = "BOOSTDIR=$EBROOTBOOST" -files_to_copy = ['bin'] +files_to_copy = ['bin','db'] sanity_check_paths = { 'files': ['bin/correlations', 'bin/neighbors', 'bin/pgen', 'bin/tcrdists'], - 'dirs': ['bin'], + 'dirs': ['bin','db'], } From 57c1c99461388b9605b6bafdbfdfdb672f25ec72 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Mon, 28 Jan 2019 15:21:53 +0000 Subject: [PATCH 0225/5331] Delete pubtcrs-master-intel-2019.01.eb --- .../p/pubtcrs/pubtcrs-master-intel-2019.01.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pubtcrs/pubtcrs-master-intel-2019.01.eb diff --git a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-master-intel-2019.01.eb b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-master-intel-2019.01.eb deleted file mode 100644 index cc743a81172..00000000000 --- a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-master-intel-2019.01.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'MakeCp' - -name = 'pubtcrs' -version = 'master' - -homepage = 'https://github.com/phbradley/pubtcrs' -description = """This repository contains C++ source code for the TCR clustering and correlation analyses described in the manuscript "Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity" by William S DeWitt III, Anajane Smith, Gary Schoch, John A Hansen, Frederick A Matsen IV and Philip Bradley, available on bioRxiv.""" - -toolchain = {'name': 'intel', 'version': '2019.01'} - -source_urls = ['https://github.com/phbradley/pubtcrs/archive/'] -sources = ['master.zip'] -checksums = ['5d38807bfaec60b1fc8765669dad18c2825f6b614a349f4dcc61e4f99add1ae3'] - -dependencies = [ - ('Boost', '1.69.0'), -] - - -buildopts = "BOOSTDIR=$EBROOTBOOST" - -files_to_copy = ['bin'] - -sanity_check_paths = { - 'files': ['bin/correlations', 'bin/neighbors', 'bin/pgen', 'bin/tcrdists'], - 'dirs': ['bin'], -} - From 4ed8d22623af77f50424e0dcfff5efd1e3f2886f Mon Sep 17 00:00:00 2001 From: sassmaj Date: Tue, 29 Jan 2019 11:54:12 +0100 Subject: [PATCH 0226/5331] Some cosmetics like missing white spaces done --- .../p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb index 750118bc4eb..8fccbc082fe 100644 --- a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb +++ b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb @@ -4,7 +4,11 @@ name = 'pubtcrs' version = 'f30b96a' homepage = 'https://github.com/phbradley/pubtcrs' -description = """This repository contains C++ source code for the TCR clustering and correlation analyses described in the manuscript "Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity" by William S DeWitt III, Anajane Smith, Gary Schoch, John A Hansen, Frederick A Matsen IV and Philip Bradley, available on bioRxiv.""" +description = """This repository contains C++ source code for the TCR clustering +and correlation analyses described in the manuscript "Human T cell receptor +occurrence patterns encode immune history, genetic background, and receptor +specificity" by William S DeWitt III, Anajane Smith, Gary Schoch, John A Hansen, +Frederick A Matsen IV and Philip Bradley, available on bioRxiv.""" toolchain = {'name': 'intel', 'version': '2019.01'} @@ -19,10 +23,10 @@ dependencies = [ buildopts = "BOOSTDIR=$EBROOTBOOST" -files_to_copy = ['bin','db'] +files_to_copy = ['bin', 'db'] sanity_check_paths = { 'files': ['bin/correlations', 'bin/neighbors', 'bin/pgen', 'bin/tcrdists'], - 'dirs': ['bin','db'], + 'dirs': ['bin', 'db'], } From 46a531b3af648f68288f94e7aa8e55729918e20f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Jan 2019 11:58:30 +0100 Subject: [PATCH 0227/5331] bump version to 3.9.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index e1310bdec96..07428d587cf 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.8.1' +VERSION = '3.9.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) From 3a03617a7ef70c5b330f5fc89c4eedd164f9d78d Mon Sep 17 00:00:00 2001 From: sassmaj Date: Tue, 29 Jan 2019 12:16:07 +0100 Subject: [PATCH 0228/5331] Removed blank line at end of file --- easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb index 8fccbc082fe..acd78413445 100644 --- a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb +++ b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb @@ -29,4 +29,3 @@ sanity_check_paths = { 'files': ['bin/correlations', 'bin/neighbors', 'bin/pgen', 'bin/tcrdists'], 'dirs': ['bin', 'db'], } - From 307635f5866b1bae2231d78cd9bb896cbb844ea2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Jan 2019 12:38:34 +0100 Subject: [PATCH 0229/5331] adding easyconfigs: EasyBuild-3.8.1.eb --- .../e/EasyBuild/EasyBuild-3.8.1.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.1.eb new file mode 100644 index 00000000000..9c444dc3b0b --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.1.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.8.1' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://files.pythonhosted.org/packages/18/59/3274a58af6af84a87f7655735b452c06c769586ee73954f5ee15d303aa29/', + # vsc-base + 'https://files.pythonhosted.org/packages/62/e5/589612e47255627e4752d99018ae7cff8f49ab0fa6b4ba7b2226a76a05d3/', + # easybuild-framework + 'https://files.pythonhosted.org/packages/14/81/21746045f034efe34f0f4efd6f193858cabb2ba4131d9eb99bb7c33b7d85/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/d1/ba/1f5f99498fb0b5d0e07fe4403b59b42e0c1b85774b2ccb918a4806ca9c31/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/87/92/b4094727f29de038abc247b31a2675508bfb77c2bcbacfad4475c9961b7f/', +] +sources = [ + 'vsc-install-0.11.3.tar.gz', + 'vsc-base-2.8.3.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '8b102ba585863769d974ad117764039ac3cea21372a3baa5cdb6b93166673ad6', # vsc-install-0.11.3.tar.gz + '9e102ca9d94ab97c2b974c63708dab7ea4dbaa3144787f06455e16445b92f204', # vsc-base-2.8.3.tar.gz + '32eec72c868d74b2d44df2949b6ded59853439466f7a39008d6cc80b4db705f5', # easybuild-framework-3.8.1.tar.gz + '15c305dd2391534e0b70f11b3e8e1be25f5bfcaaaba0219ebb563803ecd38e33', # easybuild-easyblocks-3.8.1.tar.gz + '5443b0b912a797dfbffa30d5254a27a4ffb6be0fbdd0e1bd4ade4ed334003c5c', # easybuild-easyconfigs-3.8.1.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' From a85fd5a71c1558ba21e90a3084ee1962418fee45 Mon Sep 17 00:00:00 2001 From: dugan Date: Tue, 29 Jan 2019 15:13:11 +0000 Subject: [PATCH 0230/5331] adding easyconfigs: magma-2.4.0-fosscuda-2018b.eb --- .../m/magma/magma-2.4.0-fosscuda-2018b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.4.0-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/m/magma/magma-2.4.0-fosscuda-2018b.eb b/easybuild/easyconfigs/m/magma/magma-2.4.0-fosscuda-2018b.eb new file mode 100644 index 00000000000..45f93fc03c8 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.4.0-fosscuda-2018b.eb @@ -0,0 +1,33 @@ +easyblock = "ConfigureMake" + +name = 'magma' +version = '2.4.0' + +homepage = 'http://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['http://icl.cs.utk.edu/projectsfiles/magma/downloads/'] +sources = [SOURCE_TAR_GZ] +patches = [('magma-2.3.0-fix-makefile.patch')] +checksums = [ + '4eb839b1295405fd29c8a6f5b4ed578476010bf976af46573f80d1169f1f9a4f', # magma-2.4.0.tar.gz + '47e734cf30577b563377c946fb7897da2fd53d050f7e4fe83d8bb11b8d157913', # magma-2.3.0-fix-makefile.patch +] + +skipsteps = ['configure'] + +prebuildopts = 'touch make.inc && ' +prebuildopts += 'GPU_TARGET="Kepler Maxwell Pascal Volta" ' + +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libmagma.so', 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' From f6552588554af205a9ee42c89d322958a3b925ba Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 29 Jan 2019 14:03:03 -0600 Subject: [PATCH 0231/5331] adding easyconfigs: AFNI-19.0.01-foss-2017b-Python-2.7.14.eb --- .../AFNI-19.0.01-foss-2017b-Python-2.7.14.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..441c0a252b6 --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,63 @@ +easyblock = 'ConfigureMake' + +name = 'AFNI' +version = '19.0.01' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://afni.nimh.nih.gov/' +description = """AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - + a technique for mapping human brain activity.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'openmp': True, 'pic': True} + +source_urls = ['https://github.com/afni/afni/archive/'] +sources = ['AFNI_%(version)s.tar.gz'] +patches = ['AFNI-18.1.09_omp-pragma-statement-fix.patch'] +checksums = [ + 'd3c558ac898aefc432396742e5b4d74d8b6863aa92f276d709834513848f68be', # AFNI_19.0.01.tar.gz + '8b739ddc09d6e398ac7fa86d89f6a02f26f2b58b17caea627d5c07de5282aab2', # AFNI-18.1.09_omp-pragma-statement-fix.patch +] + +builddependencies = [('M4', '1.4.18')] + +dependencies = [ + ('tcsh', '6.20.00'), + ('Python', '2.7.14'), + ('X11', '20171023'), + ('motif', '2.3.8'), + ('R', '3.4.3', '-X11-20171023'), + ('PyQt5', '5.9.2', versionsuffix), + ('expat', '2.2.5'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '1.5.2'), + ('GSL', '2.4'), + ('GLib', '2.54.3'), # must match version used in Qt5 (via PyQt5) + ('zlib', '1.2.11'), +] + +skipsteps = ['configure', 'install'] + +prebuildopts = "cd src && cp Makefile.linux_openmp_64 Makefile && " +buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%(pyshortver)s" ' +buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' +buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%(pyshortver)sm ' +buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"' +buildopts += ' INSTALLDIR=%(installdir)s' + +parallel = 1 + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['afni'], + 'dirs': [], +} + +moduleclass = 'bio' From cbfdad3ff0fcc7cffb89c7725fda514cea3222d5 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 29 Jan 2019 14:04:27 -0600 Subject: [PATCH 0232/5331] Add deps --- .../m/motif/motif-2.3.8-foss-2017b.eb | 40 +++++++++++++++++++ .../PyQt5-5.9.2-foss-2017b-Python-2.7.14.eb | 40 +++++++++++++++++++ .../SIP-4.19.8-foss-2017b-Python-2.7.14.eb | 31 ++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.19.8-foss-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb new file mode 100644 index 00000000000..66ee66896ca --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.8' + +homepage = 'http://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] + +dependencies = [ + ('X11', '20171023'), + ('libpng', '1.6.32'), + ('xbitmaps', '1.1.1', '', True), + ('freetype', '2.8'), + ('libjpeg-turbo', '1.5.2'), + ('bzip2', '1.0.6'), +] +builddependencies = [ + ('Autotools', '20170619'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('util-linux', '2.31'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..d329deb2c57 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt5' +version = '5.9.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-%(version)s'] +sources = ['%(name)s_gpl-%(version)s.tar.gz'] +checksums = ['c190dac598c97b0113ca5e7a37c71c623f02d1d713088addfacac4acfa4b8394'] + +dependencies = [ + ('Python', '2.7.14'), + ('SIP', '4.19.8', versionsuffix), + ('Qt5', '5.8.0'), +] + +configopts = "configure.py --confirm-license --verbose" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages --bindir=%(installdir)s/bin" +configopts += " --designer-plugindir=%(installdir)s/plugins/designer --qml-plugindir=%(installdir)s/plugins/PyQt5" +configopts += " --no-sip-files --no-stubs " + +options = {'modulename': '%(name)s'} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_PLUGIN_PATH': 'plugins', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19.8-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19.8-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..2a9bc73023c --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19.8-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.19.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7eaf7a2ea7d4d38a56dd6d2506574464bddf7cf284c960801679942377c297bc'] + +dependencies = [('Python', '2.7.14')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' From 087542ef1a60b0f639d8ebc2674ef81a4897ca7c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 29 Jan 2019 15:24:26 -0600 Subject: [PATCH 0233/5331] Fix deps version conflicts --- .../a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb index 441c0a252b6..9ba2f0283c4 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb @@ -28,11 +28,11 @@ dependencies = [ ('motif', '2.3.8'), ('R', '3.4.3', '-X11-20171023'), ('PyQt5', '5.9.2', versionsuffix), - ('expat', '2.2.5'), - ('libpng', '1.6.34'), + ('expat', '2.2.4'), + ('libpng', '1.6.32'), ('libjpeg-turbo', '1.5.2'), ('GSL', '2.4'), - ('GLib', '2.54.3'), # must match version used in Qt5 (via PyQt5) + ('GLib', '2.53.5'), # must match version used in Qt5 (via PyQt5) ('zlib', '1.2.11'), ] From f9a69b368e3b0399919c5304b6cf221f781d8903 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 29 Jan 2019 23:03:14 +0100 Subject: [PATCH 0234/5331] add ujson extension --- .../easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb | 4 ++++ easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb | 4 ++++ easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb | 4 ++++ easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb | 4 ++++ easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb | 4 ++++ easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb | 4 ++++ easybuild/easyconfigs/p/Python/Python-3.7.0-foss-2018b.eb | 4 ++++ easybuild/easyconfigs/p/Python/Python-3.7.0-intel-2018b.eb | 4 ++++ easybuild/easyconfigs/p/Python/Python-3.7.0-iomkl-2018b.eb | 4 ++++ 9 files changed, 36 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb index 2043bc60553..e02ad0868af 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb @@ -221,6 +221,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb index 254e9732b6f..731dcb04b29 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb @@ -225,6 +225,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb index c4d5f5c8ae9..58ce721e76c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb @@ -225,6 +225,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb index eab0bb8af3a..3aa2b82f362 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb @@ -231,6 +231,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb index db9ebaaf706..e0d49bcc75e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb @@ -235,6 +235,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb index b90e4510fb6..dd66cbcb17b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb @@ -235,6 +235,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.0-foss-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.7.0-foss-2018b.eb index 7d500c4d331..f22a09ff502 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.7.0-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.7.0-foss-2018b.eb @@ -231,6 +231,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.0-intel-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.7.0-intel-2018b.eb index 8fd6be0bbc7..54bc1938ae8 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.7.0-intel-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.7.0-intel-2018b.eb @@ -235,6 +235,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.0-iomkl-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.7.0-iomkl-2018b.eb index 8d76101f5ac..536404e8b5c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.7.0-iomkl-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.7.0-iomkl-2018b.eb @@ -235,6 +235,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), ] moduleclass = 'lang' From 091a704fd6122cb6a822b5a84075a96e67727f26 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 29 Jan 2019 20:04:26 -0600 Subject: [PATCH 0235/5331] adding easyconfigs: AFNI-19.0.01-intel-2017b-Python-2.7.14.eb --- .../AFNI-19.0.01-intel-2017b-Python-2.7.14.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..54144e6ea7f --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,63 @@ +easyblock = 'ConfigureMake' + +name = 'AFNI' +version = '19.0.01' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://afni.nimh.nih.gov/' +description = """AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - + a technique for mapping human brain activity.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'openmp': True, 'pic': True} + +source_urls = ['https://github.com/afni/afni/archive/'] +sources = ['AFNI_%(version)s.tar.gz'] +patches = ['AFNI-18.1.09_omp-pragma-statement-fix.patch'] +checksums = [ + 'd3c558ac898aefc432396742e5b4d74d8b6863aa92f276d709834513848f68be', # AFNI_19.0.01.tar.gz + '8b739ddc09d6e398ac7fa86d89f6a02f26f2b58b17caea627d5c07de5282aab2', # AFNI-18.1.09_omp-pragma-statement-fix.patch +] + +builddependencies = [('M4', '1.4.18')] + +dependencies = [ + ('tcsh', '6.20.00'), + ('Python', '2.7.14'), + ('X11', '20171023'), + ('motif', '2.3.8'), + ('R', '3.4.3', '-X11-20171023'), + ('PyQt5', '5.9.2', versionsuffix), + ('expat', '2.2.4'), + ('libpng', '1.6.32'), + ('libjpeg-turbo', '1.5.2'), + ('GSL', '2.4'), + ('GLib', '2.53.5'), # must match version used in Qt5 (via PyQt5) + ('zlib', '1.2.11'), +] + +skipsteps = ['configure', 'install'] + +prebuildopts = "cd src && cp Makefile.linux_openmp_64 Makefile && " +buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%(pyshortver)s" ' +buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' +buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%(pyshortver)sm ' +buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"' +buildopts += ' INSTALLDIR=%(installdir)s' + +parallel = 1 + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['afni'], + 'dirs': [], +} + +moduleclass = 'bio' From 73e1e76c2a245fed83aced8304317b29b54488c0 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 29 Jan 2019 20:05:26 -0600 Subject: [PATCH 0236/5331] Add deps --- .../PyQt5-5.9.2-intel-2017b-Python-2.7.14.eb | 40 +++++++++++++++++++ .../SIP-4.19.8-intel-2017b-Python-2.7.14.eb | 31 ++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..5ed59a740bb --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt5' +version = '5.9.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-%(version)s'] +sources = ['%(name)s_gpl-%(version)s.tar.gz'] +checksums = ['c190dac598c97b0113ca5e7a37c71c623f02d1d713088addfacac4acfa4b8394'] + +dependencies = [ + ('Python', '2.7.14'), + ('SIP', '4.19.8', versionsuffix), + ('Qt5', '5.8.0'), +] + +configopts = "configure.py --confirm-license --verbose" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages --bindir=%(installdir)s/bin" +configopts += " --designer-plugindir=%(installdir)s/plugins/designer --qml-plugindir=%(installdir)s/plugins/PyQt5" +configopts += " --no-sip-files --no-stubs " + +options = {'modulename': '%(name)s'} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_PLUGIN_PATH': 'plugins', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..26983c3ebbe --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.19.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7eaf7a2ea7d4d38a56dd6d2506574464bddf7cf284c960801679942377c297bc'] + +dependencies = [('Python', '2.7.14')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' From af8a6c33258625c1f55385a0ace4cfd8cd0e4774 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 30 Jan 2019 11:07:35 +0100 Subject: [PATCH 0237/5331] Add libxml2 dep to libstatialite --- .../l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb index e80b3063ea7..b064d53a1ba 100644 --- a/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-4.3.0a-foss-2018b.eb @@ -14,16 +14,14 @@ source_urls = ['http://www.gaia-gis.it/gaia-sins/'] sources = [SOURCE_TAR_GZ] checksums = ['88900030a4762904a7880273f292e5e8ca6b15b7c6c3fb88ffa9e67ee8a5a499'] -builddependencies = [ - ('CMake', '3.12.1'), - ('binutils', '2.30'), -] +builddependencies = [('CMake', '3.12.1')] dependencies = [ ('FreeXL', '1.0.5'), ('GEOS', '3.6.2', '-Python-2.7.15'), ('SQLite', '3.24.0'), ('PROJ', '5.0.0'), + ('libxml2', '2.9.8'), ] configopts = '--disable-geosadvanced' From b7b0633ed91fbe667a0d2d82e0a7fd6050461fac Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 30 Jan 2019 12:44:41 +0200 Subject: [PATCH 0238/5331] adding easyconfigs: Stacks-2.3b-foss-2018a.eb --- .../s/Stacks/Stacks-2.3b-foss-2018a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-2.3b-foss-2018a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.3b-foss-2018a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.3b-foss-2018a.eb new file mode 100644 index 00000000000..d735ea8d5fc --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.3b-foss-2018a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '2.3b' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a46786d8811a730ebcdc17891e89f50d4f4ae196734439dac86091f45c92ac72'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks', + 'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks', + 'bin/tsv2bam', 'bin/ustacks'], + 'dirs': [], +} + +moduleclass = 'bio' From 4842ac5b02374bb8cb6ac24de97e2ebd0e45886c Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Wed, 30 Jan 2019 08:13:32 -0300 Subject: [PATCH 0239/5331] Cleanup and add checksums --- ...2018b-Python-2.7.15.eb => horton-2.1.1-foss-2018b.eb} | 9 +-------- ...018b-Python-2.7.15.eb => horton-2.1.1-intel-2018b.eb} | 9 +-------- .../easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb | 3 ++- .../easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb | 3 ++- 4 files changed, 6 insertions(+), 18 deletions(-) rename easybuild/easyconfigs/h/horton/{horton-2.1.1-foss-2018b-Python-2.7.15.eb => horton-2.1.1-foss-2018b.eb} (84%) rename easybuild/easyconfigs/h/horton/{horton-2.1.1-intel-2018b-Python-2.7.15.eb => horton-2.1.1-intel-2018b.eb} (84%) diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb similarity index 84% rename from easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb rename to easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb index 9ca0c72698a..3bfb0b5491c 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] sources = [SOURCE_TAR_GZ] +checksums = ['13e3381dea62e5877c6cde94515e99c8b7872f0a9498961b0766bdeae4506fe6'] pyver = '2.7.15' pyversuffix = '-Python-%s' % pyver @@ -33,14 +34,6 @@ prebuildopts = ' '.join([ 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', ]) -# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc -#runtest = ' '.join([ -# 'export MATPLOTLIBRC=$PWD;', -# 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', -# '%s python setup.py build_ext -i; ' % prebuildopts, -# 'nosetests -v', -#]) - pyshortver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb similarity index 84% rename from easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb rename to easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb index f45e9bb1eef..ec4dd619733 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] sources = [SOURCE_TAR_GZ] +checksums = ['13e3381dea62e5877c6cde94515e99c8b7872f0a9498961b0766bdeae4506fe6'] pyver = '2.7.15' pyversuffix = '-Python-%s' % pyver @@ -33,14 +34,6 @@ prebuildopts = ' '.join([ 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', ]) -# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc -#runtest = ' '.join([ -# 'export MATPLOTLIBRC=$PWD;', -# 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', -# '%s python setup.py build_ext -i; ' % prebuildopts, -# 'nosetests -v', -#]) - pyshortver = '.'.join(pyver.split('.')[:2]) sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb index 456e6b3c095..4ae37c37d5e 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -8,7 +8,8 @@ description = """Libint library is used to evaluate the traditional (electron re toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'pic': True} -sources = ['libint-%(version)s-stable.tgz'] source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] +sources = ['libint-%(version)s-stable.tgz'] +checksums = ['5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02'] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb index 329f8d37121..80ca6acb553 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-intel-2018b.eb @@ -8,7 +8,8 @@ description = """Libint library is used to evaluate the traditional (electron re toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'pic': True} -sources = ['libint-%(version)s-stable.tgz'] source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] +sources = ['libint-%(version)s-stable.tgz'] +checksums = ['5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02'] moduleclass = 'chem' From 6a60cefba114845a88d7508ce7ad71154b1f897e Mon Sep 17 00:00:00 2001 From: sassmaj Date: Wed, 30 Jan 2019 13:44:29 +0100 Subject: [PATCH 0240/5331] adding easyconfigs: angsd-0.925-foss-2018b.eb --- .../a/angsd/angsd-0.925-foss-2018b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/angsd/angsd-0.925-foss-2018b.eb diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.925-foss-2018b.eb b/easybuild/easyconfigs/a/angsd/angsd-0.925-foss-2018b.eb new file mode 100644 index 00000000000..2bfdccb8cba --- /dev/null +++ b/easybuild/easyconfigs/a/angsd/angsd-0.925-foss-2018b.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'angsd' +version = '0.925' + +homepage = 'http://www.popgen.dk/angsd' +description = """Program for analysing NGS data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/ANGSD/angsd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['010d8b2c385b4c82f981794857b68a82f6eda0e72b75e7e7d83fd9760af78dbf'] + +dependencies = [('HTSlib', '1.9')] + +files_to_copy = [ + (['angsd', 'misc/supersim', 'misc/thetaStat', 'misc/realSFS', 'misc/msToGlf', + 'misc/smartCount', 'misc/printIcounts', 'misc/contamination', 'misc/splitgl', + 'misc/NGSadmix', 'misc/contamination2', 'misc/haploToPlink', 'misc/ngsPSMC', + 'misc/ibs'], 'bin'), + 'doc', +] + +sanity_check_paths = { + 'files': ['bin/angsd'], + 'dirs': ['doc'], +} + + +moduleclass = 'bio' From 6f43e1601dad5c38e33bcfb0099ddc0f091d25ac Mon Sep 17 00:00:00 2001 From: sassmaj Date: Wed, 30 Jan 2019 15:45:29 +0100 Subject: [PATCH 0241/5331] Some cosmetics like white spaces done --- easybuild/easyconfigs/a/angsd/angsd-0.925-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.925-foss-2018b.eb b/easybuild/easyconfigs/a/angsd/angsd-0.925-foss-2018b.eb index 2bfdccb8cba..f408a121141 100644 --- a/easybuild/easyconfigs/a/angsd/angsd-0.925-foss-2018b.eb +++ b/easybuild/easyconfigs/a/angsd/angsd-0.925-foss-2018b.eb @@ -5,7 +5,7 @@ version = '0.925' homepage = 'http://www.popgen.dk/angsd' description = """Program for analysing NGS data.""" - + toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/ANGSD/angsd/archive/'] From 241fe2ff7e5013094a17eb2e0e552faac5d3b04a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Jan 2019 18:04:08 +0100 Subject: [PATCH 0242/5331] adding easyconfigs: phonopy-1.14.2-intel-2018a-Python-2.7.14.eb --- ...honopy-1.14.2-intel-2018a-Python-2.7.14.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..4774e69fa01 --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '1.14.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://atztogo.github.io/phonopy/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['022fa8c30fa4afb128a81a35cfa537265c65a4ac19865dc67ba63adf5986b7a2'] + +dependencies = [ + ('Python', '2.7.14'), + ('matplotlib', '2.1.2', versionsuffix), + ('lxml', '4.2.0', versionsuffix), + ('PyYAML', '3.12', versionsuffix), + ('h5py', '2.7.1', versionsuffix), +] + +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From e8174b386c77b4204211a5637cc2c60185656b90 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 30 Jan 2019 14:45:36 -0600 Subject: [PATCH 0243/5331] Updated comment --- .../easyconfigs/c/cuDNN/cuDNN-7.0.5.15-fosscuda-2017b.eb | 8 +++++--- .../easyconfigs/c/cuDNN/cuDNN-7.0.5.15-intelcuda-2017b.eb | 8 +++++--- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-fosscuda-2017b.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-fosscuda-2017b.eb index 0eb2d89486c..55be3cfda91 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-fosscuda-2017b.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-fosscuda-2017b.eb @@ -22,9 +22,11 @@ toolchain = {'name': 'fosscuda', 'version': '2017b'} # Nvidia developer registration required. # Download link: # https://developer.nvidia.com/compute/machine-learning/cudnn/secure/v7.0.5/prod/9.1_20171129/cudnn-9.0-linux-x64-v7 -# Complete version number is taken from the corresponding .deb files from the same URL base -# The downloaded file must be renamed to match the following sources -# line. +# +# Complete version number is taken from the output of: +# strings -a cuda/lib64/libcudnn_static.a | grep cudnn_version_ +# +# The downloaded file must be renamed to match the following sources line. sources = ['%(namelower)s-9.0-linux-x64-v%(version)s.tgz'] checksums = ['1a3e076447d5b9860c73d9bebe7087ffcb7b0c8814fd1e506096435a2ad9ab0e'] diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-intelcuda-2017b.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-intelcuda-2017b.eb index 4ce202a361b..636b5b4cf7c 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-intelcuda-2017b.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5.15-intelcuda-2017b.eb @@ -22,9 +22,11 @@ toolchain = {'name': 'intelcuda', 'version': '2017b'} # Nvidia developer registration required. # Download link: # https://developer.nvidia.com/compute/machine-learning/cudnn/secure/v7.0.5/prod/9.1_20171129/cudnn-9.0-linux-x64-v7 -# Complete version number is taken from the corresponding .deb files from the same URL base -# The downloaded file must be renamed to match the following sources -# line. +# +# Complete version number is taken from the output of: +# strings -a cuda/lib64/libcudnn_static.a | grep cudnn_version_ +# +# The downloaded file must be renamed to match the following sources line. sources = ['%(namelower)s-9.0-linux-x64-v%(version)s.tgz'] checksums = ['1a3e076447d5b9860c73d9bebe7087ffcb7b0c8814fd1e506096435a2ad9ab0e'] From 3c4cc497fc32d2c113ede88323eb65c6197c5a8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Jan 2019 00:17:14 +0100 Subject: [PATCH 0244/5331] update phonopy 1.14.2 easyconfig to intel/2018b + Python 2.7.15 --- .../PyYAML-3.13-intel-2018b-Python-2.7.15.eb | 28 +++++++++++++++++++ ...onopy-1.14.2-intel-2018b-Python-2.7.15.eb} | 13 +++++---- 2 files changed, 35 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb rename easybuild/easyconfigs/p/phonopy/{phonopy-1.14.2-intel-2018a-Python-2.7.14.eb => phonopy-1.14.2-intel-2018b-Python-2.7.15.eb} (69%) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..af657669158 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'] + +dependencies = [ + ('Python', '2.7.15'), + ('libyaml', '0.2.1'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018b-Python-2.7.15.eb similarity index 69% rename from easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018a-Python-2.7.14.eb rename to easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018b-Python-2.7.15.eb index 4774e69fa01..4d5d1b46ccc 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.14.2-intel-2018b-Python-2.7.15.eb @@ -7,21 +7,22 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'http://atztogo.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" -toolchain = {'name': 'intel', 'version': '2018a'} +toolchain = {'name': 'intel', 'version': '2018b'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['022fa8c30fa4afb128a81a35cfa537265c65a4ac19865dc67ba63adf5986b7a2'] dependencies = [ - ('Python', '2.7.14'), - ('matplotlib', '2.1.2', versionsuffix), - ('lxml', '4.2.0', versionsuffix), - ('PyYAML', '3.12', versionsuffix), - ('h5py', '2.7.1', versionsuffix), + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), + ('lxml', '4.2.5', versionsuffix), + ('PyYAML', '3.13', versionsuffix), + ('h5py', '2.8.0', versionsuffix), ] download_dep_fail = True +use_pip = True sanity_check_paths = { 'files': ['bin/phonopy'], From 3dbc2777a4d6b20d20c36bbaff69d26f17ec9912 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 31 Jan 2019 09:12:05 +0100 Subject: [PATCH 0245/5331] install via pip --- .../p/PyCogent/PyCogent-1.9-foss-2018b-Python-2.7.15.eb | 3 +++ .../p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/PyCogent/PyCogent-1.9-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyCogent/PyCogent-1.9-foss-2018b-Python-2.7.15.eb index 4284206a75d..f7bef8b6322 100644 --- a/easybuild/easyconfigs/p/PyCogent/PyCogent-1.9-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyCogent/PyCogent-1.9-foss-2018b-Python-2.7.15.eb @@ -28,6 +28,9 @@ dependencies = [ options = {'modulename': 'cogent'} +download_dep_fail = True +use_pip = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb index 679f2ad31ec..3d6d9af5489 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb @@ -29,6 +29,9 @@ dependencies = [ options = {'modulename': '%(namelower)s'} +download_dep_fail = True +use_pip = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], From 5aa7821c93fc062ead367a4c188d7693bbf6edda Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 31 Jan 2019 11:02:13 +0200 Subject: [PATCH 0246/5331] adding easyconfigs: Theano-1.0.4-foss-2018a-Python-3.6.4.eb --- .../Theano-1.0.4-foss-2018a-Python-3.6.4.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..ef9143d53c2 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = "1.0.4" +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [] +dependencies = [('Python', '3.6.4')] + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' + From 6a8a6fe8870f31dc7b7d88cbb5ec3a20e8e02d05 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Thu, 31 Jan 2019 13:04:14 +0100 Subject: [PATCH 0247/5331] adding easyconfigs: NGSadmix-32-foss-2018b.eb --- .../n/NGSadmix/NGSadmix-32-foss-2018b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb diff --git a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb new file mode 100644 index 00000000000..e4b721eb9ca --- /dev/null +++ b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb @@ -0,0 +1,35 @@ +easyblock = 'CmdCp' + +name = 'NGSadmix' +version = '32' + +homepage = 'http://www.popgen.dk/software/index.php/NgsAdmix' +description = """This page contains information about the program called +NGSadmix, which is a very nice tool for finding admixture proportions +from NGS data. It is based on genotype likelihoods.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +# This is a bit of a hack as there is no easyblock to simply download a cpp file and compile it. +# So we download the file from the source and copy it to the build directory. + +sources = [{ +'source_urls': ['http://popgen.dk/software/download/NGSadmix/'], +'filename': 'ngsadmix32.cpp', +'download_filename': 'ngsadmix32.cpp', +'extract_cmd': 'cp %s %(builddir)s', +}] + +build_str = "g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix" +cmds_map = [('', build_str)] + +files_to_copy = ['NGSadmix'] + +sanity_check_paths = { + 'files': ['NGSadmix'], + 'dirs': [''], +} + +modextrapaths = { 'PATH': ''} + +moduleclass = 'bio' From 5d4febfd7c89a38e42a6014ffaa92ffe3740cd4c Mon Sep 17 00:00:00 2001 From: sassmaj Date: Thu, 31 Jan 2019 15:22:45 +0100 Subject: [PATCH 0248/5331] Checksum added --- easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb index e4b721eb9ca..2e5db791432 100644 --- a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb +++ b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb @@ -20,6 +20,8 @@ sources = [{ 'extract_cmd': 'cp %s %(builddir)s', }] +checksums = ['a5623b71d20114708cfd7ccc5f8c6ce38ff871d1b79af85bc89d38775f2d477e'] + build_str = "g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix" cmds_map = [('', build_str)] From e744c4bb1ea0c4b378261158b0bf5e5bc67e7721 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Thu, 31 Jan 2019 15:28:44 +0100 Subject: [PATCH 0249/5331] More cosmetic cleanups --- .../easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb index 2e5db791432..bee2d58d1f1 100644 --- a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb +++ b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb @@ -14,10 +14,10 @@ toolchain = {'name': 'foss', 'version': '2018b'} # So we download the file from the source and copy it to the build directory. sources = [{ -'source_urls': ['http://popgen.dk/software/download/NGSadmix/'], -'filename': 'ngsadmix32.cpp', -'download_filename': 'ngsadmix32.cpp', -'extract_cmd': 'cp %s %(builddir)s', + 'source_urls': ['http://popgen.dk/software/download/NGSadmix/'], + 'filename': 'ngsadmix32.cpp', + 'download_filename': 'ngsadmix32.cpp', + 'extract_cmd': 'cp %s %(builddir)s', }] checksums = ['a5623b71d20114708cfd7ccc5f8c6ce38ff871d1b79af85bc89d38775f2d477e'] @@ -32,6 +32,6 @@ sanity_check_paths = { 'dirs': [''], } -modextrapaths = { 'PATH': ''} +modextrapaths = {'PATH': ''} moduleclass = 'bio' From 8952e29acf7fdf89eb48b29c551e3bc5b3e6c6e7 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 1 Feb 2019 09:41:20 +0100 Subject: [PATCH 0250/5331] PyQtGraph 0.10.0 for Python-3.6.4-intel-2018a --- ...QtGraph-0.10.0-intel-2018a-Python-3.6.4.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2018a-Python-3.6.4.eb diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..7b68b3d1c4a --- /dev/null +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyQtGraph' +version = '0.10.0' + +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pyqtgraph.org/' +description = """PyQtGraph is a pure-python graphics and GUI library built on PyQt4/PySide and numpy.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.pyqtgraph.org/downloads/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c74597dd87c31987099bd0949a5207e5d58297bd8a663279562ca1cb334074fc'] + +dependencies = [ + ('Python', '3.6.4'), + ('PyQt5', '5.9.2', versionsuffix), +] + +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' From b94c9196956f6cd3ce2954316a604124ab193cf6 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Fri, 1 Feb 2019 11:25:46 +0100 Subject: [PATCH 0251/5331] More cosmetic cleanups --- .../easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb index bee2d58d1f1..9539af13a2d 100644 --- a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb +++ b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb @@ -14,10 +14,10 @@ toolchain = {'name': 'foss', 'version': '2018b'} # So we download the file from the source and copy it to the build directory. sources = [{ - 'source_urls': ['http://popgen.dk/software/download/NGSadmix/'], - 'filename': 'ngsadmix32.cpp', - 'download_filename': 'ngsadmix32.cpp', - 'extract_cmd': 'cp %s %(builddir)s', + 'source_urls': ['http://popgen.dk/software/download/NGSadmix/'], + 'filename': 'ngsadmix32.cpp', + 'download_filename': 'ngsadmix32.cpp', + 'extract_cmd': 'cp %s %(builddir)s', }] checksums = ['a5623b71d20114708cfd7ccc5f8c6ce38ff871d1b79af85bc89d38775f2d477e'] From 63ea68d48423693f2516791f101f5ae78e95549c Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Fri, 1 Feb 2019 17:53:04 +0200 Subject: [PATCH 0252/5331] added checksum and style-cleanup --- .../t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb index ef9143d53c2..611578980a5 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2018a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [] +checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] dependencies = [('Python', '3.6.4')] sanity_check_paths = { @@ -21,4 +21,3 @@ sanity_check_paths = { } moduleclass = 'math' - From 1ef2bdb97b95a403cf91081bf9ac3bbe3d9dd1b8 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Fri, 1 Feb 2019 18:08:19 +0200 Subject: [PATCH 0253/5331] adding easyconfigs: mkl-dnn-0.17.2-foss-2018a.eb --- .../m/mkl-dnn/mkl-dnn-0.17.2-foss-2018a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/mkl-dnn/mkl-dnn-0.17.2-foss-2018a.eb diff --git a/easybuild/easyconfigs/m/mkl-dnn/mkl-dnn-0.17.2-foss-2018a.eb b/easybuild/easyconfigs/m/mkl-dnn/mkl-dnn-0.17.2-foss-2018a.eb new file mode 100644 index 00000000000..e1de398550e --- /dev/null +++ b/easybuild/easyconfigs/m/mkl-dnn/mkl-dnn-0.17.2-foss-2018a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'mkl-dnn' +version = "0.17.2" + +homepage = 'https://01.org/mkl-dnn' +description = "Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN)" + +toolchain = {'name': 'foss', 'version': '2018a'} +source_urls = [ + 'https://github.com/01org/mkl-dnn/archive/', + 'https://github.com/intel/mkl-dnn/releases/download/v%(version)s', + 'https://github.com/intel/mkl-dnn/archive/', +] + +mklml_extract_cmd = "mkdir %(builddir)s/mkl-dnn-%(version)s/external/ && " +mklml_extract_cmd += "tar xvfz %s -C %(builddir)s/mkl-dnn-%(version)s/external/" +sources = [ + 'v%(version)s.tar.gz', + # mkl-dnn requires Intel MKL, so download minimal Intel MKL version + # actually using imkl as a dependency would be messy due to underlying icc/ifort compilers & impi MPI lib + {'filename': 'mklml_lnx_2019.0.1.20181227.tgz', 'extract_cmd': mklml_extract_cmd}, +] +checksums = ['56c3e22d4fad816059cc58fd8e78ab3bacbec76a6bbded7eaead66220d8e5134', + '0a8b39dd63494b1c5f55ef0eb7cd9a4f8cc3bcba09177b20a078c2b47e00f677'] + +builddependencies = [('CMake', '3.11.4')] + +separate_build_dir = True + +configopts = "-DFAIL_WITHOUT_MKL=1" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['include/mkldnn.h', 'include/mkldnn.hpp', 'include/mkldnn_types.h', 'lib/libmkldnn.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 310c2fb585764ef08a8f0bf6e5de22e0406047bb Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Fri, 1 Feb 2019 18:41:51 +0200 Subject: [PATCH 0254/5331] missing checksum --- easybuild/easyconfigs/f/FUSE/FUSE-3.4.1-foss-2018a.eb | 6 ++++-- .../m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb | 4 ++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.4.1-foss-2018a.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.4.1-foss-2018a.eb index 6b04d4be168..af16b58223a 100644 --- a/easybuild/easyconfigs/f/FUSE/FUSE-3.4.1-foss-2018a.eb +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.4.1-foss-2018a.eb @@ -19,10 +19,12 @@ builddependencies = [ ('Ninja', '1.8.2'), ] -configopts = '-Dutils=false' +# -Dutils=True only works as root +configopts = '-Dutils=False' sanity_check_paths = { - 'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT, 'lib64/pkgconfig/fuse%(version_major)s.pc'], + 'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT, + 'lib64/pkgconfig/fuse%(version_major)s.pc'], 'dirs': ['include/fuse%(version_major)s'], } diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb index 1c0c6a24f86..d4a975ad33a 100644 --- a/easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2018a'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = [] +checksums = ['ef893e2d64083463fe41f05d683edbe8c44bc187cd9cc66cbc2b1ce399567447'] dependencies = [ ('Python', '3.6.4'), ('Ninja', '1.8.2'), @@ -24,4 +24,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' From 51227d3884b7cc4d8f8d5888240e24a42587df73 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Feb 2019 10:46:38 -0600 Subject: [PATCH 0255/5331] Remove xbitmaps dep - now in X11 --- easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb index 66ee66896ca..b9d8b0d9c74 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb @@ -17,11 +17,11 @@ checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] dependencies = [ ('X11', '20171023'), ('libpng', '1.6.32'), - ('xbitmaps', '1.1.1', '', True), ('freetype', '2.8'), ('libjpeg-turbo', '1.5.2'), ('bzip2', '1.0.6'), ] + builddependencies = [ ('Autotools', '20170619'), ('flex', '2.6.4'), From 5499c2ccdb120dbe9775b2505d4f79e83f03205e Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Feb 2019 11:50:44 -0600 Subject: [PATCH 0256/5331] Fix order --- .../easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb index b9d8b0d9c74..280eb352e95 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2017b.eb @@ -14,6 +14,13 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] +builddependencies = [ + ('Autotools', '20170619'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('util-linux', '2.31'), +] + dependencies = [ ('X11', '20171023'), ('libpng', '1.6.32'), @@ -22,13 +29,6 @@ dependencies = [ ('bzip2', '1.0.6'), ] -builddependencies = [ - ('Autotools', '20170619'), - ('flex', '2.6.4'), - ('Bison', '3.0.4'), - ('util-linux', '2.31'), -] - # makefile is not parallel safe parallel = 1 From e29bdab787282a5d7e66a552ca1de89b7a6f1dd7 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Feb 2019 13:30:19 -0600 Subject: [PATCH 0257/5331] Removed xbitmaps now in X11 bundle --- .../m/motif/motif-2.3.7-intel-2017a.eb | 17 +++++++++-------- .../m/motif/motif-2.3.8-foss-2018a.eb | 14 +++++++------- .../m/motif/motif-2.3.8-foss-2018b.eb | 14 +++++++------- .../m/motif/motif-2.3.8-intel-2017b.eb | 14 +++++++------- .../m/motif/motif-2.3.8-intel-2018a.eb | 14 +++++++------- 5 files changed, 37 insertions(+), 36 deletions(-) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb index e0ba802b63e..3d4a1e232c2 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.7-intel-2017a.eb @@ -10,23 +10,24 @@ description = """Motif refers to both a graphical user interface (GUI) specifica toolchain = {'name': 'intel', 'version': '2017a'} -sources = ['%(name)s-%(version)s.tar.gz'] source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['8f7aadbb0f42df2093d4690735a2b9a02ea2bf69dfb15ae0a39cae28f1580d14'] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('util-linux', '2.29.2'), +] dependencies = [ ('X11', '20170314'), ('libpng', '1.6.29'), - ('xbitmaps', '1.1.1', '', True), ('freetype', '2.7.1', '-libpng-1.6.29'), ('libjpeg-turbo', '1.5.1'), ('bzip2', '1.0.6'), ] -builddependencies = [ - ('Autotools', '20150215'), - ('flex', '2.6.4'), - ('Bison', '3.0.4'), - ('util-linux', '2.29.2'), -] # makefile is not parallel safe parallel = 1 diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2018a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2018a.eb index 56749ea138d..88b16e88e27 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2018a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2018a.eb @@ -14,20 +14,20 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] +builddependencies = [ + ('Autotools', '20170619'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('util-linux', '2.31.1'), +] + dependencies = [ ('X11', '20180131'), ('libpng', '1.6.34'), - ('xbitmaps', '1.1.1', '', True), ('freetype', '2.9'), ('libjpeg-turbo', '1.5.3'), ('bzip2', '1.0.6'), ] -builddependencies = [ - ('Autotools', '20170619'), - ('flex', '2.6.4'), - ('Bison', '3.0.4'), - ('util-linux', '2.31.1'), -] # makefile is not parallel safe parallel = 1 diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2018b.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2018b.eb index 4fbe0ec2e88..a63267619e6 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2018b.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-foss-2018b.eb @@ -14,20 +14,20 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] +builddependencies = [ + ('Autotools', '20180311'), + ('flex', '2.6.4'), + ('Bison', '3.0.5'), + ('util-linux', '2.32'), +] + dependencies = [ ('X11', '20180604'), ('libpng', '1.6.34'), - ('xbitmaps', '1.1.2', '', True), ('freetype', '2.9.1'), ('libjpeg-turbo', '2.0.0'), ('bzip2', '1.0.6'), ] -builddependencies = [ - ('Autotools', '20180311'), - ('flex', '2.6.4'), - ('Bison', '3.0.5'), - ('util-linux', '2.32'), -] # makefile is not parallel safe parallel = 1 diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-intel-2017b.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-intel-2017b.eb index 2c5d6bf6070..a016139d901 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.8-intel-2017b.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-intel-2017b.eb @@ -14,20 +14,20 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] +builddependencies = [ + ('Autotools', '20170619'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('util-linux', '2.31'), +] + dependencies = [ ('X11', '20171023'), ('libpng', '1.6.32'), - ('xbitmaps', '1.1.1', '', True), ('freetype', '2.8'), ('libjpeg-turbo', '1.5.2'), ('bzip2', '1.0.6'), ] -builddependencies = [ - ('Autotools', '20170619'), - ('flex', '2.6.4'), - ('Bison', '3.0.4'), - ('util-linux', '2.31'), -] # makefile is not parallel safe parallel = 1 diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-intel-2018a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-intel-2018a.eb index ea608c2f398..2551d184d4a 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.8-intel-2018a.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-intel-2018a.eb @@ -14,20 +14,20 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] +builddependencies = [ + ('Autotools', '20170619'), + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('util-linux', '2.31.1'), +] + dependencies = [ ('X11', '20180131'), ('libpng', '1.6.34'), - ('xbitmaps', '1.1.1', '', True), ('freetype', '2.9'), ('libjpeg-turbo', '1.5.3'), ('bzip2', '1.0.6'), ] -builddependencies = [ - ('Autotools', '20170619'), - ('flex', '2.6.4'), - ('Bison', '3.0.4'), - ('util-linux', '2.31.1'), -] # makefile is not parallel safe parallel = 1 From 4448746d59cde395d9189b77eb8aaca60984a171 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 1 Feb 2019 18:19:25 -0600 Subject: [PATCH 0258/5331] adding easyconfigs: ABySS-2.0.3-foss-2017b.eb, ABySS-2.0.3-intel-2017b.eb and patches: abyss-2.0.3-BranchGroup.patch --- .../a/ABySS/ABySS-2.0.3-foss-2017b.eb | 27 ++++++++++++++++ .../a/ABySS/ABySS-2.0.3-intel-2017b.eb | 31 +++++++++++++++++++ .../a/ABySS/abyss-2.0.3-BranchGroup.patch | 19 ++++++++++++ 3 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-foss-2017b.eb create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-intel-2017b.eb create mode 100644 easybuild/easyconfigs/a/ABySS/abyss-2.0.3-BranchGroup.patch diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-foss-2017b.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-foss-2017b.eb new file mode 100644 index 00000000000..e7ed674a076 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-foss-2017b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '2.0.3' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ff4cb9c9f78e443cc5b613dbc1f949f3eba699e78f090e73f0fefe1b99d85d55'] + +dependencies = [ + ('Boost', '1.65.1'), + ('sparsehash', '2.0.3'), + ('SQLite', '3.20.1'), +] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-intel-2017b.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-intel-2017b.eb new file mode 100644 index 00000000000..25bf5095c24 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-intel-2017b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '2.0.3' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['abyss-2.0.3-BranchGroup.patch'] +checksums = [ + 'ff4cb9c9f78e443cc5b613dbc1f949f3eba699e78f090e73f0fefe1b99d85d55', # abyss-2.0.3.tar.gz + '6dac7c5641693b26e393cb43cb6d49d97fced32e6f44d0c3e50d4e223222f08d', # abyss-2.0.3-BranchGroup.patch +] + +dependencies = [ + ('Boost', '1.65.1'), + ('sparsehash', '2.0.3'), + ('SQLite', '3.20.1'), +] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ABySS/abyss-2.0.3-BranchGroup.patch b/easybuild/easyconfigs/a/ABySS/abyss-2.0.3-BranchGroup.patch new file mode 100644 index 00000000000..322b39ba047 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/abyss-2.0.3-BranchGroup.patch @@ -0,0 +1,19 @@ +The function of swap causes Intel compiler to give an error. However, because this is a pure +"assert(false)" function which indicates we can safely comment it out. See the following link: + +https://github.com/bcgsc/abyss/issues/230 + +--- abyss-2.0.3.ori/Assembly/BranchGroup.h 2019-02-01 17:55:35.908138170 -0600 ++++ abyss-2.0.3/Assembly/BranchGroup.h 2019-02-01 17:55:59.978654627 -0600 +@@ -209,9 +209,11 @@ + BranchGroupStatus m_status; + }; + ++/* + namespace std { + template <> + inline void swap(BranchGroup&, BranchGroup&) { assert(false); } + } ++*/ + + #endif From 4d649480f4da1e5c246fff07e84130105c3694a2 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 1 Feb 2019 17:53:18 +0100 Subject: [PATCH 0259/5331] SLATEC/4.1 for GCCcore/6.4.0 and intel/2018a --- .../s/SLATEC/SLATEC-4.1-GCCcore-6.4.0.eb | 40 +++++++++++++++++++ .../s/SLATEC/SLATEC-4.1-intel-2018a.eb | 36 +++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-intel-2018a.eb diff --git a/easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..90ba2bfce3e --- /dev/null +++ b/easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-GCCcore-6.4.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SLATEC' +version = '4.1' + +homepage = 'http://www.netlib.org/slatec/' +description = """SLATEC Common Mathematical Library, a comprehensive software library containing + over 1400 general purpose mathematical and statistical routines written in Fortran 77.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +sources = [{ + 'source_urls': ['http://www.netlib.org/%(namelower)s'], + 'filename': '%(namelower)s_src.tgz', + 'extract_cmd': 'tar xfvz %s', +}, { + 'source_urls': ['http://www.netlib.org/%(namelower)s'], + 'filename': '%(namelower)s4linux.tgz', + 'extract_cmd': 'tar xfvz %s -C src', +}] +checksums = [ + 'df009d9ef9c18aae06ce68711b1ae108d3533b4f174582c3cbea0915c4fdfe01', # slatec_src.tgz + 'eef9234f8fcb49e7f4905a11eda8f453ec2ca314029a9ce303fdbc99cff42bf3', # slatec4linux.tgz +] + +builddependencies = [ + ('binutils', '2.28') +] + +skipsteps = ['configure'] + +preinstallopts = "sed -i 's+/usr/local+%(installdir)s+; s+ldconfig;++' makefile &&" +preinstallopts += "mkdir -p %(installdir)s/lib %(installdir)s/man/man1 &&" + +sanity_check_paths = { + 'files': ['lib/libslatec.a', 'lib/libslatec.%s' % SHLIB_EXT], + 'dirs': ['lib', 'man/man1'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-intel-2018a.eb b/easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-intel-2018a.eb new file mode 100644 index 00000000000..dcf65ee1afd --- /dev/null +++ b/easybuild/easyconfigs/s/SLATEC/SLATEC-4.1-intel-2018a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'SLATEC' +version = '4.1' + +homepage = 'http://www.netlib.org/slatec/' +description = """SLATEC Common Mathematical Library, a comprehensive software library containing + over 1400 general purpose mathematical and statistical routines written in Fortran 77.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +sources = [{ + 'source_urls': ['http://www.netlib.org/%(namelower)s'], + 'filename': '%(namelower)s_src.tgz', + 'extract_cmd': 'tar xfvz %s', +}, { + 'source_urls': ['http://www.netlib.org/%(namelower)s'], + 'filename': '%(namelower)s4linux.tgz', + 'extract_cmd': 'tar xfvz %s -C src', +}] +checksums = [ + 'df009d9ef9c18aae06ce68711b1ae108d3533b4f174582c3cbea0915c4fdfe01', # slatec_src.tgz + 'eef9234f8fcb49e7f4905a11eda8f453ec2ca314029a9ce303fdbc99cff42bf3', # slatec4linux.tgz +] + +skipsteps = ['configure'] + +preinstallopts = "sed -i 's+/usr/local+%(installdir)s+; s+ldconfig;++' makefile &&" +preinstallopts += "mkdir -p %(installdir)s/lib %(installdir)s/man/man1 &&" + +sanity_check_paths = { + 'files': ['lib/libslatec.a', 'lib/libslatec.%s' % SHLIB_EXT], + 'dirs': ['lib', 'man/man1'] +} + +moduleclass = 'math' From a126e5e23740da16b45163269c624c46050a7da4 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 4 Feb 2019 11:54:59 +0100 Subject: [PATCH 0260/5331] adding easyconfigs: GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb --- .../GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..f5d791c3249 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/broadinstitute/gatk/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8495bfbf08fd24756b70ccafcfcf5bfdbc0603bfa5493ed0b8f812b8d545c0e7'] + +dependencies = [ + ('Python', '3.6.6'), + ('Java', '1.8', '', True), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = ["gatk --help"] + +moduleclass = 'bio' From b6fc1876b8548203a81c74cd3952ef36b07aa50a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 4 Feb 2019 12:24:49 +0100 Subject: [PATCH 0261/5331] adding easyconfigs: STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb --- ...TAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..03765f06118 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'STAR-Fusion' +version = '1.5.0' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://github.com/STAR-Fusion/STAR-Fusion' +description = """STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts + supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner + to map junction reads and spanning reads to a reference annotation set.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/STAR-Fusion/STAR-Fusion/releases/download/%(name)s-v%(version)s/'] +sources = ['%(name)s-v%(version)s.FULL.tar.gz'] +checksums = ['229cbf7980496d72de0bfab5bde7148ff3111a99b72c6169d1a04120a52508b4'] + +dependencies = [ + ('Perl', '5.28.0'), + ('STAR', '2.6.1c'), +] + +# these are the perl libraries dependencies +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('Set::IntervalTree', '0.10', { + 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/'], + 'checksums': ['e3bd9ccf0d074b5f879eef1ed88254983697bf83d02744fce62150ee46553ebc'], + }), + ('DB_File', '1.843', { + 'source_tmpl': 'DB_File-1.843.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], + 'checksums': ['de24e3d1e56b1b56c1f143590fb8ab8b812ebd9697e9c01349b0ba11c36f346a'], + }), +] + +modextrapaths = { + 'PATH': "", # add installation dir to PATH + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' +} + +sanity_check_paths = { + 'files': ['STAR-Fusion'], + 'dirs': [] +} + +moduleclass = 'bio' From bec7d64e6881c9fbb7ae56671518a44c417d971e Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Mon, 4 Feb 2019 13:57:18 +0100 Subject: [PATCH 0262/5331] Backported patches from 4.0 version --- .../OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb | 8 +- .../OpenMPI-3.1.3-backported_patches.patch | 253 ++++++++++++++++++ ....3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 8 +- 3 files changed, 267 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-backported_patches.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb index c06f2819628..f4764748be0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb @@ -10,7 +10,13 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d'] + +patches = [ '%(name)s-%(version)s-backported_patches.patch'] + +checksums = [ + '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz + '6268e34ae8c322e2a784ec3b92e8df34a3074463066c43382b3eaf248f0f17f6', # OpenMPI-3.1.3-backported_patches.eb +] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-backported_patches.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-backported_patches.patch new file mode 100644 index 00000000000..31548326d12 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-backported_patches.patch @@ -0,0 +1,253 @@ +diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.c openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx.c +--- openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.c 2018-10-29 22:31:25.000000000 +0100 ++++ openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx.c 2018-11-23 10:38:12.000000000 +0100 +@@ -14,6 +14,7 @@ + + #include "opal/runtime/opal.h" + #include "opal/mca/pmix/pmix.h" ++#include "ompi/attribute/attribute.h" + #include "ompi/message/message.h" + #include "ompi/mca/pml/base/pml_base_bsend.h" + #include "pml_ucx_request.h" +@@ -187,9 +188,9 @@ + int mca_pml_ucx_init(void) + { + ucp_worker_params_t params; +- ucs_status_t status; + ucp_worker_attr_t attr; +- int rc; ++ ucs_status_t status; ++ int i, rc; + + PML_UCX_VERBOSE(1, "mca_pml_ucx_init"); + +@@ -206,30 +207,34 @@ + &ompi_pml_ucx.ucp_worker); + if (UCS_OK != status) { + PML_UCX_ERROR("Failed to create UCP worker"); +- return OMPI_ERROR; ++ rc = OMPI_ERROR; ++ goto err; + } + + attr.field_mask = UCP_WORKER_ATTR_FIELD_THREAD_MODE; + status = ucp_worker_query(ompi_pml_ucx.ucp_worker, &attr); + if (UCS_OK != status) { +- ucp_worker_destroy(ompi_pml_ucx.ucp_worker); +- ompi_pml_ucx.ucp_worker = NULL; + PML_UCX_ERROR("Failed to query UCP worker thread level"); +- return OMPI_ERROR; ++ rc = OMPI_ERROR; ++ goto err_destroy_worker; + } + +- if (ompi_mpi_thread_multiple && attr.thread_mode != UCS_THREAD_MODE_MULTI) { ++ if (ompi_mpi_thread_multiple && (attr.thread_mode != UCS_THREAD_MODE_MULTI)) { + /* UCX does not support multithreading, disqualify current PML for now */ + /* TODO: we should let OMPI to fallback to THREAD_SINGLE mode */ +- ucp_worker_destroy(ompi_pml_ucx.ucp_worker); +- ompi_pml_ucx.ucp_worker = NULL; + PML_UCX_ERROR("UCP worker does not support MPI_THREAD_MULTIPLE"); +- return OMPI_ERROR; ++ rc = OMPI_ERR_NOT_SUPPORTED; ++ goto err_destroy_worker; + } + + rc = mca_pml_ucx_send_worker_address(); + if (rc < 0) { +- return rc; ++ goto err_destroy_worker; ++ } ++ ++ ompi_pml_ucx.datatype_attr_keyval = MPI_KEYVAL_INVALID; ++ for (i = 0; i < OMPI_DATATYPE_MAX_PREDEFINED; ++i) { ++ ompi_pml_ucx.predefined_types[i] = PML_UCX_DATATYPE_INVALID; + } + + /* Initialize the free lists */ +@@ -245,15 +250,34 @@ + PML_UCX_VERBOSE(2, "created ucp context %p, worker %p", + (void *)ompi_pml_ucx.ucp_context, + (void *)ompi_pml_ucx.ucp_worker); +- return OMPI_SUCCESS; ++ return rc; ++ ++err_destroy_worker: ++ ucp_worker_destroy(ompi_pml_ucx.ucp_worker); ++ ompi_pml_ucx.ucp_worker = NULL; ++err: ++ return OMPI_ERROR; + } + + int mca_pml_ucx_cleanup(void) + { ++ int i; ++ + PML_UCX_VERBOSE(1, "mca_pml_ucx_cleanup"); + + opal_progress_unregister(mca_pml_ucx_progress); + ++ if (ompi_pml_ucx.datatype_attr_keyval != MPI_KEYVAL_INVALID) { ++ ompi_attr_free_keyval(TYPE_ATTR, &ompi_pml_ucx.datatype_attr_keyval, false); ++ } ++ ++ for (i = 0; i < OMPI_DATATYPE_MAX_PREDEFINED; ++i) { ++ if (ompi_pml_ucx.predefined_types[i] != PML_UCX_DATATYPE_INVALID) { ++ ucp_dt_destroy(ompi_pml_ucx.predefined_types[i]); ++ ompi_pml_ucx.predefined_types[i] = PML_UCX_DATATYPE_INVALID; ++ } ++ } ++ + ompi_pml_ucx.completed_send_req.req_state = OMPI_REQUEST_INVALID; + OMPI_REQUEST_FINI(&ompi_pml_ucx.completed_send_req); + OBJ_DESTRUCT(&ompi_pml_ucx.completed_send_req); +@@ -452,6 +476,22 @@ + + int mca_pml_ucx_enable(bool enable) + { ++ ompi_attribute_fn_ptr_union_t copy_fn; ++ ompi_attribute_fn_ptr_union_t del_fn; ++ int ret; ++ ++ /* Create a key for adding custom attributes to datatypes */ ++ copy_fn.attr_datatype_copy_fn = ++ (MPI_Type_internal_copy_attr_function*)MPI_TYPE_NULL_COPY_FN; ++ del_fn.attr_datatype_delete_fn = mca_pml_ucx_datatype_attr_del_fn; ++ ret = ompi_attr_create_keyval(TYPE_ATTR, copy_fn, del_fn, ++ &ompi_pml_ucx.datatype_attr_keyval, NULL, 0, ++ NULL); ++ if (ret != OMPI_SUCCESS) { ++ PML_UCX_ERROR("Failed to create keyval for UCX datatypes: %d", ret); ++ return ret; ++ } ++ + PML_UCX_FREELIST_INIT(&ompi_pml_ucx.persistent_reqs, + mca_pml_ucx_persistent_request_t, + 128, -1, 128); +diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.h openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx.h +--- openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.h 2018-10-29 22:31:25.000000000 +0100 ++++ openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx.h 2018-11-23 10:36:28.000000000 +0100 +@@ -15,6 +15,7 @@ + #include "ompi/mca/pml/pml.h" + #include "ompi/mca/pml/base/base.h" + #include "ompi/datatype/ompi_datatype.h" ++#include "ompi/datatype/ompi_datatype_internal.h" + #include "ompi/communicator/communicator.h" + #include "ompi/request/request.h" + +@@ -37,6 +38,10 @@ + ucp_context_h ucp_context; + ucp_worker_h ucp_worker; + ++ /* Datatypes */ ++ int datatype_attr_keyval; ++ ucp_datatype_t predefined_types[OMPI_DATATYPE_MPI_MAX_PREDEFINED]; ++ + /* Requests */ + mca_pml_ucx_freelist_t persistent_reqs; + ompi_request_t completed_send_req; +diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx_datatype.c +--- openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c 2018-10-29 22:31:25.000000000 +0100 ++++ openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx_datatype.c 2018-11-23 10:36:28.000000000 +0100 +@@ -10,6 +10,7 @@ + #include "pml_ucx_datatype.h" + + #include "ompi/runtime/mpiruntime.h" ++#include "ompi/attribute/attribute.h" + + #include + +@@ -127,12 +128,25 @@ + .finish = pml_ucx_generic_datatype_finish + }; + ++int mca_pml_ucx_datatype_attr_del_fn(ompi_datatype_t* datatype, int keyval, ++ void *attr_val, void *extra) ++{ ++ ucp_datatype_t ucp_datatype = (ucp_datatype_t)attr_val; ++ ++ PML_UCX_ASSERT((void*)ucp_datatype == datatype->pml_data); ++ ++ ucp_dt_destroy(ucp_datatype); ++ datatype->pml_data = PML_UCX_DATATYPE_INVALID; ++ return OMPI_SUCCESS; ++} ++ + ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + { + ucp_datatype_t ucp_datatype; + ucs_status_t status; + ptrdiff_t lb; + size_t size; ++ int ret; + + ompi_datatype_type_lb(datatype, &lb); + +@@ -147,16 +161,33 @@ + } + + status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, +- datatype, &ucp_datatype); ++ datatype, &ucp_datatype); + if (status != UCS_OK) { + PML_UCX_ERROR("Failed to create UCX datatype for %s", datatype->name); + ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); + } + ++ datatype->pml_data = ucp_datatype; ++ ++ /* Add custom attribute, to clean up UCX resources when OMPI datatype is ++ * released. ++ */ ++ if (ompi_datatype_is_predefined(datatype)) { ++ PML_UCX_ASSERT(datatype->id < OMPI_DATATYPE_MAX_PREDEFINED); ++ ompi_pml_ucx.predefined_types[datatype->id] = ucp_datatype; ++ } else { ++ ret = ompi_attr_set_c(TYPE_ATTR, datatype, &datatype->d_keyhash, ++ ompi_pml_ucx.datatype_attr_keyval, ++ (void*)ucp_datatype, false); ++ if (ret != OMPI_SUCCESS) { ++ PML_UCX_ERROR("Failed to add UCX datatype attribute for %s: %d", ++ datatype->name, ret); ++ ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); ++ } ++ } ++ + PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) +- // TODO put this on a list to be destroyed later + +- datatype->pml_data = ucp_datatype; + return ucp_datatype; + } + +diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx_datatype.h +--- openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h 2018-10-29 22:31:25.000000000 +0100 ++++ openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx_datatype.h 2018-11-23 10:36:28.000000000 +0100 +@@ -13,6 +13,8 @@ + #include "pml_ucx.h" + + ++#define PML_UCX_DATATYPE_INVALID 0 ++ + struct pml_ucx_convertor { + opal_free_list_item_t super; + ompi_datatype_t *datatype; +@@ -23,6 +25,9 @@ + + ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype); + ++int mca_pml_ucx_datatype_attr_del_fn(ompi_datatype_t* datatype, int keyval, ++ void *attr_val, void *extra); ++ + OBJ_CLASS_DECLARATION(mca_pml_ucx_convertor_t); + + +@@ -30,7 +35,7 @@ + { + ucp_datatype_t ucp_type = datatype->pml_data; + +- if (OPAL_LIKELY(ucp_type != 0)) { ++ if (OPAL_LIKELY(ucp_type != PML_UCX_DATATYPE_INVALID)) { + return ucp_type; + } + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 5e1ef486427..e7be0c75e5a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -10,7 +10,13 @@ toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d'] + +patches = [ '%(name)s-%(version)s-backported_patches.patch'] + +checksums = [ + '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz + '6268e34ae8c322e2a784ec3b92e8df34a3074463066c43382b3eaf248f0f17f6', # OpenMPI-3.1.3-backported_patches.eb +] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] From 4c7319b4564cb8197628de1ba37a4d30c0800948 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 4 Feb 2019 14:17:43 +0100 Subject: [PATCH 0263/5331] use binary instead of source code --- .../g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb index f5d791c3249..d559c597928 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb @@ -29,9 +29,9 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['https://github.com/broadinstitute/gatk/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['8495bfbf08fd24756b70ccafcfcf5bfdbc0603bfa5493ed0b8f812b8d545c0e7'] +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['148aa061328d922a570d0120d88f27e61e5da877f542206f4d77f2d788b7d21d'] dependencies = [ ('Python', '3.6.6'), From 7e200a580dc121655485ff2b0cd0d9779d276a9e Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Mon, 4 Feb 2019 15:16:10 +0100 Subject: [PATCH 0264/5331] fix code style --- .../easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb | 6 +++--- .../OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb index f4764748be0..86e25747a22 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb @@ -11,11 +11,11 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = [ '%(name)s-%(version)s-backported_patches.patch'] +patches = ['%(name)s-%(version)s-backported_patches.patch'] checksums = [ - '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz - '6268e34ae8c322e2a784ec3b92e8df34a3074463066c43382b3eaf248f0f17f6', # OpenMPI-3.1.3-backported_patches.eb + '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz + '6268e34ae8c322e2a784ec3b92e8df34a3074463066c43382b3eaf248f0f17f6', # OpenMPI-3.1.3-backported_patches.eb ] # needed for --with-verbs diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index e7be0c75e5a..409d0b5cc11 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -11,11 +11,11 @@ toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = [ '%(name)s-%(version)s-backported_patches.patch'] +patches = ['%(name)s-%(version)s-backported_patches.patch'] checksums = [ - '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz - '6268e34ae8c322e2a784ec3b92e8df34a3074463066c43382b3eaf248f0f17f6', # OpenMPI-3.1.3-backported_patches.eb + '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz + '6268e34ae8c322e2a784ec3b92e8df34a3074463066c43382b3eaf248f0f17f6', # OpenMPI-3.1.3-backported_patches.eb ] # needed for --with-verbs From 27ee7465a3659794996992ba32e4e84a49df3b24 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 4 Feb 2019 18:43:19 +0000 Subject: [PATCH 0265/5331] {vis}[foss/2018b,intel/2018b] Mesa-18.1.1: add patch to detect MIT-SHM Query MIT-SHM before using it, to avoid issues with MobaXterm/Xming. See also patch submitted upstream here: https://gitlab.freedesktop.org/mesa/mesa/merge_requests/200 --- .../m/Mesa/Mesa-18.1.1-foss-2018b.eb | 6 ++++- .../m/Mesa/Mesa-18.1.1-intel-2018b.eb | 6 ++++- .../m/Mesa/Mesa-18.1.1-query-mit-shm.patch | 23 +++++++++++++++++++ 3 files changed, 33 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-query-mit-shm.patch diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb index eb6e1817da2..70518053e65 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb @@ -28,10 +28,14 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] sources = [SOURCELOWER_TAR_XZ] -patches = ['Mesa-17.3.6_fix-strip-llvm-flags.patch'] +patches = [ + 'Mesa-17.3.6_fix-strip-llvm-flags.patch', + 'Mesa-18.1.1-query-mit-shm.patch', +] checksums = [ 'd3312a2ede5aac14a47476b208b8e3a401367838330197c4588ab8ad420d7781', # mesa-18.1.1.tar.xz '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.3.6_fix-strip-llvm-flags.patch + 'a9df2759758318d917debbfcc2cb15f6525b3dce41bd1e481d16e2eaa592a24e', # Mesa-18.1.1-query-mit-shm.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-intel-2018b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-intel-2018b.eb index 7fd276dfe7c..70d6d337b34 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-intel-2018b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-intel-2018b.eb @@ -28,10 +28,14 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] sources = [SOURCELOWER_TAR_XZ] -patches = ['Mesa-17.3.6_fix-strip-llvm-flags.patch'] +patches = [ + 'Mesa-17.3.6_fix-strip-llvm-flags.patch', + 'Mesa-18.1.1-query-mit-shm.patch', +] checksums = [ 'd3312a2ede5aac14a47476b208b8e3a401367838330197c4588ab8ad420d7781', # mesa-18.1.1.tar.xz '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.3.6_fix-strip-llvm-flags.patch + 'a9df2759758318d917debbfcc2cb15f6525b3dce41bd1e481d16e2eaa592a24e', # Mesa-18.1.1-query-mit-shm.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-query-mit-shm.patch b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-query-mit-shm.patch new file mode 100644 index 00000000000..771bb3b722b --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-query-mit-shm.patch @@ -0,0 +1,23 @@ +#Query MIT-SHM before using it, to avoid issues with MobaXterm/Xming. +#https://gitlab.freedesktop.org/mesa/mesa/merge_requests/200 +# Bart Oldeman Feb 4, 2019 +--- mesa-18.3.1/src/gallium/winsys/sw/xlib/xlib_sw_winsys.c~ 2018-12-11 21:13:57.000000000 +0000 ++++ mesa-18.3.1/src/gallium/winsys/sw/xlib/xlib_sw_winsys.c 2019-02-03 02:33:35.354730123 +0000 +@@ -396,6 +396,7 @@ + { + struct xlib_displaytarget *xlib_dt; + unsigned nblocksy, size; ++ int ignore; + + xlib_dt = CALLOC_STRUCT(xlib_displaytarget); + if (!xlib_dt) +@@ -410,7 +411,8 @@ + xlib_dt->stride = align(util_format_get_stride(format, width), alignment); + size = xlib_dt->stride * nblocksy; + +- if (!debug_get_option_xlib_no_shm()) { ++ if (!debug_get_option_xlib_no_shm() && ++ XQueryExtension(xlib_dt->display, "MIT-SHM", &ignore, &ignore, &ignore)) { + xlib_dt->data = alloc_shm(xlib_dt, size); + if (xlib_dt->data) { + xlib_dt->shm = True; From 6335d93b978545d82ae31ba2edd2722c836fde0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 5 Feb 2019 07:53:20 +0100 Subject: [PATCH 0266/5331] switch to GCCcore toolchain --- .../{ncdu-1.13-foss-2018b.eb => ncdu-1.13-GCCcore-7.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/n/ncdu/{ncdu-1.13-foss-2018b.eb => ncdu-1.13-GCCcore-7.3.0.eb} (95%) diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.13-foss-2018b.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.13-GCCcore-7.3.0.eb similarity index 95% rename from easybuild/easyconfigs/n/ncdu/ncdu-1.13-foss-2018b.eb rename to easybuild/easyconfigs/n/ncdu/ncdu-1.13-GCCcore-7.3.0.eb index 90807c35030..999c72802e2 100644 --- a/easybuild/easyconfigs/n/ncdu/ncdu-1.13-foss-2018b.eb +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.13-GCCcore-7.3.0.eb @@ -11,7 +11,7 @@ description = """Ncdu is a disk usage analyzer with an ncurses interface. It is desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed.""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = ['https://dev.yorhel.nl/download/'] sources = [SOURCE_TAR_GZ] From bf123b2d6e1320deff247dac0b0c067827550ccb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 5 Feb 2019 08:56:22 +0100 Subject: [PATCH 0267/5331] add binutils as build dependency --- easybuild/easyconfigs/n/ncdu/ncdu-1.13-GCCcore-7.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.13-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.13-GCCcore-7.3.0.eb index 999c72802e2..900b3a8011a 100644 --- a/easybuild/easyconfigs/n/ncdu/ncdu-1.13-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.13-GCCcore-7.3.0.eb @@ -21,6 +21,8 @@ checksums = [ '70a75350f362bf54e3738de5c198da8fa1b5d2ce59c54419668a5143eb6aa424', # ncdu-1.13_large-file-counts.patch ] +builddependencies = [('binutils', '2.30')] + dependencies = [('ncurses', '6.1')] sanity_check_paths = { From 410fe89de57e2e2a7d0282fae321ca796a86d9b6 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Tue, 5 Feb 2019 11:34:51 +0100 Subject: [PATCH 0268/5331] adding easyconfigs: Java-1.9.0.4.eb --- easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb b/easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb new file mode 100644 index 00000000000..9e03a5e8f56 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb @@ -0,0 +1,19 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +name = 'Java' +version = '1.9.0.4' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from +# http://www.oracle.com/technetwork/java/javase/downloads/index.html +altver = version.split('.',1)[1] +sources = ['jdk-%s_linux-x64_bin.tar.gz' % altver] +checksums = ['90c4ea877e816e3440862cfa36341bc87d05373d53389ec0f2d54d4e8c95daa2'] + +moduleclass = 'lang' From 2e80032cd4f5a075867c9b386810d6072f708661 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Tue, 5 Feb 2019 12:00:31 +0100 Subject: [PATCH 0269/5331] Some cosmetics like white spaces done --- easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb b/easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb index 9e03a5e8f56..ce860f4a217 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # download the tar.gz directly from # http://www.oracle.com/technetwork/java/javase/downloads/index.html -altver = version.split('.',1)[1] +altver = version.split('.', 1)[1] sources = ['jdk-%s_linux-x64_bin.tar.gz' % altver] checksums = ['90c4ea877e816e3440862cfa36341bc87d05373d53389ec0f2d54d4e8c95daa2'] From b57834f0b28ff99ac6637d00e3dd395966310740 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 5 Feb 2019 14:42:37 +0100 Subject: [PATCH 0270/5331] adding easyconfigs: BLAST+-2.8.1-foss-2018b.eb --- .../b/BLAST+/BLAST+-2.8.1-foss-2018b.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.8.1-foss-2018b.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.8.1-foss-2018b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.8.1-foss-2018b.eb new file mode 100644 index 00000000000..100287a5e15 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.8.1-foss-2018b.eb @@ -0,0 +1,51 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.8.1' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['e03dd1a30e37cb8a859d3788a452c5d70ee1f9102d1ee0f93b2fbd145925118f'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('PCRE', '8.41'), + ('Boost', '1.67.0'), + ('GMP', '6.1.2'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '2.0.0'), + ('LMDB', '0.9.22'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' From 5d0e785eae4050ec1f66ed99d235c866ef6a2f7c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 5 Feb 2019 09:21:24 +0100 Subject: [PATCH 0271/5331] adding easyconfigs: HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb --- .../HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..5bb33ab8a40 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonPackage' + +name = 'HTSeq' +version = '0.11.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www-huber.embl.de/users/anders/%(name)s/' +description = "A framework to process and analyze data from high-throughput sequencing (HTS) assays" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +checksums = ['65c4c13968506c7df92e97124df96fdd041c4476c12a548d67350ba8b436bcfc'] + +builddependencies = [('SWIG', '3.0.12', versionsuffix)] + +dependencies = [ + ('Pysam', '0.15.1', versionsuffix), + ('Python', '3.6.6'), + ('matplotlib', '3.0.0', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg'], +} + +sanity_check_commands = ['%(namelower)s-count --help'] + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' From 483d0bd33f1223a16aef599e71135a4ec37b3807 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 5 Feb 2019 15:07:36 +0100 Subject: [PATCH 0272/5331] adding easyconfigs: scikit-learn-0.20.2-foss-2018b-Python-3.6.6.eb --- ...it-learn-0.20.2-foss-2018b-Python-3.6.6.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-3.6.6.eb new file mode 100755 index 00000000000..192a4e462ce --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.20.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['bc5bc7c7ee2572a1edcb51698a6caf11fae554194aaab9a38105d9ec419f29e6'] + +dependencies = [ + ('Python', '3.6.6'), + ('matplotlib', '3.0.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' From b22fd965782ce9816cca9b72cffb04dea8611390 Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Tue, 5 Feb 2019 17:57:34 +0200 Subject: [PATCH 0273/5331] adding easyconfigs: Ploticus-2.42-GCCcore-7.3.0.eb and patches: Ploticus-2.42-fix-makefile.patch --- .../p/Ploticus/Ploticus-2.42-GCCcore-7.3.0.eb | 35 +++++++++++++++++++ .../Ploticus/Ploticus-2.42-fix-makefile.patch | 34 ++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-fix-makefile.patch diff --git a/easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..090cbf43c55 --- /dev/null +++ b/easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-GCCcore-7.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Ploticus' +version = '2.42' + +homepage = 'http://ploticus.sourceforge.net/doc/welcome.html' +description = """Ploticus is a free GPL software utility that can produce various types of plots and graphs""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s%s_src.tar.gz' % version.replace('.', '')] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + '3f29e4b9f405203a93efec900e5816d9e1b4381821881e241c08cab7dd66e0b0', # ploticus242_src.tar.gz + '56f7e9914c76a3401ff5dbfdb24617ee507db9ddfbecc90e19790a3ec8efc1be', # Ploticus-2.42-fix-makefile.patch +] + +start_dir = 'src' + +buildopts = 'INSTALLDIR=%(installdir)s plpng' + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.34') +] + +files_to_copy = [(['pl'], 'bin'), 'prefabs'] + +sanity_check_paths = { + 'files': ['bin/pl'], + 'dirs': ['prefabs'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-fix-makefile.patch b/easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-fix-makefile.patch new file mode 100644 index 00000000000..415197ca965 --- /dev/null +++ b/easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-fix-makefile.patch @@ -0,0 +1,34 @@ +# Use EB values in Makefile +# wpoely86@gmail.com +diff -ur ploticus242/src/Makefile ploticus242.new/src/Makefile +--- ploticus242/src/Makefile 2013-06-07 19:05:43.000000000 +0200 ++++ ploticus242.new/src/Makefile 2019-02-05 16:47:23.430213501 +0100 +@@ -7,7 +7,7 @@ + + + # defaults.. +-CC = gcc ++CC := $(CC) + PLATFORM = UNIX + RMCOM = rm -f + NOX11 = -DNOX11 +@@ -92,8 +92,8 @@ + + ########### Option 1: use bundled GD16 (PNG only). Requires libpng and zlib. + exetarget: plpng +-GD16LIBS = -lpng -lz +-GD16H = -I/usr/local/include ++GD16LIBS = -L$(EBROOTLIBPNG)/lib -L$(EBROOTZLIB)/lib -lpng -lz ++GD16H = -I$(EBROOTLIBPNG)/include -I$(EBROOTZLIB)/include + ZFLAG = -DWZ + ### These should remain commented unless your libs are not in usual places, then alter to suit... + ### GD16LIBS = /home/scg/lib/libpng.a /home/scg/lib/libz.a +@@ -140,7 +140,7 @@ + + + #### If you do a "make install", where do you want the executable(s) to be moved to? +-INSTALLBIN = /usr/local/bin ++INSTALLBIN := $(INSTALLDIR) + + + #### For LOCALE support (non-roman alphabets & collation), uncomment the following.. From 2602c14a47c2d1a6d436816909fe5728be5de694 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Tue, 5 Feb 2019 17:28:26 +0100 Subject: [PATCH 0274/5331] adding easyconfigs: JUnit-4.12-Java-1.8.0_202.eb --- .../j/JUnit/JUnit-4.12-Java-1.8.0_202.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_202.eb diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_202.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_202.eb new file mode 100644 index 00000000000..ea0f123dd61 --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_202.eb @@ -0,0 +1,26 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'JAR' + +name = 'JUnit' +version = '4.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] +sources = ['%(namelower)s-%(version)s.jar'] +checksums = ['59721f0805e223d84b90677887d9ff567dc534d7c502ca903c0c2b17f05c116a'] + +dependencies = [('Java', '1.8.0_202')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' From 8e5b96e2b682d4db001d8f5564835c4a6b461010 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Tue, 5 Feb 2019 17:29:03 +0100 Subject: [PATCH 0275/5331] adding easyconfigs: ant-1.10.1-Java-1.8.0_202.eb --- .../a/ant/ant-1.10.1-Java-1.8.0_202.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_202.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_202.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_202.eb new file mode 100644 index 00000000000..ce1c6d73ca9 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_202.eb @@ -0,0 +1,30 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +name = 'ant' +version = '1.10.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +checksums = ['68f7ced0aa15d1f9f672f23d67c86deaf728e9576936313cfbff4f7a0e6ce382'] + +dependencies = [('Java', '1.8.0_202')] + +builddependencies = [('JUnit', '4.12', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 846a9958f15ea89822fc0e13852d9d83c5fe9c9a Mon Sep 17 00:00:00 2001 From: sassmaj Date: Tue, 5 Feb 2019 17:29:48 +0100 Subject: [PATCH 0276/5331] adding easyconfigs: ImageJ-1.51a.eb --- .../easyconfigs/i/ImageJ/ImageJ-1.51a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb new file mode 100644 index 00000000000..c01cfb1dbdb --- /dev/null +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb @@ -0,0 +1,32 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'PackedBinary' + +name = 'ImageJ' +version = '1.51a' + +homepage = 'https://imagej.nih.gov/ij' +description = "Image Processing and Analysis in Java" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://imagej.nih.gov/ij/download/src/'] +sources = ['ij%(version_major)s%(version_minor)s-src.zip'] + +dependencies = [ + ('Java', '1.8.0_202'), +] + +builddependencies = [('ant', '1.10.1', '-Java-%(javaver)s')] + +install_cmd = 'cd source && ant build && cp ij.jar %(installdir)s' + +sanity_check_paths = { + 'files': ['ij.jar'], + 'dirs': [], +} + +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar'\n" + +moduleclass = 'tools' From 2d2bc7e24173ce64f1432afcdea76c34f2a34c4e Mon Sep 17 00:00:00 2001 From: sassmaj Date: Tue, 5 Feb 2019 17:30:33 +0100 Subject: [PATCH 0277/5331] adding easyconfigs: Java-1.8.0_202.eb --- easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb new file mode 100644 index 00000000000..38430bf5120 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb @@ -0,0 +1,17 @@ +name = 'Java' +version = '1.8.0_202' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download the tar.gz directly from +# http://www.oracle.com/technetwork/java/javase/downloads/index.html +(vp, vs) = version.split('_') +altver = '%su%s' % (vp.split('.')[1], vs) +sources = ['jdk-%s-linux-x64.tar.gz' % altver] +checksums = ['9a5c32411a6a06e22b69c495b7975034409fa1652d03aeb8eb5b6f59fd4594e0'] + +moduleclass = 'lang' From 9d3e1af26dd80fdd0fe605aa0bc8aa1762d99f99 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Tue, 5 Feb 2019 17:33:18 +0100 Subject: [PATCH 0278/5331] Comment regarding author added --- easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb index 38430bf5120..0fbdf71c830 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb @@ -1,3 +1,6 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + name = 'Java' version = '1.8.0_202' From cdb4b2e2e42cce641a520a862825e410373b8e54 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 5 Feb 2019 20:28:51 +0100 Subject: [PATCH 0279/5331] Add binutils build dep --- easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-GCCcore-7.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-GCCcore-7.3.0.eb index 090cbf43c55..a1078a6b8a0 100644 --- a/easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/p/Ploticus/Ploticus-2.42-GCCcore-7.3.0.eb @@ -20,6 +20,8 @@ start_dir = 'src' buildopts = 'INSTALLDIR=%(installdir)s plpng' +builddependencies = [('binutils', '2.30')] + dependencies = [ ('zlib', '1.2.11'), ('libpng', '1.6.34') From 084f66fa6f5f44d783abfe4669cc3644c99b9329 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 5 Feb 2019 15:02:09 -0600 Subject: [PATCH 0280/5331] adding easyconfigs: MINC-2.4.03-foss-2017b.eb, MINC-2.4.03-intel-2017b.eb --- .../m/MINC/MINC-2.4.03-foss-2017b.eb | 31 +++++++++++++++++++ .../m/MINC/MINC-2.4.03-intel-2017b.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2017b.eb create mode 100644 easybuild/easyconfigs/m/MINC/MINC-2.4.03-intel-2017b.eb diff --git a/easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2017b.eb b/easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2017b.eb new file mode 100644 index 00000000000..aa63811a28e --- /dev/null +++ b/easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2017b.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MINC' +version = '2.4.03' + +homepage = 'https://github.com/BIC-MNI/libminc' +description = "Medical Image NetCDF or MINC isn't netCDF." + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/BIC-MNI/libminc/archive'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['138eded8a4958e2735178ce41e687af25d4c7a4127b67b853a40165d5d1962f5'] + +builddependencies = [ + ('CMake', '3.9.5'), +] +dependencies = [ + ('HDF5', '1.10.1'), + ('netCDF', '4.5.0'), + ('NIfTI', '2.0.0'), +] + +configopts = "-DLIBMINC_USE_SYSTEM_NIFTI=ON" + +sanity_check_paths = { + 'files': ['lib/libminc%(version_major)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MINC/MINC-2.4.03-intel-2017b.eb b/easybuild/easyconfigs/m/MINC/MINC-2.4.03-intel-2017b.eb new file mode 100644 index 00000000000..16828918e03 --- /dev/null +++ b/easybuild/easyconfigs/m/MINC/MINC-2.4.03-intel-2017b.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MINC' +version = '2.4.03' + +homepage = 'https://github.com/BIC-MNI/libminc' +description = "Medical Image NetCDF or MINC isn't netCDF." + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://github.com/BIC-MNI/libminc/archive'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['138eded8a4958e2735178ce41e687af25d4c7a4127b67b853a40165d5d1962f5'] + +builddependencies = [ + ('CMake', '3.9.5'), +] +dependencies = [ + ('HDF5', '1.10.1'), + ('netCDF', '4.5.0'), + ('NIfTI', '2.0.0'), +] + +configopts = "-DLIBMINC_USE_SYSTEM_NIFTI=ON" + +sanity_check_paths = { + 'files': ['lib/libminc%(version_major)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 8b27054920ed0eba48771fca0708f78fc9e39e02 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 5 Feb 2019 15:56:57 -0600 Subject: [PATCH 0281/5331] Add description --- easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2018a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2018a.eb b/easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2018a.eb index 8d90ff0c2b7..34058328495 100644 --- a/easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2018a.eb +++ b/easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2018a.eb @@ -4,7 +4,7 @@ name = 'MINC' version = '2.4.03' homepage = 'https://github.com/BIC-MNI/libminc' -description = "This is an example description." +description = "Medical Image NetCDF or MINC isn't netCDF." toolchain = {'name': 'foss', 'version': '2018a'} @@ -28,4 +28,4 @@ sanity_check_paths = { 'dirs': ['include'], } -moduleclass = 'lib' +moduleclass = 'lib' \ No newline at end of file From b5e02608c0180451eabc54f0488fab02292da2b7 Mon Sep 17 00:00:00 2001 From: HPC-uniOldenburg Date: Wed, 6 Feb 2019 11:23:28 +0100 Subject: [PATCH 0282/5331] adding easyconfigs: KNIME-3.6.2.eb --- easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb | 28 ++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb diff --git a/easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb b/easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb new file mode 100644 index 00000000000..f9a39e9fd5d --- /dev/null +++ b/easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'KNIME' +version = '3.6.2' + +homepage = 'https://www.knime.com/' + +description = """ +KNIME Analytics Platform is the open source software +for creating data science applications and services. +KNIME stands for KoNstanz Information MinEr. +""" + +source_urls = ['https://download.knime.org/analytics-platform/linux/'] +sources = ['%(namelower)s_%(version)s.linux.gtk.x86_64.tar.gz'] +checksums = ['78a44bb5d3d86ed7251181d2d25d3d93c297b652027c6884f66ba45e49025119'] + +toolchain = {'name': 'dummy', 'version': 'dummy'} +dependencies = [('Java', '1.8.0_172')] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['knime'], + 'dirs': ['p2'] +} + +moduleclass = 'bio' From d5006779d99408d4aebe590dbb6560ce7e91bdfb Mon Sep 17 00:00:00 2001 From: HPC-uniOldenburg Date: Wed, 6 Feb 2019 11:57:25 +0100 Subject: [PATCH 0283/5331] adding easyconfigs: Salmon-0.11.2-intel-2018a-Python-2.7.14.eb --- ...Salmon-0.11.2-intel-2018a-Python-2.7.14.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..8460f531e29 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '0.11.2' +versionsuffix = '-Python-2.7.14' + +toolchainopts = {'cstd': 'c++14'} + +homepage = 'https://github.com/COMBINE-lab/%(namelower)s' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'optarch': True, 'pic': True, 'openmp': True} + +source_urls = ['https://github.com/COMBINE-lab/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Salmon-%(version)s_Intel-compilers.patch'] +checksums = [ + 'bbdb70173be3c54d1bff8ab370efab74a7b6c45c509b83d28ae24f85da15b5ab', # v0.11.2.tar.gz + '420c248e0e494fa75ded42aae6218adf84fb6682d9a0a29a3dfb2ecf8b9113a9', # Salmon-0.11.2_Intel-compilers.patch +] + +builddependencies = [('CMake', '3.9.5', '', ('GCCcore', '6.4.0'))] + +dependencies = [ + ('Boost', '1.66.0', '', ('intel', '2018a')), + ('tbb', '2018_U3'), + ('Jellyfish', '2.2.10'), + ('bzip2', '1.0.6', '', ('GCCcore', '6.4.0')) +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' From 5185a058f6669342d47a529a7a99619bf86a36c3 Mon Sep 17 00:00:00 2001 From: HPC-uniOldenburg Date: Wed, 6 Feb 2019 12:48:02 +0100 Subject: [PATCH 0284/5331] Patch added --- .../Salmon-0.11.2_Intel-compilers.patch | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.11.2_Intel-compilers.patch diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2_Intel-compilers.patch b/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2_Intel-compilers.patch new file mode 100644 index 00000000000..7343498a474 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2_Intel-compilers.patch @@ -0,0 +1,31 @@ +--- CMakeLists.txt.orig 2018-08-28 10:48:05.642565702 +0200 ++++ CMakeLists.txt 2018-08-28 11:06:52.694742007 +0200 +@@ -187,6 +187,15 @@ + else() + set (PTHREAD_LIB "pthread") + endif() ++elseif ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Intel") ++ execute_process( ++ COMMAND ${CMAKE_CXX_COMPILER} -dumpversion OUTPUT_VARIABLE INTEL_VERSION) ++ set (INTEL TRUE) ++ set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static-libstdc++") ++ set (BOOST_TOOLSET "intel-linux") ++ set (BOOST_CONFIGURE_TOOLSET "--with-toolset=intel-linux") ++ set (BCXX_FLAGS "-std=c++14") ++ set (BOOST_EXTRA_FLAGS toolset=intel-linux cxxflags=${BCXX_FLAGS}) + else () + message(FATAL_ERROR "Your C++ compiler does not support C++14.") + endif () +--- include/atomicops.h.orig 2018-08-28 11:10:46.299480092 +0200 ++++ include/atomicops.h 2018-08-28 11:15:37.560437277 +0200 +@@ -82,8 +82,8 @@ + + } // end namespace moodycamel + +-#if (defined(AE_VCPP) && (_MSC_VER < 1700 || defined(__cplusplus_cli))) || \ +- defined(AE_ICC) ++#if (defined(AE_VCPP) && (_MSC_VER < 1700 || defined(__cplusplus_cli))) // || \ ++// defined(AE_ICC) + // VS2010 and ICC13 don't support std::atomic_*_fence, implement our own fences + + #include From 2e0621170e842fc299e488b2beb6c2bafca405eb Mon Sep 17 00:00:00 2001 From: sassmaj Date: Wed, 6 Feb 2019 13:21:55 +0100 Subject: [PATCH 0285/5331] adding easyconfigs: Maven-3.6.0.eb --- easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb | 23 ++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb b/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb new file mode 100644 index 00000000000..6647e33d6a1 --- /dev/null +++ b/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PackedBinary' + +name = 'Maven' +version = '3.6.0' + +homepage = 'http://maven.apache.org/index.html' +description = """Binary maven install, Apache Maven is a software project management and comprehension tool. Based on +the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a +central piece of information. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['apache-maven-%(version)s-bin.tar.gz'] +source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] +checksums = ['6a1b346af36a1f1a491c1c1a141667c5de69b42e6611d3687df26868bc0f4637'] + +sanity_check_paths = { + 'files': ['bin/mvn'], + 'dirs': [], +} + +moduleclass = 'devel' From 6a635dbfe874df13a671b0d7a345d637da9cc809 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Wed, 6 Feb 2019 13:25:51 +0100 Subject: [PATCH 0286/5331] Comment regarding author added --- easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb b/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb index 6647e33d6a1..069a173f79f 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb @@ -1,3 +1,6 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + easyblock = 'PackedBinary' name = 'Maven' From 60136d7b1a6e1f3cf6556af957bd1b1cec709827 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Wed, 6 Feb 2019 18:50:58 +0100 Subject: [PATCH 0287/5331] Java-wrapper added --- .../{JUnit-4.12-Java-1.8.0_202.eb => JUnit-4.12-Java-1.8.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/j/JUnit/{JUnit-4.12-Java-1.8.0_202.eb => JUnit-4.12-Java-1.8.eb} (83%) diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_202.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb similarity index 83% rename from easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_202.eb rename to easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb index ea0f123dd61..a98374886f7 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_202.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb @@ -16,7 +16,8 @@ source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(ver sources = ['%(namelower)s-%(version)s.jar'] checksums = ['59721f0805e223d84b90677887d9ff567dc534d7c502ca903c0c2b17f05c116a'] -dependencies = [('Java', '1.8.0_202')] +# specify dependency on Java/1.8 "wrapper", rather than a specific Java version +dependencies = [('Java', '1.8', '', True)] sanity_check_paths = { 'files': sources, From 97fcd5af6767c2d62aec200cf22d2cb0a20282da Mon Sep 17 00:00:00 2001 From: sassmaj Date: Wed, 6 Feb 2019 18:52:02 +0100 Subject: [PATCH 0288/5331] Java-wrapper added --- .../{ant-1.10.1-Java-1.8.0_202.eb => ant-1.10.1-Java-1.8.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/a/ant/{ant-1.10.1-Java-1.8.0_202.eb => ant-1.10.1-Java-1.8.eb} (88%) diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_202.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb similarity index 88% rename from easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_202.eb rename to easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb index ce1c6d73ca9..dc2a62675eb 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_202.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb @@ -16,7 +16,8 @@ source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] sources = ['apache-%(name)s-%(version)s-src.tar.gz'] checksums = ['68f7ced0aa15d1f9f672f23d67c86deaf728e9576936313cfbff4f7a0e6ce382'] -dependencies = [('Java', '1.8.0_202')] +# specify dependency on Java/1.8 "wrapper", rather than a specific Java version +dependencies = [('Java', '1.8', '', True)] builddependencies = [('JUnit', '4.12', versionsuffix)] From 99bb7809fc9a1c8413f35bed931eed305a7ca232 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Feb 2019 21:00:51 +0100 Subject: [PATCH 0289/5331] adding easyconfigs: SQLite-3.26.0-GCCcore-8.2.0.eb, Tcl-8.6.9-GCCcore-8.2.0.eb, libreadline-8.0-GCCcore-8.2.0.eb --- .../libreadline-8.0-GCCcore-8.2.0.eb | 43 ++++++++++++++++++ .../s/SQLite/SQLite-3.26.0-GCCcore-8.2.0.eb | 45 +++++++++++++++++++ .../t/Tcl/Tcl-8.6.9-GCCcore-8.2.0.eb | 45 +++++++++++++++++++ 3 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.26.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.9-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..4f68be0f053 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.0-GCCcore-8.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.0' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' + +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['e339f51971478d369f8a053a330a190781acb9864cf4c541060f12078948e461'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('ncurses', '6.1'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.26.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.26.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..7ba7c468641 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.26.0-GCCcore-8.2.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.26.0' + +homepage = 'http://www.sqlite.org/' + +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +source_urls = ['http://www.sqlite.org/2018/'] +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] +checksums = ['5daa6a3fb7d1e8c767cd59c4ded8da6e4b00c61d3b466d0685e35c4dd6d7bf5d'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('libreadline', '8.0'), + ('Tcl', '8.6.9'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.9-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.9-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..0b0415a8da8 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.9-GCCcore-8.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.9' + +homepage = 'http://www.tcl.tk/' + +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['ad0cd2de2c87b9ba8086b43957a0de3eb2eb565c7159d5f53ccbba3feb915f4e'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = [ + 'ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh' +] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' From 78b7aa71fad3586a08a2a86467bcc417b0b813e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Feb 2019 09:54:32 +0100 Subject: [PATCH 0290/5331] {bio}[intel/2018b] Trim_Galore v0.5.0, cutadapt v1.18 w/ Python 3.6.6 --- .../cutadapt-1.18-intel-2018b-Python-3.6.6.eb | 35 +++++++++++++++++++ ...m_Galore-0.5.0-intel-2018b-Python-3.6.6.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb create mode 100755 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..e5515ceeae8 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modufied by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS + +easyblock = 'PythonPackage' + +name = 'cutadapt' +version = '1.18' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['17aabf9b19d09a426d96030a83ad003c97b26dba9d45bf5570d33088fcd533f9'] + +dependencies = [ + ('Python', '3.6.6'), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb new file mode 100755 index 00000000000..54a9e8723f4 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'Trim_Galore' +version = '0.5.0' +versionsuffix = '-Python-3.6.6' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """A wrapper tool around Cutadapt and FastQC to consistently apply + quality and adapter trimming to FastQ files, with some extra functionality for + MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9a7966bcfdea5d8c4f14c669904fb44693ac5d9392caa4d49dd11254a0a6753d'] + +dependencies = [ + ('FastQC', '0.11.8', '-Java-1.8', True), + ('cutadapt', '1.18', versionsuffix), +] + +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s", +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' From 11e7acf3335e04a6fc8dbf7a37d0cd1935ba41ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Feb 2019 10:08:37 +0100 Subject: [PATCH 0291/5331] {lib}[intel/2018a] phonopy v2.0.0 w/ Python 2.7.14 --- ...phonopy-2.0.0-intel-2018a-Python-2.7.14.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-2.0.0-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.0.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.0.0-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..ec0fc78b950 --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.0.0-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '2.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://atztogo.github.io/phonopy/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['46baf7c4571fe75374071674727c2beb0388cf57073e0623d8457f04b1c54495'] + +dependencies = [ + ('Python', '2.7.14'), + ('matplotlib', '2.1.2', versionsuffix), + ('lxml', '4.2.0', versionsuffix), + ('PyYAML', '3.12', versionsuffix), + ('h5py', '2.7.1', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From a1ce8ec48fcf852fd2eae1f1b6acb5e48ce55f04 Mon Sep 17 00:00:00 2001 From: HPC-uniOldenburg Date: Thu, 7 Feb 2019 10:40:46 +0100 Subject: [PATCH 0292/5331] Style change and change to Java wrapper --- easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb b/easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb index f9a39e9fd5d..32355d287f7 100644 --- a/easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb +++ b/easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb @@ -11,12 +11,13 @@ for creating data science applications and services. KNIME stands for KoNstanz Information MinEr. """ +toolchain = {'name': 'dummy', 'version': 'dummy'} + source_urls = ['https://download.knime.org/analytics-platform/linux/'] sources = ['%(namelower)s_%(version)s.linux.gtk.x86_64.tar.gz'] checksums = ['78a44bb5d3d86ed7251181d2d25d3d93c297b652027c6884f66ba45e49025119'] -toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('Java', '1.8.0_172')] +dependencies = [('Java', '1.8')] modextrapaths = {'PATH': ''} From 3a49f9d9c55ad652f78dbba89dfaf74bef95f733 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Feb 2019 11:07:23 +0100 Subject: [PATCH 0293/5331] {math}[foss/2018b] NIMBLE v0.7.0 w/ R 3.5.1 --- .../NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb diff --git a/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb new file mode 100644 index 00000000000..eb15010718a --- /dev/null +++ b/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'NIMBLE' +version = '0.7.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://r-nimble.org' +description = """NIMBLE is a system for building and sharing analysis methods for statistical models, + especially for hierarchical models and computationally-intensive methods.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/nimble/', +] +sources = ['%(namelower)s_%(version)s.tar.gz'] +checksums = ['661a5bb626164c145ae9c5ba5c3d9c30b0ecc1b83d86eae25d83745324906f7e'] + +dependencies = [ + ('R', '3.5.1'), + ('Eigen', '3.3.7', '', True), +] + +installopts = '--configure-args="--enable-dylib=true --with-eigen=$EBROOTEIGEN/include" ' + +sanity_check_paths = { + 'files': ['nimble/CppCode/libnimble.%s' % SHLIB_EXT, 'nimble/libs/nimble.%s' % SHLIB_EXT], + 'dirs': [], +} + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'math' From bed158466359a870321b35249f95e2a5ad1e8d10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Feb 2019 11:58:13 +0100 Subject: [PATCH 0294/5331] Eigen is just a build dependency for NIMBLE --- .../n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb index eb15010718a..492ce96c1a9 100644 --- a/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb @@ -17,10 +17,9 @@ source_urls = [ sources = ['%(namelower)s_%(version)s.tar.gz'] checksums = ['661a5bb626164c145ae9c5ba5c3d9c30b0ecc1b83d86eae25d83745324906f7e'] -dependencies = [ - ('R', '3.5.1'), - ('Eigen', '3.3.7', '', True), -] +builddependencies = [('Eigen', '3.3.7', '', True)] + +dependencies = [('R', '3.5.1')] installopts = '--configure-args="--enable-dylib=true --with-eigen=$EBROOTEIGEN/include" ' From afc9e559b74879359497330ba7db3821fd471368 Mon Sep 17 00:00:00 2001 From: HPC-uniOldenburg Date: Thu, 7 Feb 2019 15:35:05 +0100 Subject: [PATCH 0295/5331] Added patch author, deleted subtoolchain, new checksum, add. minor changes --- .../s/Salmon/Salmon-0.11.2-intel-2018a.eb | 37 +++++++++++++++++++ .../Salmon-0.11.2_Intel-compilers.patch | 6 +++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a.eb diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a.eb new file mode 100644 index 00000000000..a44f90e0914 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '0.11.2' + +homepage = 'https://github.com/COMBINE-lab/%(namelower)s' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/COMBINE-lab/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Salmon-%(version)s_Intel-compilers.patch'] +checksums = [ + 'bbdb70173be3c54d1bff8ab370efab74a7b6c45c509b83d28ae24f85da15b5ab', # v0.11.2.tar.gz + '647cfda4ef4bd931be6f9a5b96f1980a3107efab210cfa8266ac84cbd62b1578', # Salmon-0.11.2_Intel-compilers.patch +] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('Boost', '1.66.0'), + ('tbb', '2018_U3'), + ('Jellyfish', '2.2.10'), + ('bzip2', '1.0.6') +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2_Intel-compilers.patch b/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2_Intel-compilers.patch index 7343498a474..5ee9696b12b 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2_Intel-compilers.patch +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2_Intel-compilers.patch @@ -1,3 +1,9 @@ +fix support for building Salmon 0.11.2 with Intel compilers +* fix detection of C++11-compatible compiler in CMakeLists.txt +* uncomment preprocessor directive that guard workaround for Intel compilers that is not required for recent versions +author: Kenneth Hoste (HPC-UGent) +adopted by Fynn Schwietzer (HPC-UniOldenburg) + --- CMakeLists.txt.orig 2018-08-28 10:48:05.642565702 +0200 +++ CMakeLists.txt 2018-08-28 11:06:52.694742007 +0200 @@ -187,6 +187,15 @@ From 56681a698d112a91b0f7bc4b3e3cd43884bd7a88 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 7 Feb 2019 15:35:26 +0100 Subject: [PATCH 0296/5331] adding easyconfigs: BlobTools-20180528-foss-2018b-Python-2.7.15.eb and patches: BlobTools-20180528_fix_deps.patch --- ...Tools-20180528-foss-2018b-Python-2.7.15.eb | 41 ++++++++++++++++ .../BlobTools-20180528_fix_deps.patch | 49 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/b/BlobTools/BlobTools-20180528_fix_deps.patch diff --git a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..4ce91976f69 --- /dev/null +++ b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,41 @@ +easyblock = 'CmdCp' + +name = 'BlobTools' +version = '20180528' +commit = 'a14630e' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://blobtools.readme.io/docs' +description = """ A modular command-line solution for visualisation, + quality control and taxonomic partitioning of genome datasets. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/drl/blobtools/archive/'] +sources = [{'download_filename': '%s.tar.gz' % commit, 'filename': SOURCE_TAR_GZ}] +patches = ['BlobTools-20180528_fix_deps.patch'] +checksums = [ + '316c22cceec6b6ac4e3751d06ec6effb88ea35d746abb957239c75e1f4eed9a9', # BlobTools-20180528.tar.gz + 'db0c4501303b0bf17f6cadeafbe109d3a2c4e34e029d4ea272e6a8d4287a50fd', # BlobTools-20180528_fix_deps.patch +] + +dependencies = [ + ('Python', '2.7.15'), + ('matplotlib','2.2.3', versionsuffix), + ('SAMtools', '1.9'), +] + +cmds_map = [('.*', './install')] + +files_to_copy = ['data', 'example', 'lib', 'blobtools'] + +modextrapaths = {'PATH': ''} + +sanity_check_commands = ['blobtools -h'] + +sanity_check_paths = { + 'files': ['blobtools', 'data/nodesDB.txt'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528_fix_deps.patch b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528_fix_deps.patch new file mode 100644 index 00000000000..f3f55c23445 --- /dev/null +++ b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528_fix_deps.patch @@ -0,0 +1,49 @@ +Don't install Python dependencies +Don't install SAMtools +Don't use self-installed SAMtools +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ur blobtools-master.orig/install blobtools-master/install +--- blobtools-master.orig/install 2018-05-29 15:39:21.000000000 +0200 ++++ blobtools-master/install 2019-01-29 16:31:54.613784312 +0100 +@@ -30,16 +30,6 @@ + exit + fi + fi +-# Install python dependencies +-echo "[+] Installing python dependencies..." +-$python setup.py install --quiet +-if [ $? -eq 0 ]; then +- echo "[+] Python dependencies installed." +- else +- echo "FAIL." +- echo "[X] - Python dependencies could not be installed. Make sure you are using Python 2.7 and have a functional installation of pip." +- exit +-fi + + # Create executable + echo -n "[+] Creating BlobTools executable..." +@@ -124,12 +114,6 @@ + fi + } + +-# install samtools +-samtools_tar=$DIR/samtools-1.5.tar.bz2 +-if [ ! -f "$samtools_tar" ]; then +- download_samtools +-fi +-install_samtools + + # get taxdump + taxdump=$DIR/data/taxdump.tar.gz +diff -ur blobtools-master.orig/lib/blobtools.py blobtools-master/lib/blobtools.py +--- blobtools-master.orig/lib/blobtools.py 2018-05-29 15:39:21.000000000 +0200 ++++ blobtools-master/lib/blobtools.py 2019-01-29 16:34:20.702264497 +0100 +@@ -45,7 +45,7 @@ + LIBDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '')) + MAINDIR = os.path.abspath(os.path.join(LIBDIR, '../')) + DATADIR = os.path.abspath(os.path.join(MAINDIR, 'data/')) +-SAMTOOLS = os.path.abspath(os.path.join(MAINDIR, 'samtools/bin/samtools')) ++SAMTOOLS = 'samtools' + + if __name__ == '__main__': + args = docopt(__doc__, From bd2e9ccb0fbd68c92662007c7370efe1bd185c5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Feb 2019 10:43:36 +0100 Subject: [PATCH 0297/5331] adding easyconfigs: VTune-2019_update2.eb --- .../easyconfigs/v/VTune/VTune-2019_update2.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2019_update2.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update2.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update2.eb new file mode 100644 index 00000000000..ec66a000137 --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update2.eb @@ -0,0 +1,19 @@ +name = 'VTune' +version = '2019_update2' + +homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vtune_amplifier_%(version)s.tar.gz'] +checksums = ['25a3d9af6cc630c6aabcd724b8faef2703b16e96e4731970ebed37cf6a2e9b16'] + +license_file = HOME + '/licenses/intel/license.lic' +# +# Use this configuration to use a license server: +# license_file = '12345@license.example.com' +# + +moduleclass = 'tools' From 7f6c8b64ff09e3e1bd1f2a69bb310058e62a13a2 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 8 Feb 2019 11:55:45 +0100 Subject: [PATCH 0298/5331] adding easyconfigs: CellRanger-3.0.2.eb --- .../c/CellRanger/CellRanger-3.0.2.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.2.eb diff --git a/easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.2.eb b/easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.2.eb new file mode 100644 index 00000000000..ff29a375024 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.2.eb @@ -0,0 +1,36 @@ +# The STAR binary included in this version has been vectorized with AVX +# hence it is not recommended for systems that do not support it. + +easyblock = 'Tarball' + +name = 'CellRanger' +version = '3.0.2' + +homepage = 'https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger' +description = """Cell Ranger is a set of analysis pipelines that process Chromium + single-cell RNA-seq output to align reads, generate gene-cell matrices and perform + clustering and gene expression analysis.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest +sources = [SOURCELOWER_TAR_GZ] +checksums = ['882c9170703f9c57c3e1970b0bd7d679f511683c65ce8c63fcad3fcb88733f38'] + +dependencies = [('Java', '1.8')] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ["cellranger", "cellranger-shell"], + 'dirs': ["cellranger-cs", "cellranger-tiny-fastq", "cellranger-tiny-ref", + "lz4", "martian-cs", "miniconda-cr-cs", "STAR"], +} + +modextrapaths = { + 'PATH': ['cellranger-cs/%(version)s/bin', 'STAR/5dda596'] +} + +tests = ['%(installdir)s/cellranger testrun --id=tiny'] + +moduleclass = 'bio' From f91c6279c2945df6405371dd301ff05850878956 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Fri, 8 Feb 2019 13:32:09 +0100 Subject: [PATCH 0299/5331] add missing space --- .../b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb index 4ce91976f69..eb5ac47669e 100644 --- a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb @@ -21,7 +21,7 @@ checksums = [ dependencies = [ ('Python', '2.7.15'), - ('matplotlib','2.2.3', versionsuffix), + ('matplotlib', '2.2.3', versionsuffix), ('SAMtools', '1.9'), ] From 6d64e21e413aff41b42e3966ca1e2ca90bb108db Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 8 Feb 2019 07:22:48 -0600 Subject: [PATCH 0300/5331] adding easyconfigs: lpsolve-5.5.2.5-foss-2017b.eb, lpsolve-5.5.2.5-intel-2017b.eb --- .../l/lpsolve/lpsolve-5.5.2.5-foss-2017b.eb | 33 +++++++++++++++++++ .../l/lpsolve/lpsolve-5.5.2.5-intel-2017b.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-foss-2017b.eb create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2017b.eb diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-foss-2017b.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-foss-2017b.eb new file mode 100644 index 00000000000..14982bb032a --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-foss-2017b.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.5' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a'] + +lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % lpsolve_ver + +comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +comp_cmd += "sh ccc" +cmds_map = [('.*', comp_cmd)] + +lpsolve_libname = 'liblpsolve%s' % lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % lpsolve_libname, 'bin/ux64/%s.%s' % (lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % lpsolve_libname, 'lib/%s.%s' % (lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2017b.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2017b.eb new file mode 100644 index 00000000000..14acb31fd93 --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2017b.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.5' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a'] + +lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % lpsolve_ver + +comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +comp_cmd += "sh ccc" +cmds_map = [('.*', comp_cmd)] + +lpsolve_libname = 'liblpsolve%s' % lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % lpsolve_libname, 'bin/ux64/%s.%s' % (lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % lpsolve_libname, 'lib/%s.%s' % (lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' From 94f0ae48beb6fb2844a249469339389f0ebb3f68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Feb 2019 15:56:25 +0100 Subject: [PATCH 0301/5331] adding easyconfigs: itac-2019.2.026.eb --- .../easyconfigs/i/itac/itac-2019.2.026.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/i/itac/itac-2019.2.026.eb diff --git a/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb b/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb new file mode 100644 index 00000000000..9249d901083 --- /dev/null +++ b/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb @@ -0,0 +1,21 @@ +name = 'itac' +version = '2019.2.026' + +homepage = 'http://software.intel.com/en-us/intel-trace-analyzer/' +description = """The Intel Trace Collector is a low-overhead tracing library that performs + event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application + activities gathered by the Intel Trace Collector through graphical displays. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_itac_p_%(version)s.tgz'] +checksums = ['c66890beaf6e81da0f2ecb9695059a6686c95f6f01f467e32a076eb84ca8e40e'] + +dontcreateinstalldir = 'True' + +preferredmpi = 'impi5' + +# license file +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' From 50b93b80d926e8be946af142aa1980afccebcdf2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Feb 2019 17:52:56 +0100 Subject: [PATCH 0302/5331] add 'asnipe' as extension to R 3.5.1 easyconfigs --- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 3 +++ easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index f1f876546a5..2573f954659 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -2063,6 +2063,9 @@ exts_list = [ ('bridgedist', '0.1.0', { 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], }), + ('asnipe', '1.1.11', { + 'checksums': ['982b9f34dbcf98136a8406b9ce4717faf155c7d5d923dcdf0dca6a9d53e27219'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 82241a05558..da852d607f8 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -2061,6 +2061,9 @@ exts_list = [ ('bridgedist', '0.1.0', { 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], }), + ('asnipe', '1.1.11', { + 'checksums': ['982b9f34dbcf98136a8406b9ce4717faf155c7d5d923dcdf0dca6a9d53e27219'], + }), ] moduleclass = 'lang' From 8b0d6433819790d64c8489adead5dc1d8878a04c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Feb 2019 21:27:42 +0100 Subject: [PATCH 0303/5331] adding easyconfigs: QuTiP-4.3.1-intel-2018b-Python-3.6.6.eb --- .../QuTiP-4.3.1-intel-2018b-Python-3.6.6.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuTiP/QuTiP-4.3.1-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/q/QuTiP/QuTiP-4.3.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/q/QuTiP/QuTiP-4.3.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..8d813807aa6 --- /dev/null +++ b/easybuild/easyconfigs/q/QuTiP/QuTiP-4.3.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'QuTiP' +version = '4.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://qutip.org' +description = "QuTiP is open-source software for simulating the dynamics of open quantum systems." + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e2d243a24b5b8577337cfc57fe1efbe12cb3f4a0d6e14c06aa9583dbe68d53f4'] + +dependencies = [ + ('Python', '3.6.6'), + ('matplotlib', '3.0.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'quantum' From 84cf3d25a3422219f25abb7e21ff53b10285206f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Feb 2019 20:48:49 +0100 Subject: [PATCH 0304/5331] verify QuTiP installation --- .../q/QuTiP/QuTiP-4.3.1-intel-2018b-Python-3.6.6.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/q/QuTiP/QuTiP-4.3.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/q/QuTiP/QuTiP-4.3.1-intel-2018b-Python-3.6.6.eb index 8d813807aa6..2ba443438c8 100644 --- a/easybuild/easyconfigs/q/QuTiP/QuTiP-4.3.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/q/QuTiP/QuTiP-4.3.1-intel-2018b-Python-3.6.6.eb @@ -26,4 +26,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +# verify installation (takes a while), +# see also http://qutip.org/docs/latest/installation.html#verifying-the-installation +sanity_check_commands = ["python -c 'import qutip.testing as qt; qt.run()'"] + moduleclass = 'quantum' From 76e09e073b6a119f1cced0bdd51b553a746a5812 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 10 Feb 2019 11:21:47 +0100 Subject: [PATCH 0305/5331] adding easyconfigs: MultiQC-1.7-foss-2018b-Python-3.6.6.eb --- .../MultiQC-1.7-foss-2018b-Python-3.6.6.eb | 107 ++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..c071cb07206 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,107 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('matplotlib', '3.0.0', versionsuffix), + ('PyYAML', '3.13', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('click', '7.0', { + 'source_tmpl': 'Click-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('simplejson', '3.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('networkx', '2.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], + 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], + }), + ('colormath', '3.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('certifi', '2018.11.29', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + }), + ('urllib3', '1.24.1', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('idna', '2.8', { + 'source_urls': ['https://pypi.io/packages/source/i/idna'], + 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], + }), + ('requests', '2.21.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], + }), + ('Markdown', '3.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], + 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], + }), + ('future', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], + 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], + }), + ('lzstring', '1.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('multiqc', version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], + 'checksums': ['02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +moduleclass = 'bio' From 9608dc16419438ddd02790a62fafe16644251200 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Feb 2019 12:49:57 +0100 Subject: [PATCH 0306/5331] Spyder 3.3.2 requires spyder-kernels < 1.0 --- .../s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb index 9d2024f4b17..f095dcaf11a 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-3.3.2-foss-2018b-Python-3.6.6.eb @@ -34,10 +34,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], 'checksums': ['f169a8523a40eb0a3452e1878aac31da6759409fbafa51dd50d89d4a6b42bcf1'], }), - ('spyder-kernels', '1.1.0', { + ('spyder-kernels', '0.4.2', { 'modulename': 'spyder_kernels', 'source_urls': ['https://pypi.python.org/packages/source/s/spyder-kernels'], - 'checksums': ['7e4d6a55e679757bdbae833f9fcdc4239f0086a8ba38439a252612cd113ac4fa'], + 'checksums': ['a13cefb569ef9f63814cb5fcf3d0db66e09d2d7e6cc68c703d5118b2d7ba062b'], }), ('QtPy', '1.5.2', { 'source_urls': ['https://pypi.python.org/packages/source/Q/QtPy'], From aedeeadb3d2b9d96894243dfa245bc51e83691bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Feb 2019 14:04:35 +0100 Subject: [PATCH 0307/5331] {quantum}[intel/2018b] ProjectQ v0.4.2 w/ Python 3.6.6 (+ deps) --- ...ProjectQ-0.4.2-intel-2018b-Python-3.6.6.eb | 53 +++++++++++++++++ ...pybind11-2.2.4-intel-2018b-Python-3.6.6.eb | 35 +++++++++++ .../pytest-3.8.2-intel-2018b-Python-3.6.6.eb | 58 +++++++++++++++++++ 3 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/p/ProjectQ/ProjectQ-0.4.2-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/ProjectQ/ProjectQ-0.4.2-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/ProjectQ/ProjectQ-0.4.2-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..f4d389c23d8 --- /dev/null +++ b/easybuild/easyconfigs/p/ProjectQ/ProjectQ-0.4.2-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'ProjectQ' +version = '0.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://projectq.ch' +description = "An open source software framework for quantum computing" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('networkx', '2.2', versionsuffix), + ('pybind11', '2.2.4', versionsuffix), + ('pytest', '3.8.2', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('future', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], + 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], + }), + ('py', '1.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + 'checksums': ['bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694'], + }), + ('pluggy', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + 'checksums': ['8ddc32f03971bfdf900a81961a48ccf2fb677cf7715108f85295c67405798616'], + }), + ('more-itertools', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + ('attrs', '18.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], + 'modulename': 'attr', + }), + ('atomicwrites', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], + }), + ('projectq', version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/projectq/'], + 'checksums': ['45a45fb51f6961754fee0cb2baabcc2969fa8c882b8288627a6bbdfe2f695717'], + }), +] + +moduleclass = 'quantum' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..2b717d25076 --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'pybind11' +version = '2.2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b69e83658513215b8d1443544d0549b7d231b9f201f6fc787a2b2218b408181e'] + +builddependencies = [ + ('CMake', '3.12.1'), + ('Eigen', '3.3.4', '', True), + ('pytest', '3.8.2', versionsuffix), +] +dependencies = [('Python', '3.6.6')] + +installopts = " && export PYBIND11_USE_CMAKE=1 && pip install --prefix %(installdir)s . " + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/pybind11', 'lib/python%(pyshortver)s/site-packages/pybind11', 'share/cmake/pybind11'], +} + +sanity_check_commands = ["python -c 'import pybind11'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..a3813148956 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-3.8.2-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '3.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [('Python', '3.6.6')] + +use_pip = True + +exts_list = [ + ('py', '1.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + 'checksums': ['bf92637198836372b520efcba9e020c330123be8ce527e535d185ed4b6f45694'], + }), + ('attrs', '18.2.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], + }), + ('pluggy', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + 'checksums': ['447ba94990e8014ee25ec853339faf7b0fc8050cdc3289d4d71f7f410fb90095'], + }), + ('atomicwrites', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + 'checksums': ['ec9ae8adaae229e4f8446952d204a3e4b5fdd2d099f9be3aaf556120135fb3ee'], + }), + ('more-itertools', '4.3.0', { + 'modulename': 'more_itertools', + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + 'checksums': ['c476b5d3a34e12d40130bc2f935028b5f636df8f372dc2c1c01dc19681b2039e'], + }), + ('scandir', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], + }), + ('pathlib2', '2.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + 'checksums': ['9332147e9af2dcf46cd7ceb14d5acadb6564744ddff1fe8c17f0ce60ece7d9a2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From f724532f3b56d5ace0328c1b795e366e003c271b Mon Sep 17 00:00:00 2001 From: murfreesboro Date: Mon, 11 Feb 2019 09:23:48 -0600 Subject: [PATCH 0308/5331] downgrade the foss to GCC 6.4 --- ...solve-5.5.2.5-foss-2017b.eb => lpsolve-5.5.2.5-GCC-6.4.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/lpsolve/{lpsolve-5.5.2.5-foss-2017b.eb => lpsolve-5.5.2.5-GCC-6.4.0.eb} (95%) diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-foss-2017b.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0.eb similarity index 95% rename from easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-foss-2017b.eb rename to easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0.eb index 14982bb032a..7d93b51bb92 100644 --- a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-foss-2017b.eb +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0.eb @@ -6,7 +6,7 @@ version = '5.5.2.5' homepage = 'https://sourceforge.net/projects/lpsolve/' description = "Mixed Integer Linear Programming (MILP) solver" -toolchain = {'name': 'foss', 'version': '2017b'} +toolchain = {'name': 'GCC', 'version': '6.4.0'} source_urls = [SOURCEFORGE_SOURCE] sources = ['lp_solve_%(version)s_source.tar.gz'] From f8de9b5035212175818a00434798fa154fad47b0 Mon Sep 17 00:00:00 2001 From: murfreesboro Date: Mon, 11 Feb 2019 09:29:51 -0600 Subject: [PATCH 0309/5331] downgrade the intel toolchain to iccifort --- ...eb => lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/lpsolve/{lpsolve-5.5.2.5-intel-2017b.eb => lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb} (92%) diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2017b.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb similarity index 92% rename from easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2017b.eb rename to easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 14acb31fd93..a63a3263953 100644 --- a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2017b.eb +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '5.5.2.5' homepage = 'https://sourceforge.net/projects/lpsolve/' description = "Mixed Integer Linear Programming (MILP) solver" -toolchain = {'name': 'intel', 'version': '2017b'} +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} source_urls = [SOURCEFORGE_SOURCE] sources = ['lp_solve_%(version)s_source.tar.gz'] From 25004ca9d5a6f4a56b043298af63b274e54bc291 Mon Sep 17 00:00:00 2001 From: murfreesboro Date: Mon, 11 Feb 2019 09:35:08 -0600 Subject: [PATCH 0310/5331] correct the mistypo in the GCC toolchain --- easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0.eb index 7d93b51bb92..bd7854d8b4d 100644 --- a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0.eb +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0.eb @@ -6,7 +6,7 @@ version = '5.5.2.5' homepage = 'https://sourceforge.net/projects/lpsolve/' description = "Mixed Integer Linear Programming (MILP) solver" -toolchain = {'name': 'GCC', 'version': '6.4.0'} +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = [SOURCEFORGE_SOURCE] sources = ['lp_solve_%(version)s_source.tar.gz'] From 6aa453e6f7a99bfd86d8121c7df18f698788f5c4 Mon Sep 17 00:00:00 2001 From: murfreesboro Date: Mon, 11 Feb 2019 09:36:22 -0600 Subject: [PATCH 0311/5331] also update the file name for GCC eb file --- ...lve-5.5.2.5-GCC-6.4.0.eb => lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/lpsolve/{lpsolve-5.5.2.5-GCC-6.4.0.eb => lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb} (100%) diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb similarity index 100% rename from easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0.eb rename to easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb From 22ac91fb16de238c935c67106dce2b15142888fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Feb 2019 17:40:23 +0100 Subject: [PATCH 0312/5331] adding easyconfigs: SHAPEIT-2.r904.glibcv2.17.eb --- .../s/SHAPEIT/SHAPEIT-2.r904.glibcv2.17.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r904.glibcv2.17.eb diff --git a/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r904.glibcv2.17.eb b/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r904.glibcv2.17.eb new file mode 100644 index 00000000000..9c8e01c0566 --- /dev/null +++ b/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r904.glibcv2.17.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'SHAPEIT' +version = '2.r904' +versionsuffix = '.glibcv2.17' + +homepage = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html' +description = """SHAPEIT is a fast and accurate method for estimation of +haplotypes (aka phasing) from genotype or sequencing data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] +sources = ['shapeit.v%(version)s%(versionsuffix)s.linux.tar.gz'] +checksums = ['a5c3445c82fa45b1fa604582f003a491ecce8de6316e210be831127da09ea9e6'] + +sanity_check_paths = { + 'files': ["bin/shapeit", "LICENCE"], + 'dirs': ["example"] +} + +moduleclass = 'bio' From 33718543523eb1f9767d3b818a060cea9bf7b08f Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Mon, 11 Feb 2019 20:50:03 +0100 Subject: [PATCH 0313/5331] Add header to patches --- .../OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb | 2 +- ...e_attribute_to_release_ucp_datatype.patch} | 94 +++++++++++++------ ....3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- 3 files changed, 69 insertions(+), 29 deletions(-) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-3.1.3-backported_patches.patch => OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch} (72%) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb index 86e25747a22..6bdef1e19cd 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb @@ -15,7 +15,7 @@ patches = ['%(name)s-%(version)s-backported_patches.patch'] checksums = [ '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz - '6268e34ae8c322e2a784ec3b92e8df34a3074463066c43382b3eaf248f0f17f6', # OpenMPI-3.1.3-backported_patches.eb + '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch ] # needed for --with-verbs diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-backported_patches.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch similarity index 72% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-backported_patches.patch rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch index 31548326d12..08041b82b19 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-backported_patches.patch +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch @@ -1,15 +1,30 @@ -diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.c openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx.c ---- openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.c 2018-10-29 22:31:25.000000000 +0100 -+++ openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx.c 2018-11-23 10:38:12.000000000 +0100 -@@ -14,6 +14,7 @@ +From 4763822a64c9002f24429aef95d87f6abfc45c06 Mon Sep 17 00:00:00 2001 +From: Yossi Itigin +Date: Tue, 9 Oct 2018 16:38:49 +0300 +Subject: [PATCH 1/2] pml_ucx: add ompi datatype attribute to release + ucp_datatype + +Signed-off-by: Yossi Itigin +--- + ompi/mca/pml/ucx/pml_ucx.c | 62 ++++++++++++++++++++++++----- + ompi/mca/pml/ucx/pml_ucx.h | 5 +++ + ompi/mca/pml/ucx/pml_ucx_datatype.c | 37 +++++++++++++++-- + ompi/mca/pml/ucx/pml_ucx_datatype.h | 7 +++- + 4 files changed, 96 insertions(+), 15 deletions(-) + +diff --git a/ompi/mca/pml/ucx/pml_ucx.c b/ompi/mca/pml/ucx/pml_ucx.c +index 1f37212c58f..d92ad5a58cb 100644 +--- a/ompi/mca/pml/ucx/pml_ucx.c ++++ b/ompi/mca/pml/ucx/pml_ucx.c +@@ -16,6 +16,7 @@ #include "opal/runtime/opal.h" #include "opal/mca/pmix/pmix.h" +#include "ompi/attribute/attribute.h" #include "ompi/message/message.h" #include "ompi/mca/pml/base/pml_base_bsend.h" - #include "pml_ucx_request.h" -@@ -187,9 +188,9 @@ + #include "opal/mca/common/ucx/common_ucx.h" +@@ -190,9 +191,9 @@ int mca_pml_ucx_close(void) int mca_pml_ucx_init(void) { ucp_worker_params_t params; @@ -21,7 +36,7 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.c openmpi-3.1.3/ompi/mca/p PML_UCX_VERBOSE(1, "mca_pml_ucx_init"); -@@ -206,30 +207,34 @@ +@@ -209,30 +210,34 @@ int mca_pml_ucx_init(void) &ompi_pml_ucx.ucp_worker); if (UCS_OK != status) { PML_UCX_ERROR("Failed to create UCP worker"); @@ -65,12 +80,10 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.c openmpi-3.1.3/ompi/mca/p } /* Initialize the free lists */ -@@ -245,15 +250,34 @@ - PML_UCX_VERBOSE(2, "created ucp context %p, worker %p", +@@ -249,14 +254,33 @@ int mca_pml_ucx_init(void) (void *)ompi_pml_ucx.ucp_context, (void *)ompi_pml_ucx.ucp_worker); -- return OMPI_SUCCESS; -+ return rc; + return OMPI_SUCCESS; + +err_destroy_worker: + ucp_worker_destroy(ompi_pml_ucx.ucp_worker); @@ -101,7 +114,7 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.c openmpi-3.1.3/ompi/mca/p ompi_pml_ucx.completed_send_req.req_state = OMPI_REQUEST_INVALID; OMPI_REQUEST_FINI(&ompi_pml_ucx.completed_send_req); OBJ_DESTRUCT(&ompi_pml_ucx.completed_send_req); -@@ -452,6 +476,22 @@ +@@ -398,6 +422,22 @@ int mca_pml_ucx_del_procs(struct ompi_proc_t **procs, size_t nprocs) int mca_pml_ucx_enable(bool enable) { @@ -124,9 +137,10 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.c openmpi-3.1.3/ompi/mca/p PML_UCX_FREELIST_INIT(&ompi_pml_ucx.persistent_reqs, mca_pml_ucx_persistent_request_t, 128, -1, 128); -diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.h openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx.h ---- openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.h 2018-10-29 22:31:25.000000000 +0100 -+++ openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx.h 2018-11-23 10:36:28.000000000 +0100 +diff --git a/ompi/mca/pml/ucx/pml_ucx.h b/ompi/mca/pml/ucx/pml_ucx.h +index da1b3ef0c57..484ad5ebe1c 100644 +--- a/ompi/mca/pml/ucx/pml_ucx.h ++++ b/ompi/mca/pml/ucx/pml_ucx.h @@ -15,6 +15,7 @@ #include "ompi/mca/pml/pml.h" #include "ompi/mca/pml/base/base.h" @@ -134,8 +148,8 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.h openmpi-3.1.3/ompi/mca/p +#include "ompi/datatype/ompi_datatype_internal.h" #include "ompi/communicator/communicator.h" #include "ompi/request/request.h" - -@@ -37,6 +38,10 @@ + #include "opal/mca/common/ucx/common_ucx.h" +@@ -42,6 +43,10 @@ struct mca_pml_ucx_module { ucp_context_h ucp_context; ucp_worker_h ucp_worker; @@ -146,9 +160,10 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx.h openmpi-3.1.3/ompi/mca/p /* Requests */ mca_pml_ucx_freelist_t persistent_reqs; ompi_request_t completed_send_req; -diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx_datatype.c ---- openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c 2018-10-29 22:31:25.000000000 +0100 -+++ openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx_datatype.c 2018-11-23 10:36:28.000000000 +0100 +diff --git a/ompi/mca/pml/ucx/pml_ucx_datatype.c b/ompi/mca/pml/ucx/pml_ucx_datatype.c +index 98b7b190df7..74b5fbe19c3 100644 +--- a/ompi/mca/pml/ucx/pml_ucx_datatype.c ++++ b/ompi/mca/pml/ucx/pml_ucx_datatype.c @@ -10,6 +10,7 @@ #include "pml_ucx_datatype.h" @@ -157,7 +172,7 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c openmpi-3.1.3/o #include -@@ -127,12 +128,25 @@ +@@ -127,12 +128,25 @@ static ucp_generic_dt_ops_t pml_ucx_generic_datatype_ops = { .finish = pml_ucx_generic_datatype_finish }; @@ -183,7 +198,7 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c openmpi-3.1.3/o ompi_datatype_type_lb(datatype, &lb); -@@ -147,16 +161,33 @@ +@@ -147,16 +161,33 @@ ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) } status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, @@ -220,9 +235,10 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c openmpi-3.1.3/o return ucp_datatype; } -diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx_datatype.h ---- openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h 2018-10-29 22:31:25.000000000 +0100 -+++ openmpi-3.1.3/ompi/mca/pml/ucx/pml_ucx_datatype.h 2018-11-23 10:36:28.000000000 +0100 +diff --git a/ompi/mca/pml/ucx/pml_ucx_datatype.h b/ompi/mca/pml/ucx/pml_ucx_datatype.h +index 26b1835a153..f5207cecc75 100644 +--- a/ompi/mca/pml/ucx/pml_ucx_datatype.h ++++ b/ompi/mca/pml/ucx/pml_ucx_datatype.h @@ -13,6 +13,8 @@ #include "pml_ucx.h" @@ -232,7 +248,7 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h openmpi-3.1.3/o struct pml_ucx_convertor { opal_free_list_item_t super; ompi_datatype_t *datatype; -@@ -23,6 +25,9 @@ +@@ -23,6 +25,9 @@ struct pml_ucx_convertor { ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype); @@ -242,7 +258,7 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h openmpi-3.1.3/o OBJ_CLASS_DECLARATION(mca_pml_ucx_convertor_t); -@@ -30,7 +35,7 @@ +@@ -30,7 +35,7 @@ static inline ucp_datatype_t mca_pml_ucx_get_datatype(ompi_datatype_t *datatype) { ucp_datatype_t ucp_type = datatype->pml_data; @@ -251,3 +267,27 @@ diff -Nur openmpi-3.1.3.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h openmpi-3.1.3/o return ucp_type; } + +From 40ac9e477165616ab98085e2d590dbbbe4874b9f Mon Sep 17 00:00:00 2001 +From: Yossi Itigin +Date: Wed, 10 Oct 2018 12:10:28 +0300 +Subject: [PATCH 2/2] pml_ucx: fix return code from mca_pml_ucx_init() + +Signed-off-by: Yossi Itigin +--- + ompi/mca/pml/ucx/pml_ucx.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/ompi/mca/pml/ucx/pml_ucx.c b/ompi/mca/pml/ucx/pml_ucx.c +index d92ad5a58cb..2e10a3b768c 100644 +--- a/ompi/mca/pml/ucx/pml_ucx.c ++++ b/ompi/mca/pml/ucx/pml_ucx.c +@@ -253,7 +253,7 @@ int mca_pml_ucx_init(void) + PML_UCX_VERBOSE(2, "created ucp context %p, worker %p", + (void *)ompi_pml_ucx.ucp_context, + (void *)ompi_pml_ucx.ucp_worker); +- return OMPI_SUCCESS; ++ return rc; + + err_destroy_worker: + ucp_worker_destroy(ompi_pml_ucx.ucp_worker); diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 409d0b5cc11..413f6c97c42 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -15,7 +15,7 @@ patches = ['%(name)s-%(version)s-backported_patches.patch'] checksums = [ '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz - '6268e34ae8c322e2a784ec3b92e8df34a3074463066c43382b3eaf248f0f17f6', # OpenMPI-3.1.3-backported_patches.eb + '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch ] # needed for --with-verbs From 64f952a2fa4c63c5f281eafcd4559430459b88a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 12 Feb 2019 07:29:22 +0100 Subject: [PATCH 0314/5331] adding easyconfigs: ChimPipe-0.9.5-foss-2018b.eb --- .../c/ChimPipe/ChimPipe-0.9.5-foss-2018b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/ChimPipe/ChimPipe-0.9.5-foss-2018b.eb diff --git a/easybuild/easyconfigs/c/ChimPipe/ChimPipe-0.9.5-foss-2018b.eb b/easybuild/easyconfigs/c/ChimPipe/ChimPipe-0.9.5-foss-2018b.eb new file mode 100644 index 00000000000..ed339f69d2e --- /dev/null +++ b/easybuild/easyconfigs/c/ChimPipe/ChimPipe-0.9.5-foss-2018b.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PackedBinary' + +name = 'ChimPipe' +version = '0.9.5' + +homepage = 'https://%(namelower)s.readthedocs.org/' +description = """ChimPipe is a computational method for the detection of novel transcription-induced + chimeric transcripts and fusion genes from Illumina Paired-End RNA-seq data. It combines junction + spanning and paired-end read information to accurately detect chimeric splice junctions at base-pair + resolution.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +github_account = 'Chimera-tools' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['0ab55a0a38dd86845334125459b3961e11e427564ed14b22185c9cc17467c000'] + +dependencies = [ + ('BEDTools', '2.27.1'), + ('SAMtools', '0.1.20'), + ('BLAST+', '2.8.1'), +] + +sanity_check_paths = { + 'files': ['%(name)s.sh', 'bin/gtfToGenePred'], + 'dirs': ['bin/gemtools-1.7.1-i3', 'src/awk', 'src/bash', 'tools'], +} + +moduleclass = 'bio' From 6c376600f028c2211e4e8bda2f250f24928e8593 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 12 Feb 2019 10:11:17 +0100 Subject: [PATCH 0315/5331] adding easyconfigs: Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb, Kraken-1.1-foss-2018b-Perl-5.28.0.eb, Jellyfish-1.1.12-foss-2018b.eb, libidn-1.35-GCCcore-7.3.0.eb, wget-1.20.1-GCCcore-7.3.0.eb and patches: Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch, Kraken-1.1_CXX-CXXFLAGS.patch --- .../Jellyfish/Jellyfish-1.1.12-foss-2018b.eb | 29 +++++++++++ .../Kraken-1.1-foss-2018b-Perl-5.28.0.eb | 48 +++++++++++++++++ .../k/Kraken/Kraken-1.1_CXX-CXXFLAGS.patch | 12 +++++ ...aken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb | 51 +++++++++++++++++++ .../Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch | 12 +++++ .../l/libidn/libidn-1.35-GCCcore-7.3.0.eb | 22 ++++++++ .../w/wget/wget-1.20.1-GCCcore-7.3.0.eb | 48 +++++++++++++++++ 7 files changed, 222 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.12-foss-2018b.eb create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken-1.1_CXX-CXXFLAGS.patch create mode 100644 easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb create mode 100644 easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.35-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.12-foss-2018b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.12-foss-2018b.eb new file mode 100644 index 00000000000..0acc34299ed --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.12-foss-2018b.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '1.1.12' + +homepage = 'http://www.cbcb.umd.edu/software/%(namelower)s/' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'foss', 'version': '2018b'} + +github_account = 'gmarcais' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['1ae32d3775e551272a757608671dc1d69d0659d253b174e393b6cb24f6a7e181'] + +builddependencies = [('Autotools', '20180311')] + +preconfigopts = "autoreconf -i && " + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..39ecfad1069 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PackedBinary' + +name = 'Kraken' +version = '1.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# Part is compiled with CXX, the rest is in Perl +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'openmp': True} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_CXX-CXXFLAGS.patch'] +checksums = [ + 'a4ac74c54c10920f431741c80d8a172670be12c3b352912000030fb5ea4c87a7', # v1.1.tar.gz + '84c017d6a80ccaac1e23561c83cac90bcc3d62baa8d31657a7dafbc2c3f29726', # Kraken-1.1_CXX-CXXFLAGS.patch +] + +dependencies = [ + ('Perl', '5.28.0'), + ('Jellyfish', '1.1.12'), + ('wget', '1.20.1', '-GCCcore-7.3.0', True), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_%(namelower)s.sh %(installdir)s' + +sanity_check_paths = { + 'files': ['add_to_library.sh', 'build_kraken_db.sh', 'check_for_jellyfish.sh', 'classify', 'clean_db.sh', + 'cp_into_tempfile.pl', 'db_shrink', 'db_sort', 'download_genomic_library.sh', + 'download_taxonomy.sh', 'kraken', 'kraken-build', 'kraken-filter', 'krakenlib.pm', + 'kraken-mpa-report', 'kraken-report', 'kraken-translate', 'make_seqid_to_taxid_map', + 'read_merger.pl', 'report_gi_numbers.pl', 'set_lcas', 'shrink_db.sh', + 'standard_installation.sh', 'upgrade_db.sh', 'verify_gi_numbers.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-1.1_CXX-CXXFLAGS.patch b/easybuild/easyconfigs/k/Kraken/Kraken-1.1_CXX-CXXFLAGS.patch new file mode 100644 index 00000000000..d07e8618c01 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken-1.1_CXX-CXXFLAGS.patch @@ -0,0 +1,12 @@ +tweak Makefile such that $CXX and $CXXFLAGS are picked up from the environment +B. Hajgato (Free University Brussels, VUB), Kenneth Hoste (HPC-UGent) +--- kraken-1.0/src/Makefile.orig 2018-05-04 11:37:07.631634957 +0200 ++++ kraken-1.0/src/Makefile 2018-05-04 11:38:07.013115388 +0200 +@@ -1,5 +1,5 @@ +-CXX = g++ +-CXXFLAGS = -Wall -fopenmp -O3 ++CXX ?= g++ ++CXXFLAGS ?= -Wall -fopenmp -O3 + PROGS = db_sort set_lcas classify make_seqid_to_taxid_map db_shrink kmer_estimator + + .PHONY: all install clean diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..91f1f9ee61f --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,51 @@ +easyblock = 'PackedBinary' + +name = 'Kraken2' +version = '2.0.7-beta' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.ccb.jhu.edu/software/%(namelower)s/' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# part is compiled with $CXX, the rest is in Perl +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_CXX-CXXFLAGS.patch'] +checksums = [ + 'baa160f5aef73327e1a79e6d1c54b64b2fcdaee0be31b456f7bc411d1897a744', # v2.0.7-beta.tar.gz + '191291e51a846d193a12486ab84496d5dd221a05c84648688b1351bb84d7adb2', # Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch +] + +dependencies = [ + ('Perl', '5.28.0'), + ('BLAST+', '2.8.1'), + ('wget', '1.20.1', '-GCCcore-7.3.0', True), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken2.sh %(installdir)s' + +sanity_check_paths = { + 'files': [ + '16S_gg_installation.sh', '16S_rdp_installation.sh', '16S_silva_installation.sh', 'add_to_library.sh', + 'build_db', 'build_gg_taxonomy.pl', 'build_kraken2_db.sh', 'build_rdp_taxonomy.pl', 'build_silva_taxonomy.pl', + 'classify', 'clean_db.sh', 'cp_into_tempfile.pl', 'download_genomic_library.sh', 'download_taxonomy.sh', + 'dump_table', 'estimate_capacity', 'kraken2', 'kraken2-build', 'kraken2-inspect', 'kraken2lib.pm', + 'lookup_accession_numbers.pl', 'make_seqid2taxid_map.pl', 'mask_low_complexity.sh', 'rsync_from_ncbi.pl', + 'scan_fasta_file.pl'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch new file mode 100644 index 00000000000..0acdcfb8bfe --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch @@ -0,0 +1,12 @@ +tweak Makefile such that $CXX and $CXXFLAGS are picked up from the environment +B. Hajgato (Free University Brussels, VUB), Kenneth Hoste (HPC-UGent) +--- kraken2-2.0.6-beta/src/Makefile.orig 2018-06-26 21:19:26.000000000 +0200 ++++ kraken2-2.0.6-beta/src/Makefile 2018-07-09 14:00:54.566891002 +0200 +@@ -1,5 +1,5 @@ +-CXX = g++ +-CXXFLAGS = -fopenmp -Wall -std=c++11 -O3 ++CXX ?= g++ ++CXXFLAGS ?= -fopenmp -Wall -std=c++11 -O3 + CXXFLAGS += -DLINEAR_PROBING + + .PHONY: all clean install diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.35-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.35-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..c04481b1912 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.35-GCCcore-7.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.35' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f11af1005b46b7b15d057d7f107315a1ad46935c7fcdf243c16e46ec14f0fe1e'] + +builddependencies = [('binutils', '2.30')] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..286b76c0e4f --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.20.1' + +homepage = 'https://www.gnu.org/software/%(name)s/' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b783b390cb571c837b392857945f5a1f00ec6b043177cc42abb8ee1b542ee1b3'] + +builddependencies = [ + ('binutils', '2.30'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('PCRE', '8.41'), + ('libidn', '1.35'), + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0h'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.4.11'), +] + +# make sure pkg-config picks up system packages (OpenSSL & co) +preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +configopts = '--with-ssl=openssl ' + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'devel' From a187c054d0697ab140af08ec093ea789dc7dad63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Feb 2019 11:06:36 +0100 Subject: [PATCH 0316/5331] {numlib}[intel/2018b] SuiteSparse v5.4.0 --- .../m/METIS/METIS-5.1.0-GCCcore-7.3.0.eb | 38 +++++++++++++++++++ ...iteSparse-5.4.0-intel-2018b-METIS-5.1.0.eb | 26 +++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-intel-2018b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..9e84a428400 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-7.3.0.eb @@ -0,0 +1,38 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +# We use 32bit for indices and 64bit for content +patches = ['%(name)s-%(version)s-use-doubles.patch'] + +checksums = [ + '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2', # source + '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67', # patch +] + +builddependencies = [ + ('binutils', '2.30'), + ('CMake', '3.12.1'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-intel-2018b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-intel-2018b-METIS-5.1.0.eb new file mode 100644 index 00000000000..c96223725c5 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-intel-2018b-METIS-5.1.0.eb @@ -0,0 +1,26 @@ +name = 'SuiteSparse' +version = '5.4.0' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] +checksums = ['374dd136696c653e34ef3212dc8ab5b61d9a67a6791d5ec4841efb838e94dbd1'] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [('METIS', metis_ver)] + +parallel = 1 + +prebuildopts = "sed -i 's/-openmp/-fopenmp/g' SuiteSparse_config/SuiteSparse_config.mk && " +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts += "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From 7141c090e87fc73ee5989a8eb2518748eda27d5a Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Tue, 12 Feb 2019 12:04:05 +0100 Subject: [PATCH 0317/5331] Requeted changes in horton eb and other fixes --- ... horton-2.1.1-foss-2018b-Python-2.7.15.eb} | 24 ++++++++++++------- ...horton-2.1.1-intel-2018b-Python-2.7.15.eb} | 24 ++++++++++++------- ...oss-2018b.eb => libxc-2.2.2-foss-2018b.eb} | 4 ++-- ...el-2018b.eb => libxc-2.2.2-intel-2018b.eb} | 4 ++-- 4 files changed, 34 insertions(+), 22 deletions(-) rename easybuild/easyconfigs/h/horton/{horton-2.1.1-foss-2018b.eb => horton-2.1.1-foss-2018b-Python-2.7.15.eb} (66%) rename easybuild/easyconfigs/h/horton/{horton-2.1.1-intel-2018b.eb => horton-2.1.1-intel-2018b-Python-2.7.15.eb} (67%) rename easybuild/easyconfigs/l/libxc/{libxc-2.2.3-foss-2018b.eb => libxc-2.2.2-foss-2018b.eb} (88%) rename easybuild/easyconfigs/l/libxc/{libxc-2.2.3-intel-2018b.eb => libxc-2.2.2-intel-2018b.eb} (90%) diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb similarity index 66% rename from easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb rename to easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb index 3bfb0b5491c..b1b552d8b8d 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-foss-2018b-Python-2.7.15.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'horton' version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://theochem.github.io/horton' description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written @@ -16,16 +17,14 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] sources = [SOURCE_TAR_GZ] -checksums = ['13e3381dea62e5877c6cde94515e99c8b7872f0a9498961b0766bdeae4506fe6'] +checksums = ['4b3f87920d881030ba80f097326a744de2cfee5316aa4499cc9a6501f64b5060'] -pyver = '2.7.15' -pyversuffix = '-Python-%s' % pyver dependencies = [ - ('Python', pyver), - ('h5py', '2.8.0', pyversuffix), - ('matplotlib', '2.2.3', pyversuffix), + ('Python', '2.7.15'), + ('h5py', '2.8.0', versionsuffix), + ('matplotlib', '2.2.3', versionsuffix), ('Libint', '2.0.3'), - ('libxc', '2.2.3'), + ('libxc', '2.2.2'), ] prebuildopts = ' '.join([ @@ -34,10 +33,17 @@ prebuildopts = ' '.join([ 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', ]) -pyshortver = '.'.join(pyver.split('.')[:2]) +# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc +runtest = ' '.join([ + 'export MATPLOTLIBRC=$PWD;', + 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', + '%s python setup.py build_ext -i; ' % prebuildopts, + 'nosetests -v', +]) + sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/horton' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/horton'], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb similarity index 67% rename from easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb rename to easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb index ec4dd619733..2f77a2c0bf3 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2018b-Python-2.7.15.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'horton' version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://theochem.github.io/horton' description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written @@ -16,16 +17,14 @@ toolchain = {'name': 'intel', 'version': '2018b'} source_urls = ['https://github.com/theochem/horton/releases/download/%s' % version] sources = [SOURCE_TAR_GZ] -checksums = ['13e3381dea62e5877c6cde94515e99c8b7872f0a9498961b0766bdeae4506fe6'] +checksums = ['4b3f87920d881030ba80f097326a744de2cfee5316aa4499cc9a6501f64b5060'] -pyver = '2.7.15' -pyversuffix = '-Python-%s' % pyver dependencies = [ - ('Python', pyver), - ('h5py', '2.8.0', pyversuffix), - ('matplotlib', '2.2.3', pyversuffix), + ('Python', '2.7.15'), + ('h5py', '2.8.0', versionsuffix), + ('matplotlib', '2.2.3', versionsuffix), ('Libint', '2.0.3'), - ('libxc', '2.2.3'), + ('libxc', '2.2.2'), ] prebuildopts = ' '.join([ @@ -34,10 +33,17 @@ prebuildopts = ' '.join([ 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', ]) -pyshortver = '.'.join(pyver.split('.')[:2]) +# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc +runtest = ' '.join([ + 'export MATPLOTLIBRC=$PWD;', + 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', + '%s python setup.py build_ext -i; ' % prebuildopts, + 'nosetests -v', +]) + sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%s/site-packages/horton' % pyshortver], + 'dirs': ['lib/python%(pyshortver)s/site-packages/horton'], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2018b.eb similarity index 88% rename from easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb rename to easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2018b.eb index 561661417d2..6cd124752b3 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2018b.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libxc' -version = '2.2.3' +version = '2.2.2' homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] sources = [SOURCE_TAR_GZ] -checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] +checksums = ['6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642'] configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2018b.eb similarity index 90% rename from easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb rename to easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2018b.eb index 85d607baacc..5dfa0de3524 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2018b.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libxc' -version = '2.2.3' +version = '2.2.2' homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. @@ -14,7 +14,7 @@ toolchainopts = {'lowopt': True, 'optarch': False} source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] sources = [SOURCE_TAR_GZ] -checksums = ['2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7'] +checksums = ['6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642'] configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' From ef40135960c289e641280527d887d6f01e298cbb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 12 Feb 2019 13:33:14 +0100 Subject: [PATCH 0318/5331] adding easyconfigs: IGVTools-2.4.18-Java-1.8.eb --- .../i/IGVTools/IGVTools-2.4.18-Java-1.8.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGVTools/IGVTools-2.4.18-Java-1.8.eb diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.4.18-Java-1.8.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.4.18-Java-1.8.eb new file mode 100644 index 00000000000..2acadf08862 --- /dev/null +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.4.18-Java-1.8.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'IGVTools' +version = '2.4.18' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://software.broadinstitute.org/software/igv/%(namelower)s' +description = """ This package contains command line utilities for preprocessing, + computing feature count density (coverage), sorting, and indexing data files. + See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s/'] +sources = ['%(namelower)s_%(version)s.zip'] +checksums = ['8236e31e4264e63e39956c1070028b83284a3fd56f46353504e47a12daa58dd2'] + +dependencies = [('Java', '1.8')] + +# add the installation dir to PATH +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['lib/%(namelower)s.jar', '%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s help'] + +moduleclass = 'bio' From 22362e76cfde10bbe60b5271705e404831fee6d7 Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Tue, 12 Feb 2019 14:11:36 +0100 Subject: [PATCH 0319/5331] Fix line length --- .../easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb | 3 ++- .../OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb index 6bdef1e19cd..9c7955082ae 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb @@ -15,7 +15,8 @@ patches = ['%(name)s-%(version)s-backported_patches.patch'] checksums = [ '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz - '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch + # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch + '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', ] # needed for --with-verbs diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 413f6c97c42..05be968255f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -15,7 +15,8 @@ patches = ['%(name)s-%(version)s-backported_patches.patch'] checksums = [ '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz - '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch + # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch + '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', ] # needed for --with-verbs From 6848e96c63b4a4444ef49a50c2cc634e777c89b0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 12 Feb 2019 14:28:26 +0100 Subject: [PATCH 0320/5331] Blobtools: pre-download taxdump --- ...obTools-20180528-foss-2018b-Python-2.7.15.eb | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb index eb5ac47669e..79be229404e 100644 --- a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb @@ -11,12 +11,23 @@ description = """ A modular command-line solution for visualisation, toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['https://github.com/drl/blobtools/archive/'] -sources = [{'download_filename': '%s.tar.gz' % commit, 'filename': SOURCE_TAR_GZ}] +source_urls = [ + 'https://github.com/drl/blobtools/archive/', + 'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/', +] +sources = [ + { + 'download_filename': '%s.tar.gz' % commit, + 'filename': SOURCE_TAR_GZ, + 'extract_cmd': "tar -xzf %s -C %(builddir)s --strip-components 1", + }, + {'filename': 'taxdump.tar.gz', 'extract_cmd': "cp %s %(builddir)s/data/"}, +] patches = ['BlobTools-20180528_fix_deps.patch'] checksums = [ '316c22cceec6b6ac4e3751d06ec6effb88ea35d746abb957239c75e1f4eed9a9', # BlobTools-20180528.tar.gz - 'db0c4501303b0bf17f6cadeafbe109d3a2c4e34e029d4ea272e6a8d4287a50fd', # BlobTools-20180528_fix_deps.patch + '24399e6711ff09e27a3d457cfbf4567615e4f5b990ff15681e60248ef7852df6', # taxdump.tar.gz + 'f26cfc74a1d90cf692a4655d251be236920feb8b0c636cd3358c4eda0c50cc82', # BlobTools-20180528_fix_deps.patch ] dependencies = [ From 8f107b3f41e6e53b2fdebe80295b34d9d873e38c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 12 Feb 2019 15:58:14 +0200 Subject: [PATCH 0321/5331] adding easyconfigs: TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb --- ...RT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..5f2d6faba6f --- /dev/null +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,36 @@ +name = 'TensorRT' +version = '4.0.1.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://developer.nvidia.com/tensorrt' +description = """NVIDIA TensorRT is a platform for high-performance deep learning inference""" + +sources = ['%(name)s-%(version)s.Ubuntu-16.04.4.x86_64-gnu.cuda-9.2.cudnn7.1.tar.gz'] +checksums = ['fc5fd2ba86225ed62e60870cc24896107770a59829363fcb49229c82bb1f4fb5'] + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +builddependencies = [ + ('protobuf', '3.6.1'), +] + +dependencies = [ + ('Python', '2.7.15'), + ('cuDNN', '7.1.4.18'), +] + +extract_sources = True +keepsymlinks = True + +exts_list = [ + ('protobuf-python', '3.6.1', { + 'modulename': 'google.protobuf', + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + 'start_dir': 'python', + 'use_pip': False, + 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + }), +] + +moduleclass = 'lib' From a5ae4a0bc4c9b6c77aeca860e29ff48898d3abe6 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 12 Feb 2019 07:59:45 -0600 Subject: [PATCH 0322/5331] adding easyconfigs: CLAPACK-3.2.1-GCC-6.4.0-2.28.eb, CLAPACK-3.2.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb --- .../c/CLAPACK/CLAPACK-3.2.1-GCC-6.4.0-2.28.eb | 49 +++++++++++++++++++ ....2.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 49 +++++++++++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..2eb15e82800 --- /dev/null +++ b/easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-GCC-6.4.0-2.28.eb @@ -0,0 +1,49 @@ +# +# The CLAPACK needs to run the command of "ulimit -s unlimited" before running the eb file, +# else if directly compiled the CLAPACK, it gives the following error: +# +# NEP: Testing Nonsymmetric Eigenvalue Problem routines +# ./xeigtstz < nep.in > znep.out 2>&1 +# /bin/sh: line 1: 4778 Segmentation fault ./xeigtstz < nep.in > znep.out 2>&1 +# make[1]: *** [znep.out] Error 139 +# +# The solution of "ulimit -s unlimited" is provided in the link: +# +# https://unix.stackexchange.com/questions/428394/lapack-make-fails-recipe-for-target-znep-out-failed-error +# +# As described in another link, the error only pertains to the testing module; which related to improperly +# setting the testing matrix: +# +# https://github.com/Reference-LAPACK/lapack/issues/85 +# +# Therefore there's nothing harmful for the code section. +# +easyblock = 'ConfigureMake' + +name = 'CLAPACK' +version = '3.2.1' + +homepage = 'http://www.netlib.org/clapack' +description = "C version of LAPACK" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = ['http://www.netlib.org/clapack/'] +sources = [SOURCELOWER_TGZ] +checksums = ['6dc4c382164beec8aaed8fd2acc36ad24232c406eda6db462bd4c41d5e455fac'] + +unpack_options = '--strip-components=1' +buildininstalldir = True +skipsteps = ['configure', 'install'] + +prebuildopts = 'ulimit -s unlimited && cp make.inc.example make.inc && ' +buildopts = 'CC="$CC" LOADER="$CC" ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['lapack_LINUX.a', 'tmglib_LINUX.a'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..7e8fe272eb3 --- /dev/null +++ b/easybuild/easyconfigs/c/CLAPACK/CLAPACK-3.2.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,49 @@ +# +# The CLAPACK needs to run the command of "ulimit -s unlimited" before running the eb file, +# else if directly compiled the CLAPACK, it gives the following error: +# +# NEP: Testing Nonsymmetric Eigenvalue Problem routines +# ./xeigtstz < nep.in > znep.out 2>&1 +# /bin/sh: line 1: 4778 Segmentation fault ./xeigtstz < nep.in > znep.out 2>&1 +# make[1]: *** [znep.out] Error 139 +# +# The solution of "ulimit -s unlimited" is provided in the link: +# +# https://unix.stackexchange.com/questions/428394/lapack-make-fails-recipe-for-target-znep-out-failed-error +# +# As described in another link, the error only pertains to the testing module; which related to improperly +# setting the testing matrix: +# +# https://github.com/Reference-LAPACK/lapack/issues/85 +# +# Therefore there's nothing harmful for the code section. +# +easyblock = 'ConfigureMake' + +name = 'CLAPACK' +version = '3.2.1' + +homepage = 'http://www.netlib.org/clapack' +description = "C version of LAPACK" + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +source_urls = ['http://www.netlib.org/clapack/'] +sources = [SOURCELOWER_TGZ] +checksums = ['6dc4c382164beec8aaed8fd2acc36ad24232c406eda6db462bd4c41d5e455fac'] + +unpack_options = '--strip-components=1' +buildininstalldir = True +skipsteps = ['configure', 'install'] + +prebuildopts = 'ulimit -s unlimited && cp make.inc.example make.inc && ' +buildopts = 'CC="$CC" LOADER="$CC" ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['lapack_LINUX.a', 'tmglib_LINUX.a'], + 'dirs': [], +} + +moduleclass = 'math' From 99a73be7bc76aeba13fc89b8203a2cc863820b7e Mon Sep 17 00:00:00 2001 From: Oriol Mula-Valls Date: Tue, 12 Feb 2019 16:20:09 +0100 Subject: [PATCH 0323/5331] fix patches lines --- .../easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb | 2 +- .../OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb index 9c7955082ae..a990de595f7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s-backported_patches.patch'] +patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] checksums = [ '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 05be968255f..5d12763daa5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s-backported_patches.patch'] +patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] checksums = [ '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz From 0a70df15b3a2c9e8f68a09beba212ec065ae4338 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 09:56:23 -0600 Subject: [PATCH 0324/5331] adding easyconfigs: Biopython-1.70-foss-2017b-Python-2.7.14.eb, Biopython-1.70-foss-2017b-Python-2.7.14.eb, Biopython-1.70-intel-2017b-Python-3.6.3.eb --- ...Biopython-1.70-foss-2017b-Python-2.7.14.eb | 39 +++++++++++++++++++ ...Biopython-1.70-intel-2017b-Python-3.6.3.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..c66d3961e38 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.70' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b'] + +dependencies = [ + ('Python', '2.7.14') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..8c44145be0b --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.70' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b'] + +dependencies = [ + ('Python', '3.6.3') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From 4926f11e1d10436c2e7fd6f2a2c647d977f1cfb6 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 10:02:56 -0600 Subject: [PATCH 0325/5331] Add one more easyconfig --- .../Biopython-1.70-foss-2017b-Python-3.6.3.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..ffb30f9fd25 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.70' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.biopython.org' +description = """Biopython is a set of freely available tools for biological computation written +in Python by an international team of developers. It is a distributed collaborative effort to +develop Python libraries and applications which address the needs of current and future work in +bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b'] + +dependencies = [ + ('Python', '3.6.3') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From ec23199a1bc5f05777c0b8903ba9a51821178969 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 10:07:00 -0600 Subject: [PATCH 0326/5331] Use pip and fail on deps download --- .../b/Biopython/Biopython-1.70-foss-2017b-Python-2.7.14.eb | 3 +++ .../b/Biopython/Biopython-1.70-foss-2017b-Python-3.6.3.eb | 3 +++ .../b/Biopython/Biopython-1.70-intel-2017b-Python-2.7.14.eb | 3 +++ .../b/Biopython/Biopython-1.70-intel-2017b-Python-3.6.3.eb | 3 +++ 4 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-2.7.14.eb index c66d3961e38..34bca17400f 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-2.7.14.eb @@ -29,6 +29,9 @@ dependencies = [ ('Python', '2.7.14') ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-3.6.3.eb index ffb30f9fd25..b1fbb4037b4 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-foss-2017b-Python-3.6.3.eb @@ -29,6 +29,9 @@ dependencies = [ ('Python', '3.6.3') ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-2.7.14.eb index 689d75041af..342e88e3dcc 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-2.7.14.eb @@ -29,6 +29,9 @@ dependencies = [ ('Python', '2.7.14') ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-3.6.3.eb index 8c44145be0b..f18795f259f 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.70-intel-2017b-Python-3.6.3.eb @@ -29,6 +29,9 @@ dependencies = [ ('Python', '3.6.3') ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', 'lib/python%(pyshortver)s/site-packages/BioSQL'] From a4a1a6ad554bf27338d9f28ed6a3e2ad657a016d Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 10:25:42 -0600 Subject: [PATCH 0327/5331] adding easyconfigs: VCFtools-0.1.15-foss-2017b-Perl-5.26.0.eb, VCFtools-0.1.15-intel-2017b-Perl-5.26.0.eb --- .../VCFtools-0.1.15-foss-2017b-Perl-5.26.0.eb | 31 +++++++++++++++++++ ...VCFtools-0.1.15-intel-2017b-Perl-5.26.0.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.15-foss-2017b-Perl-5.26.0.eb create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.15-intel-2017b-Perl-5.26.0.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.15-foss-2017b-Perl-5.26.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.15-foss-2017b-Perl-5.26.0.eb new file mode 100644 index 00000000000..fb001c01cc3 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.15-foss-2017b-Perl-5.26.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.15' +versionsuffix = '-Perl-%(perlver)s' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['31e47afd5be679d89ece811a227525925b6907cce4af2c86f10f465e080383e3'] + +dependencies = [ + ('Perl', '5.26.0'), + ('tabix', '0.2.6'), + ('zlib', '1.2.11'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.15-intel-2017b-Perl-5.26.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.15-intel-2017b-Perl-5.26.0.eb new file mode 100644 index 00000000000..ac69deaaba7 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.15-intel-2017b-Perl-5.26.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.15' +versionsuffix = '-Perl-%(perlver)s' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['31e47afd5be679d89ece811a227525925b6907cce4af2c86f10f465e080383e3'] + +dependencies = [ + ('Perl', '5.26.0'), + ('tabix', '0.2.6'), + ('zlib', '1.2.11'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' From b461ed9127fa4155b1f7ef07815c2dd03d742656 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 10:36:01 -0600 Subject: [PATCH 0328/5331] adding easyconfigs: Valgrind-3.13.0-foss-2017b.eb --- .../v/Valgrind/Valgrind-3.13.0-foss-2017b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-foss-2017b.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-foss-2017b.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-foss-2017b.eb new file mode 100644 index 00000000000..a3e35d98a63 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.13.0-foss-2017b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.13.0' + +homepage = 'http://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'optarch': False} + +source_urls = [ + 'ftp://sourceware.org/pub/valgrind/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['d76680ef03f00cd5e970bbdcd4e57fb1f6df7d2e2c071635ef2be74790190c3b'] + +configopts = ' --with-mpicc="$MPICC"' + +binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'debugger' From 878ee8f89e68e304ef63b7b5ba9e108e9c0642b2 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 12 Feb 2019 10:58:02 -0600 Subject: [PATCH 0329/5331] change the patch name from abyss to ABySS --- ...byss-2.0.3-BranchGroup.patch => ABySS-2.0.3-BranchGroup.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/ABySS/{abyss-2.0.3-BranchGroup.patch => ABySS-2.0.3-BranchGroup.patch} (100%) diff --git a/easybuild/easyconfigs/a/ABySS/abyss-2.0.3-BranchGroup.patch b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-BranchGroup.patch similarity index 100% rename from easybuild/easyconfigs/a/ABySS/abyss-2.0.3-BranchGroup.patch rename to easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-BranchGroup.patch From 017691d0789728a3a47cdfc2ca42a1a4b774c1e1 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 12 Feb 2019 10:59:06 -0600 Subject: [PATCH 0330/5331] modify the eb file for the patch name modification --- easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-intel-2017b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-intel-2017b.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-intel-2017b.eb index 25bf5095c24..48adc9641e4 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-intel-2017b.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.3-intel-2017b.eb @@ -11,10 +11,10 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['abyss-2.0.3-BranchGroup.patch'] +patches = ['ABySS-%(version)s-BranchGroup.patch'] checksums = [ 'ff4cb9c9f78e443cc5b613dbc1f949f3eba699e78f090e73f0fefe1b99d85d55', # abyss-2.0.3.tar.gz - '6dac7c5641693b26e393cb43cb6d49d97fced32e6f44d0c3e50d4e223222f08d', # abyss-2.0.3-BranchGroup.patch + '6dac7c5641693b26e393cb43cb6d49d97fced32e6f44d0c3e50d4e223222f08d', # ABySS-2.0.3-BranchGroup.patch ] dependencies = [ From 70bb0f505c8a5837b7279b6824bc34c286379d6e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Feb 2019 18:02:44 +0100 Subject: [PATCH 0331/5331] adding easyconfigs: CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb, SuiteSparse-5.4.0-foss-2018b-METIS-5.1.0.eb --- .../CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb | 40 +++++++++++++++++++ ...uiteSparse-5.4.0-foss-2018b-METIS-5.1.0.eb | 25 ++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2018b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..8de4194ac15 --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,40 @@ +easyblock = "PythonPackage" + +name = 'CVXOPT' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['CVXOPT-1.2.1-fix-setup-py.patch'] +checksums = [ + 'ea62a2a1b8e2db3a6ae44ac394f58e4620149af226c250c6f2b18739b48cfc21', # cvxopt-1.2.3.tar.gz + '85d8475098895e9af45f330489a712b5b944489c5fb4a6c67f59bef8fed4303d', # CVXOPT-1.2.1-fix-setup-py.patch +] + +dependencies = [ + ('Python', '3.6.6'), + ('SuiteSparse', '5.4.0', '-METIS-5.1.0'), + ('GSL', '2.5'), +] + +prebuildopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' +prebuildopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' + +installopts = ' && nosetests' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2018b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2018b-METIS-5.1.0.eb new file mode 100644 index 00000000000..33a1038bfb2 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2018b-METIS-5.1.0.eb @@ -0,0 +1,25 @@ +name = 'SuiteSparse' +version = '5.4.0' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] +checksums = ['374dd136696c653e34ef3212dc8ab5b61d9a67a6791d5ec4841efb838e94dbd1'] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [('METIS', metis_ver)] + +parallel = 1 + +prebuildopts = "sed -i 's/-openmp/-fopenmp/g' SuiteSparse_config/SuiteSparse_config.mk && " +prebuildopts += "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From effc3f30903385656d92d127efd7889525f46eef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Feb 2019 18:05:47 +0100 Subject: [PATCH 0332/5331] adding easyconfigs: networkx-2.2-foss-2018b-Python-3.6.6.eb --- .../networkx-2.2-foss-2018b-Python-3.6.6.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..89256354661 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] +checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] + +dependencies = [('Python', '3.6.6')] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 6c41a5fa89e6b033943c55b20bd81df268bb54b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Feb 2019 18:06:21 +0100 Subject: [PATCH 0333/5331] adding easyconfigs: Ninja-1.9.0-foss-2018b.eb --- .../n/Ninja/Ninja-1.9.0-foss-2018b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-foss-2018b.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-foss-2018b.eb new file mode 100644 index 00000000000..5ea2081b987 --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-foss-2018b.eb @@ -0,0 +1,26 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.9.0' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5d7ec75828f8d3fd1a0c2f31b5b0cea780cdfe1031359228c428c1a48bfcd5b9'] + +builddependencies = [('Python', '3.6.6')] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +moduleclass = 'tools' From 941da35ef62efc692f227db937973edd03a13893 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Feb 2019 18:09:54 +0100 Subject: [PATCH 0334/5331] {quantum}[foss/2018b] Qiskit v0.7.2 w/ Python 3.6.6 --- .../Qiskit-0.7.2-foss-2018b-Python-3.6.6.eb | 106 ++++++++++++++++++ 1 file changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qiskit/Qiskit-0.7.2-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.7.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.7.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..d0c238e4f9e --- /dev/null +++ b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.7.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,106 @@ +easyblock = 'PythonBundle' + +name = 'Qiskit' +version = '0.7.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://qiskit.org' +description = """Qiskit is an open-source framework for working with noisy quantum computers + at the level of pulses, circuits, and algorithms.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +# required for building/installing qiskit-aer +builddependencies = [ + ('CMake', '3.12.1'), + ('Ninja', '1.9.0'), +] + +dependencies = [ + ('Python', '3.6.6'), + ('sympy', '1.3', versionsuffix), + ('Pillow', '5.3.0', versionsuffix), + ('networkx', '2.2', versionsuffix), + ('h5py', '2.8.0', versionsuffix), + ('scikit-learn', '0.20.0', versionsuffix), + ('CVXOPT', '1.2.3', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('setuptools', '40.8.0', { + 'source_tmpl': 'setuptools-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['6e4eec90337e849ade7103723b9a99631c1f0d19990d6e8412dc42f5ae8b304d'], + }), + ('ntlm-auth', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/ntlm-auth/'], + 'checksums': ['7bc02a3fbdfee7275d3dc20fce8028ed8eb6d32364637f28be9e9ae9160c6d5c'], + }), + ('requests_ntlm', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests_ntlm/'], + 'checksums': ['9189c92e8c61ae91402a64b972c4802b2457ce6a799d658256ebf084d5c7eb71'], + }), + ('psutil', '5.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil/'], + 'checksums': ['1aba93430050270750d046a179c5f3d6e1f5f8b96c20399ba38c596b28fc4d37'], + }), + ('ply', '3.11', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ply/'], + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('marshmallow', '2.18.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/marshmallow/'], + 'checksums': ['958e6640bec9a04ca15701e3d99b12c4269d0f43be596f00eeca1f2baf530abc'], + }), + ('marshmallow-polyfield', '3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/m/marshmallow-polyfield/'], + 'checksums': ['72980cb9a43a7c750580b4b08e9d01a8cbd583e1f59360f1924a1ed60f065a4c'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], + }), + ('qiskit-terra', '0.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-terra/'], + 'checksums': ['9cc57da08896627d0f34cf6ae76bd3358a5e6e155f612137ff343dd787134720'], + 'modulename': 'qiskit.qobj', + }), + ('packaging', '19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + }), + ('wheel', '0.33.0', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wheel/'], + }), + ('scikit-build', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-build/'], + 'checksums': ['2aa4411a7de928d395eca240a6a794aa05c8d1c42ee53a4ae48fa324693902c2'], + 'modulename': 'skbuild', + }), + ('qiskit-aer', '0.1.1', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/Qiskit/qiskit-aer/archive/'], + 'checksums': ['98d74e2a362e5620b59d9f91edf25d20a909766bd1cea6e910913521913136ac'], + 'modulename': 'qiskit.providers.aer', + }), + ('qiskit', version, { + 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit/'], + 'checksums': ['08c7f7ccd32a5cb0c0a0c4f63d6ff068d659c9c0b51e2df6f2054e586e8bfa19'], + }), + ('qiskit-aqua', '0.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-aqua/'], + 'checksums': ['53098c1c57d8ec956826badcbade41ac7b5a047ef562c2d4384a02a5b33c71a2'], + }), + ('qiskit-chemistry', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-chemistry/'], + 'checksums': ['d6164517a41f88c388795e7f3c1162a32c167bd84378ec4a0e28602b7dff038d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/qiskit_aqua_cmd', 'bin/qiskit_chemistry_cmd'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'quantum' From ea6a2987f5c05df2b43ee75d560173154a168514 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 11:16:19 -0600 Subject: [PATCH 0335/5331] adding easyconfigs: SuiteSparse-5.1.2-foss-2017b-ParMETIS-4.0.3.eb, SuiteSparse-5.1.2-intel-2017b-ParMETIS-4.0.3.eb --- ...eSparse-5.1.2-foss-2017b-ParMETIS-4.0.3.eb | 20 +++++++++++++++++++ ...Sparse-5.1.2-intel-2017b-ParMETIS-4.0.3.eb | 20 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-foss-2017b-ParMETIS-4.0.3.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2017b-ParMETIS-4.0.3.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-foss-2017b-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-foss-2017b-ParMETIS-4.0.3.eb new file mode 100644 index 00000000000..719eac1c6c1 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-foss-2017b-ParMETIS-4.0.3.eb @@ -0,0 +1,20 @@ +name = 'SuiteSparse' +version = '5.1.2' +parmetis_ver = '4.0.3' +versionsuffix = '-ParMETIS-%s' % parmetis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4ec8d344bd8e95b898132ddffd7ee93bfbb2c1224925d11bab844b08f9b4c3b7'] + +dependencies = [('ParMETIS', parmetis_ver)] + +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2017b-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2017b-ParMETIS-4.0.3.eb new file mode 100644 index 00000000000..ba01b64cb9f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2017b-ParMETIS-4.0.3.eb @@ -0,0 +1,20 @@ +name = 'SuiteSparse' +version = '5.1.2' +parmetis_ver = '4.0.3' +versionsuffix = '-ParMETIS-%s' % parmetis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4ec8d344bd8e95b898132ddffd7ee93bfbb2c1224925d11bab844b08f9b4c3b7'] + +dependencies = [('ParMETIS', parmetis_ver)] + +parallel = 1 + +moduleclass = 'numlib' From 1939ffac3f30ec484e479c0ec742f21c5ae94461 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 12 Feb 2019 19:27:48 +0200 Subject: [PATCH 0336/5331] Add comment about download, fix style, drop things now in easyblock. --- .../TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb index 5f2d6faba6f..b9ae131ade4 100644 --- a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb @@ -5,11 +5,13 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://developer.nvidia.com/tensorrt' description = """NVIDIA TensorRT is a platform for high-performance deep learning inference""" +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +# Requires manual download from +# https://developer.nvidia.com/nvidia-tensorrt-4x-download sources = ['%(name)s-%(version)s.Ubuntu-16.04.4.x86_64-gnu.cuda-9.2.cudnn7.1.tar.gz'] checksums = ['fc5fd2ba86225ed62e60870cc24896107770a59829363fcb49229c82bb1f4fb5'] -toolchain = {'name': 'fosscuda', 'version': '2018b'} - builddependencies = [ ('protobuf', '3.6.1'), ] @@ -19,9 +21,6 @@ dependencies = [ ('cuDNN', '7.1.4.18'), ] -extract_sources = True -keepsymlinks = True - exts_list = [ ('protobuf-python', '3.6.1', { 'modulename': 'google.protobuf', From 3e98ad5e5d2b61dd05af5afb7ce8e05bbce75e15 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 11:55:28 -0600 Subject: [PATCH 0337/5331] Fix newline --- easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2018a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2018a.eb b/easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2018a.eb index 34058328495..a6e3c220d0d 100644 --- a/easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2018a.eb +++ b/easybuild/easyconfigs/m/MINC/MINC-2.4.03-foss-2018a.eb @@ -28,4 +28,4 @@ sanity_check_paths = { 'dirs': ['include'], } -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' From 0371f0fc0878d9abbbd2487049fe8bcf945e1f97 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 13:58:14 -0600 Subject: [PATCH 0338/5331] Update checksum --- .../a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb index 54144e6ea7f..9ba3747062c 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/afni/afni/archive/'] sources = ['AFNI_%(version)s.tar.gz'] patches = ['AFNI-18.1.09_omp-pragma-statement-fix.patch'] checksums = [ - 'd3c558ac898aefc432396742e5b4d74d8b6863aa92f276d709834513848f68be', # AFNI_19.0.01.tar.gz + 'da4b49e90dc542101bc69a471fae45e2fe95558b9c83c8146aa7b1999bb70835', # AFNI_19.0.01.tar.gz '8b739ddc09d6e398ac7fa86d89f6a02f26f2b58b17caea627d5c07de5282aab2', # AFNI-18.1.09_omp-pragma-statement-fix.patch ] From 51c395ea3877c1388a9da7a42fa2e3d8823280c5 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 14:00:51 -0600 Subject: [PATCH 0339/5331] Update checksum --- .../easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb index 9ba2f0283c4..0732a36f665 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/afni/afni/archive/'] sources = ['AFNI_%(version)s.tar.gz'] patches = ['AFNI-18.1.09_omp-pragma-statement-fix.patch'] checksums = [ - 'd3c558ac898aefc432396742e5b4d74d8b6863aa92f276d709834513848f68be', # AFNI_19.0.01.tar.gz + 'da4b49e90dc542101bc69a471fae45e2fe95558b9c83c8146aa7b1999bb70835', # AFNI_19.0.01.tar.gz '8b739ddc09d6e398ac7fa86d89f6a02f26f2b58b17caea627d5c07de5282aab2', # AFNI-18.1.09_omp-pragma-statement-fix.patch ] From 9f7cf16c815ace593fa797157af1a78799e7aee5 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 17:04:28 -0600 Subject: [PATCH 0340/5331] adding easyconfigs: Python-2.7.14-fosscuda-2017b.eb, Python-2.7.14-intelcuda-2017b.eb, Python-3.6.3-fosscuda-2017b.eb, Python-3.6.3-intelcuda-2017b.eb --- .../p/Python/Python-2.7.14-fosscuda-2017b.eb | 217 +++++++++++++++++ .../p/Python/Python-2.7.14-intelcuda-2017b.eb | 217 +++++++++++++++++ .../p/Python/Python-3.6.3-fosscuda-2017b.eb | 219 +++++++++++++++++ .../p/Python/Python-3.6.3-intelcuda-2017b.eb | 227 ++++++++++++++++++ 4 files changed, 880 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2017b.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.14-intelcuda-2017b.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2017b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2017b.eb new file mode 100644 index 00000000000..7376a94e0e2 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-fosscuda-2017b.eb @@ -0,0 +1,217 @@ +name = 'Python' +version = '2.7.14' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.20.1'), + ('GMP', '6.1.2'), # required for pycrypto + ('libffi', '3.2.1'), # required for cryptography + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2l'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +exts_download_dep_fail = True + +# order is important! +# package versions updated September 18th 2017 +exts_list = [ + ('setuptools', '36.5.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['ce2007c1cea3359870b80657d634253a0765b0c7dc5a988d77ba803fc86f2c64'], + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('numpy', '1.13.1', { + 'patches': ['numpy-1.12.0-mkl.patch'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'checksums': [ + 'c9b0283776085cb2804efff73e9955ca279ba4edafd58d3ead70b61d209c4fbb', # numpy-1.13.1.zip + 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch + ], + }), + ('scipy', '0.19.1', { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '3.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], + }), + ('Cython', '0.26.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + 'checksums': ['c2e63c4794161135adafa8aa4a855d6068073f421c83ffacc39369497a189dd5'], + }), + ('six', '1.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], + }), + ('dateutil', '2.6.1', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'checksums': ['c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b'], + }), + ('decorator', '4.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], + }), + ('arff', '2.1.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], + }), + ('ipaddress', '1.0.22', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], + 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], + }), + ('asn1crypto', '0.24.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], + 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], + }), + ('idna', '2.7', { + 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], + 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], + }), + ('cryptography', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['d04bb2425086c3fe86f7bc48915290b13e798497839fbb18ab7f6dffcf98cc3a'], + }), + ('pyasn1', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), + ('pycparser', '2.18', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], + 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], + }), + ('cffi', '1.11.5', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), + ('PyNaCl', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], + 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], + 'modulename': 'nacl', + }), + ('bcrypt', '3.1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], + 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], + }), + ('paramiko', '2.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + 'checksums': ['ff94ae65379914ec3c960de731381f49092057b6dd1d24d18842ead5a2eb2277'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], + }), + ('netifaces', '0.10.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], + }), + ('pytz', '2017.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + 'checksums': ['f5c056e8f62d45ba8215e5cb8f50dfccb198b4b9fbea8500674f3443e4689589'], + }), + ('pandas', '0.20.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], + }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], + 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], + }), + ('xlrd', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], + 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], + }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.14-intelcuda-2017b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.14-intelcuda-2017b.eb new file mode 100644 index 00000000000..1d0891f54ba --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.14-intelcuda-2017b.eb @@ -0,0 +1,217 @@ +name = 'Python' +version = '2.7.14' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.20.1'), + ('GMP', '6.1.2'), # required for pycrypto + ('libffi', '3.2.1'), # required for cryptography + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2l'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +exts_download_dep_fail = True + +# order is important! +# package versions updated September 18th 2017 +exts_list = [ + ('setuptools', '36.5.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['ce2007c1cea3359870b80657d634253a0765b0c7dc5a988d77ba803fc86f2c64'], + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('numpy', '1.13.1', { + 'patches': ['numpy-1.12.0-mkl.patch'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'checksums': [ + 'c9b0283776085cb2804efff73e9955ca279ba4edafd58d3ead70b61d209c4fbb', # numpy-1.13.1.zip + 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch + ], + }), + ('scipy', '0.19.1', { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '3.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], + }), + ('Cython', '0.26.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + 'checksums': ['c2e63c4794161135adafa8aa4a855d6068073f421c83ffacc39369497a189dd5'], + }), + ('six', '1.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], + }), + ('dateutil', '2.6.1', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'checksums': ['c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b'], + }), + ('decorator', '4.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], + }), + ('arff', '2.1.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], + }), + ('ipaddress', '1.0.22', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], + 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], + }), + ('asn1crypto', '0.24.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], + 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], + }), + ('idna', '2.7', { + 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], + 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], + }), + ('cryptography', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['d04bb2425086c3fe86f7bc48915290b13e798497839fbb18ab7f6dffcf98cc3a'], + }), + ('pyasn1', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), + ('pycparser', '2.18', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], + 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], + }), + ('cffi', '1.11.5', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), + ('PyNaCl', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], + 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], + 'modulename': 'nacl', + }), + ('bcrypt', '3.1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], + 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], + }), + ('paramiko', '2.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + 'checksums': ['ff94ae65379914ec3c960de731381f49092057b6dd1d24d18842ead5a2eb2277'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], + }), + ('netifaces', '0.10.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], + }), + ('pytz', '2017.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + 'checksums': ['f5c056e8f62d45ba8215e5cb8f50dfccb198b4b9fbea8500674f3443e4689589'], + }), + ('pandas', '0.20.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], + }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], + 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], + }), + ('xlrd', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], + 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], + }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb new file mode 100644 index 00000000000..52314a666e7 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb @@ -0,0 +1,219 @@ +name = 'Python' +version = '3.6.3' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +patches = ['Python-3.6.1_fix_stupid_comment_in_comment.patch'] +checksums = [ + 'ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91', # Python-3.6.3.tgz + # Python-3.6.1_fix_stupid_comment_in_comment.patch + 'c664b16ae9a2d2ef9dcca39a3b959a0e48c8d57258e5ab403d988e39b359b48e', +] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.20.1'), + ('GMP', '6.1.2'), + ('XZ', '5.2.3'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2l'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +exts_download_dep_fail = True + +# order is important! +# package versions updated October 16th 2017 +exts_list = [ + ('setuptools', '36.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['62074589522a798da243f47348f38020d55b6c945652e2f2c09d3a96299812b7'], + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('numpy', '1.13.3', { + 'patches': ['numpy-1.12.0-mkl.patch'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'checksums': [ + '36ee86d5adbabc4fa2643a073f93d5504bdfed37a149a3a49f4dde259f35a750', # numpy-1.13.3.zip + 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch + ], + }), + ('scipy', '0.19.1', { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], + }), + ('paycheck', '1.0.2', { + 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'checksums': [ + '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz + # paycheck-1.0.2_setup-open-README-utf8.patch + 'ceb7f08aebf016cdcd94ae41c1c76c8c120907f85cbfce240d3a112afb264d79', + ], + }), + ('pbr', '3.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('Cython', '0.27.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + 'checksums': ['e6840a2ba2704f4ffb40e454c36f73aeb440a4005453ee8d7ff6a00d812ba176'], + }), + ('six', '1.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], + }), + ('dateutil', '2.6.1', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], + }), + ('deap', '1.0.2', { + 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'checksums': [ + 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz + # deap-1.0.2_setup-open-README-utf8.patch + '39a3a08359321189a1b27a382eb309dfd4470cba9101997a6d527a2fd3a0ce93', + ], + }), + ('decorator', '4.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], + }), + ('arff', '2.1.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], + }), + ('ipaddress', '1.0.22', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], + 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], + }), + ('asn1crypto', '0.24.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], + 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], + }), + ('idna', '2.7', { + 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], + 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], + }), + ('pycparser', '2.19', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], + 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], + }), + ('cryptography', '2.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['2699ed21e1f73dd1bdb7b0b22a517295de07809d535b23e200dd22166037fe6f'], + }), + ('pyasn1', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), + ('cffi', '1.11.5', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), + ('PyNaCl', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], + 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], + 'modulename': 'nacl', + }), + ('bcrypt', '3.1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], + 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], + }), + ('paramiko', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + 'checksums': ['fa6b4f5c9d88f27c60fd9578146ff24e99d4b9f63391ff1343305bfd766c4660'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], + }), + ('netifaces', '0.10.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], + }), + ('pytz', '2017.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], + }), + ('pandas', '0.20.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], + }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], + 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], + }), + ('xlrd', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], + 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], + }), + ('tabulate', '0.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], + 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb new file mode 100644 index 00000000000..64a6eddec81 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb @@ -0,0 +1,227 @@ +name = 'Python' +version = '3.6.3' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +patches = ['Python-3.6.1_fix_stupid_comment_in_comment.patch'] +checksums = [ + 'ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91', # Python-3.6.3.tgz + # Python-3.6.1_fix_stupid_comment_in_comment.patch + 'c664b16ae9a2d2ef9dcca39a3b959a0e48c8d57258e5ab403d988e39b359b48e', +] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('SQLite', '3.20.1'), + ('GMP', '6.1.2'), + ('XZ', '5.2.3'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2l'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +exts_download_dep_fail = True + +# try and make sure stack limit is set to unlimited, to avoid compilation errors for hashlib with Intel compilers +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/6484 +ulimit_unlimited = True + +# workaround for "undefined symbol: __stack_chk_guard" +# see also https://software.intel.com/en-us/forums/intel-c-compiler/topic/610514 +buildopts = 'LDFLAGS="$LDFLAGS -lssp"' + +# order is important! +# package versions updated October 16th 2017 +exts_list = [ + ('setuptools', '36.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['62074589522a798da243f47348f38020d55b6c945652e2f2c09d3a96299812b7'], + }), + ('pip', '9.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + 'checksums': ['09f243e1a7b461f654c26a725fa373211bb7ff17a9300058b205c61658ca940d'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('numpy', '1.13.3', { + 'patches': ['numpy-1.12.0-mkl.patch'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'checksums': [ + '36ee86d5adbabc4fa2643a073f93d5504bdfed37a149a3a49f4dde259f35a750', # numpy-1.13.3.zip + 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch + ], + }), + ('scipy', '0.19.1', { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + 'checksums': ['a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('mpi4py', '2.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['6543a05851a7aa1e6d165e673d422ba24e45c41e4221f0993fe1e5924a00cb81'], + }), + ('paycheck', '1.0.2', { + 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'checksums': [ + '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz + # paycheck-1.0.2_setup-open-README-utf8.patch + 'ceb7f08aebf016cdcd94ae41c1c76c8c120907f85cbfce240d3a112afb264d79', + ], + }), + ('pbr', '3.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + 'checksums': ['05f61c71aaefc02d8e37c0a3eeb9815ff526ea28b3b76324769e6158d7f95be1'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('Cython', '0.27.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + 'checksums': ['e6840a2ba2704f4ffb40e454c36f73aeb440a4005453ee8d7ff6a00d812ba176'], + }), + ('six', '1.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], + }), + ('dateutil', '2.6.1', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'checksums': ['891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca'], + }), + ('deap', '1.0.2', { + 'patches': ['deap-1.0.2_setup-open-README-utf8.patch'], + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'checksums': [ + 'c52bd32b8f0143db3a0b90f2b976c920b588638d6999ca0d038d8b1c07f7950b', # deap-1.0.2.post2.tar.gz + # deap-1.0.2_setup-open-README-utf8.patch + '39a3a08359321189a1b27a382eb309dfd4470cba9101997a6d527a2fd3a0ce93', + ], + }), + ('decorator', '4.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + 'checksums': ['7cb64d38cb8002971710c8899fbdfb859a23a364b7c99dab19d1f719c2ba16b5'], + }), + ('arff', '2.1.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'checksums': ['b8ef2c64ae5318f6884dc0e20b8491b0b1c96151a40077a479e0f57257cab817'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], + }), + ('ipaddress', '1.0.22', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], + 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], + }), + ('asn1crypto', '0.24.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], + 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], + }), + ('idna', '2.7', { + 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], + 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], + }), + ('pycparser', '2.19', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], + 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], + }), + ('cryptography', '2.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['2699ed21e1f73dd1bdb7b0b22a517295de07809d535b23e200dd22166037fe6f'], + }), + ('pyasn1', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), + ('cffi', '1.11.5', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), + ('PyNaCl', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], + 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], + 'modulename': 'nacl', + }), + ('bcrypt', '3.1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], + 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], + }), + ('paramiko', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + 'checksums': ['fa6b4f5c9d88f27c60fd9578146ff24e99d4b9f63391ff1343305bfd766c4660'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], + }), + ('netifaces', '0.10.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + 'checksums': ['0c4da523f36d36f1ef92ee183f2512f3ceb9a9d2a45f7d19cda5a42c6689ebe0'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], + }), + ('pytz', '2017.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + 'checksums': ['fae4cffc040921b8a2d60c6cf0b5d662c1190fe54d718271db4eb17d44a185b7'], + }), + ('pandas', '0.20.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + 'checksums': ['a777e07633d83d546c55706420179551c8e01075b53c497dcf8ae4036766bc66'], + }), + ('virtualenv', '15.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + 'checksums': ['02f8102c2436bb03b3ee6dede1919d1dac8a427541652e5ec95171ec8adbc93a'], + }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt'], + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib'], + 'checksums': ['7b8fd56df36d9731a83729395ccb85a3b401f62a96255deb1a77220c00ed4085'], + }), + ('xlrd', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], + 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], + }), + ('tabulate', '0.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], + 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], + }), +] + +moduleclass = 'lang' From 6cc95b5cb4b10e546ee09976275aaf48a86d23f6 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 18:31:59 -0600 Subject: [PATCH 0341/5331] adding easyconfigs: R-bundle-Bioconductor-3.6-foss-2017b-R-3.4.3.eb --- ...dle-Bioconductor-3.6-foss-2017b-R-3.4.3.eb | 527 ++++++++++++++++++ 1 file changed, 527 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-foss-2017b-R-3.4.3.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-foss-2017b-R-3.4.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-foss-2017b-R-3.4.3.eb new file mode 100644 index 00000000000..caed54adac4 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.6-foss-2017b-R-3.4.3.eb @@ -0,0 +1,527 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.6' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [ + ('R', '3.4.3', '-X11-20171023'), + ('HDF5', '1.10.1'), # for rhdf5 + ('MariaDB-connector-c', '2.3.4'), # for RMySQL +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.6/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.6/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.6/data/experiment/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on Dec 19th 2017 +exts_list = [ + ('BiocGenerics', '0.24.0', { + 'checksums': ['517d31c47d7d807170031e116af3ffeba57baca3980ef4d85b37c2ec3bdc9d0f'], + }), + ('Biobase', '2.38.0', { + 'checksums': ['6fa2f0dc214d42f2d0afcc42d2f4da2223ebe67a2f79ff69fba6dc19940cf5b1'], + }), + ('S4Vectors', '0.16.0', { + 'checksums': ['8043a0a9f76e00ab96d4214a0ac888d7cf26c0917bb5b3e48ed5503bc6df480f'], + }), + ('IRanges', '2.12.0', { + 'checksums': ['a51e7219a9adedcc3ec708db570dbe8ed1156b0bd2bc882fbf5577cad3fa0cef'], + }), + ('GenomeInfoDbData', '1.0.0', { + 'checksums': ['d7bb73db4a76960e65c5f6d8ccdcb9480a48cea529a30ea2399f8e4c9887e876'], + }), + ('GenomeInfoDb', '1.14.0', { + 'checksums': ['d7db65fe2a494c3a1a0a087a2776eb69cca914024476b920db8f30356b0415ca'], + }), + ('AnnotationDbi', '1.40.0', { + 'checksums': ['8c5a98056d4ab3c215d6a01b64953589d127be71940cfd0031f694a382c604b6'], + }), + ('zlibbioc', '1.24.0', { + 'checksums': ['22f9bb05a415ae3ce828a904abc0f290aede5ae5fdb212fc75f4c152e08229ff'], + }), + ('XVector', '0.18.0', { + 'checksums': ['b36e985344cc3d033d567e2206029e272e1fc23dc5e0ce66c8149ddcdb1c91c4'], + }), + ('Biostrings', '2.46.0', { + 'checksums': ['f353f6c1fdbc520a685b880ef05f61245f04397adfcaae4c1395e14e1b06e56d'], + }), + ('GenomicRanges', '1.30.2', { + 'checksums': ['d2ae992511355061e8433e0496d544708173c451b8a9a1e5276b0f604a097930'], + }), + ('BiocParallel', '1.12.0', { + 'checksums': ['0de25aa5c7a1b1cce8da0d5f42a00eaccc50de1edf4ab30174833ecd851dcf8e'], + }), + ('Rsamtools', '1.30.0', { + 'checksums': ['ba2a6f2c13e7d001fb8e1a00bd73130a6a748c8d9daf41a16fceae2d5df1565e'], + }), + ('lambda.r', '1.2', { + 'checksums': 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['f1e3f92fd55deb37d6489751aeb7aead5e0ea260d5e393781ee346894ba2a68a'], + }), + ('RSpectra', '0.12-0', { + 'checksums': ['c0a9e7467200e08c945ea2f497a1abb1104d92c48516f5affd6f00f9611d4329'], + }), + ('rARPACK', '0.11-0', { + 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], + }), + ('mixOmics', '6.3.1', { + 'checksums': ['1883f0c60e4f0dfa0beb62a9b0f377624cc310efef1646b9c4ba57927a5f742f'], + }), + ('minfi', '1.24.0', { + 'checksums': ['27b66608e7aceed1b701b5f85fb35d0356b9c964164b1545cf2afef4b7d265de'], + }), + ('FDb.InfiniumMethylation.hg19', '2.2.0', { + 'checksums': ['605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f'], + }), + ('methylumi', '2.24.1', { + 'checksums': ['2c81232bb11f2494a57b70d3664a70f21b31799e96a477ba5c301dc6748f1c16'], + }), + ('lumi', '2.30.0', { + 'checksums': ['52a98db2580c6404ad7b0b674c26c3eb7df629784f63a806ae5dd002cf08c0bf'], + }), + ('widgetTools', '1.56.0', { + 'checksums': ['59bf079ca10fa2af25c778fc9546ab09e205b7e8639e2c966ec96bf251d36a76'], + }), + ('tkWidgets', '1.56.0', { + 'checksums': ['ee39ae67415ea2279df7667d4eda45dcd09efc18f824268bcd7bfbea2d683b7c'], + }), + ('Mfuzz', '2.38.0', { + 'checksums': ['316c3dbca6900baf57ab1b32ce8d86338e51361d976560c32662ade6d11b88a1'], + }), + ('venn', '1.5', { + 'checksums': ['51218e1838b1323fb58635c085ba160036cf8eb5f20080090a28d93a89416855'], + }), + ('maSigPro', '1.50.0', { + 'checksums': ['a06d8b226f47c66dcc4cca92dad943d2899d93617969bd345eee6a41aae3d9b4'], + }), + ('SPIA', '2.30.0', { + 'checksums': ['03f7906c3e07165c1f3021652ea2a015a564fde28b6629384aed6d20bfd95b54'], + }), + ('Gviz', '1.22.3', { + 'checksums': ['2a45bd2c3722b72ea6b5a749cb005d9e3f379d6d5bdfbdae3885cf7f65fe32bf'], + }), + ('cummeRbund', '2.20.0', { + 'checksums': ['8034f5509d507057d3ba491ae51b93ee9be303ce51a977ecc5561b7d1d106907'], + }), + ('GenomicFiles', '1.14.0', { + 'checksums': ['3669d0da57f3d4eac35a7736c968d6668c5be5d3825938d90c8e795974ae1c64'], + }), + ('derfinderHelper', '1.12.0', { + 'checksums': ['2b4ca09478fa851e1c6a290bcab429a7760ebbbc27764503bb47d48d12145219'], + }), + ('derfinder', '1.12.6', { + 'checksums': ['80d6bae5a63d354123e2a3d534b2a96c821e38716419543e6736b35207c7e8ae'], + }), + ('polyester', '1.14.0', { + 'checksums': ['ba4f3221e9a8589cb1ce94b35ebb33f9261b0990b54862032da165eb989db4df'], + }), + ('Rsubread', '1.28.1', { + 'checksums': ['205b2e24c1d6f8edf483f7eb5df13646d5cb77a6460ee9223c28f55d254273bb'], + }), + ('pcaMethods', '1.70.0', { + 'checksums': ['68aeb04c7b0fffcf2a9e3fce039d69db2c102d122e3b86e01489800e5e192246'], + }), + ('marray', '1.56.0', { + 'checksums': ['2caad6eab11df6f58022ebbfb357e03af6b4cd07945cd415b1f2306f501c8991'], + }), + ('CGHbase', '1.38.0', { + 'checksums': ['9562f906d128261bd2b2239799fa0c0b6654a2452c770b6232f7ad2635dbd63b'], + }), + ('sigaR', '1.26.0', { + 'checksums': ['b380854cbbf25afb685d2ce56e768dae6f12e58451a4425bdd29e2ecd290d2a4'], + }), + ('HCsnip', '1.17.0', { + 'checksums': ['426026207e86888ae16d609b4b1b2170b5ebfe3d6fbb14a151c0ed6f43dd3a81'], + }), + ('metagenomeSeq', '1.20.1', { + 'checksums': ['b713d70b7b2cb8f31e2151ada1cadb7ca46c9c2d2f10fcc3d455831ca9312b96'], + }), + ('gdsfmt', '1.14.1', { + 'checksums': ['e183b9b979512e61dea13bfbb63279d4f018faff5effbca614dccf526591fe34'], + }), + ('SNPRelate', '1.12.2', { + 'patches': ['SNPRelate-1.6.5_no-SSE-intr.patch'], + 'checksums': [ + '7166a26e89d9dfd300e3fb6d6a2beed21946c5832015ac1393dbcfbfbc94a017', # SNPRelate_1.12.2.tar.gz + '258558d4ed00178b2feab0d932955aaeb20a8c08992d88e5ddfc853d4cd79d2a', # SNPRelate-1.6.5_no-SSE-intr.patch + ], + }), + ('rhdf5', '2.22.0', { + 'checksums': ['81110d0f79b2ed1599c90d2a254671ad0eeb07fef92ed66b3456f5f0302aa890'], + }), + ('biomformat', '1.6.0', { + 'checksums': ['7aa98827b119f1cac4b49e777d789ab9f387a791596b05a6844db5a39805476b'], + }), + ('phyloseq', '1.22.3', { + 'checksums': ['c0de813c5eeb68c02d20455552a6feda97a59d2391777dc35a727fcb40115e36'], + }), + ('ALDEx2', '1.10.0', { + 'checksums': ['a3fcadb525906ed3b113a8591c7078c0544f103aa896b2a137dc4052add3c360'], + }), + ('RcppParallel', '4.3.20', { + 'checksums': ['0fac9b63c4c294619388138a048b507efee2e990c447924c309a0421611183c1'], + }), + ('dada2', '1.6.0', { + 'checksums': ['79b65f611f7a4da5b08c9d258ab69540139d8159b24481bbbc2e786604e48e51'], + }), + ('LEA', '2.0.0', { + 'checksums': ['b6e9575b503464a70bb5a04ae828894540795c588194e318599b5655c5173dc0'], + }), + ('tximport', '1.6.0', { + 'checksums': ['505c8d721b09897519cfa0e82fabbfe97a536ce0587c86e59be175185265d8bf'], + }), + ('SingleCellExperiment', '1.0.0', { + 'checksums': ['3a2be57963077d8fac43f40b7213489aae23e713259947db2e8a187e523447e4'], + }), + ('Rhdf5lib', '1.0.0', { + 'checksums': ['3ce431b69998878c074184aece188c3b249ae64ca491be3617162f996f266c4e'], + }), + ('HDF5Array', '1.6.0', { + 'checksums': ['500275365ecf557798e9f40248097a93c7c55520a8e17de9361b2b1d88fa8d4d'], + }), + ('beachmat', '1.0.2', { + 'checksums': ['1ff356bf49dea190aeab405c7785f18e7048eb31b2c7b3b86aa42f5794fccd2c'], + }), + ('scater', '1.6.3', { + 'checksums': ['b69d2b7264b35fb4ac826332d7321f7d1de925a0b76e27700b4a69e49e497a60'], + }), + ('scran', '1.6.7', { + 'checksums': ['ab42b13bf450329706ef8b93f347174af135bf69f8f94e121aebdbdc512cd57d'], + }), + ('SC3', '1.7.7', { + 'checksums': ['3c703f15cdaf47d7543107afc0295bbd3befbbffc1a095fa25892b8b41213df5'], + }), + ('ComplexHeatmap', '1.17.1', { + 'checksums': ['9e71eec1020eed2075e87aad460df1c247674b820c0fdae0424d631c4bb9d3f4'], + }), + ('GENIE3', '1.0.0', { + 'checksums': ['a361f25fb8b56114e95fcf9a223956fe6e10213b65094c6bb60281b5299cabd3'], + }), + ('dupRadar', '1.8.0', { + 'checksums': ['f6b605828f02480259adc6a692a0a90e96387457d4bb5cd4a2b0daa65b03609d'], + }), + ('DNAcopy', '1.52.0', { + 'checksums': ['51f192baca80ba98965893a5760306e0a250ede8c468c821951f864773a1f188'], + }), + ('MAST', '1.4.1', { + 'checksums': ['524b5dfa4131581649410852ff999d007ed57c4b1f6ae2244b60fbff0afa5871'], + }), + ('fitdistrplus', '1.0-9', { + 'checksums': ['e68fdee3dde1a35cde0f0deeaecf74f1eb3846dc70cc610e290da5f24821a9a3'], + }), + ('splatter', '1.2.1', { + 'checksums': ['af641527ae3fb21966d11201fa227bf0934973c6b5cfcb38bac52a576b485745'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('blockmodeling', '0.1.9', { + 'checksums': ['c93a74d439de861fc7a1c484dc0cc983a7330904f1cdef15a03ee1b2b98ba8e5'], + }), + ('EBSeq', '1.18.0', { + 'checksums': ['bc9eeeeb1ac825d74d9f325d8c10fee39e7bf76958655486cfc372629cea275f'], + }), + ('scDD', '1.2.0', { + 'checksums': ['81950bef464c80a3e070693f5909e7c7193fa76293ad2b458a63a23d9380a411'], + }), + ('DDRTree', '0.1.5', { + 'checksums': ['d351ec029461b43c0dcc7c30d9f378753b31ba16c6dbf667869df279b874459b'], + }), + ('HSMMSingleCell', '0.112.0', { + 'checksums': ['11b6dcb7a3ee86323740aa4c3627abb4c546a890ad0d3e0a262fcf2aa49be773'], + }), + ('ggrepel', '0.7.0', { + 'checksums': ['28187a10eb37ef0432cbdfdb39829096c61b0d413db021c8113b87f34c75183c'], + }), + ('densityClust', '0.3', { + 'checksums': ['23749ba57d1d7886e0fe9ba535d7f30dd2cbb7ebf451afcec8f54be5d4063eff'], + }), + ('qlcMatrix', '0.9.5', { + 'checksums': ['4e13c2413dc28ecda0eff05ae6d6a0e4ed4597c368ce9a2031e2cad57c4ca43a'], + }), + ('RUnit', '0.4.31', { + 'checksums': ['9d764092216391c9d7e13bbe1585f5d00c357ed8b04c7e66ed82d229c34119cb'], + }), + ('biocViews', '1.46.0', { + 'checksums': ['ad868c40c54bbcac5b38776bc56afca95bc514f091ea042b4d08303c83c4fe27'], + }), + ('monocle', '2.6.1', { + 'checksums': ['7b43d5e97e5506170b8a6b5861abcdecce43a8fb774ad2755b142c2f11226fe8'], + }), + ('scde', '2.6.0', { + 'checksums': ['226c6ac1699c507546144313027b844280092e311da1fb4cb10b288d6854aa33'], + }), + ('ROTS', '1.6.0', { + 'checksums': ['509202ea048cf3e62f7d06dde89c03ceaa22aa0dc4e158488d41fc18315fb889'], + }), + ('DESeq', '1.30.0', { + 'checksums': ['693b7b5af137c05fda2fe4815f8e62d932a39451ffe8fed1e43c9ae0d9e0c556'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/uniqueAtomMat/'], + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('QuasiSeq', '1.0-10-1', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/QuasiSeq/'], + 'checksums': ['47921c3204848614dc22961a3adca4fe740b704380742e17884f8b61183ba415'], + }), + ('aod', '1.3', { + 'checksums': ['e377effe345987850ece985eabf79750ca1979d75469d17a323c21515ad1dda8'], + }), + ('ExomeDepth', '1.1.10', { + 'checksums': ['2678ff4c4d024e08a843f08cb932707a11ce7274ab48bfc2632669ca930d8f86'], + }), + ('WES.1KG.WUGSC', '1.10.0', { + 'checksums': ['d204b8b1c2e1a0857c1686807229e69a0f4ed0b90f6baa73fe6f4376578f7f34'], + }), + ('CODEX', '1.10.0', { + 'checksums': ['d83685a70122cf8beeb9795b2d601c69ce2edc997a2a3308b1f9210b627ccece'], + }), + ('DEXSeq', '1.24.4', { + 'checksums': ['a59920d174e7d95f38721eeb1e5769c0c1bb7cd3359eadf061a53b41cef600a9'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' From f0ea7af035e8e6305eda649872717235f3fa33e1 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Feb 2019 18:33:41 -0600 Subject: [PATCH 0342/5331] Add dependency --- .../MariaDB-connector-c-2.3.4-foss-2017b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-foss-2017b.eb diff --git a/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-foss-2017b.eb b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-foss-2017b.eb new file mode 100644 index 00000000000..507fca0c1e7 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-foss-2017b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB-connector-c' +version = '2.3.4' + +homepage = 'https://downloads.mariadb.org/connector-c/' +description = "MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases." + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://downloads.mariadb.org/f/connector-c-%(version)s'] +sources = ['mariadb-connector-c-%(version)s-src.tar.gz'] +checksums = ['8beb0513da8a24ed2cb47836564c8b57045c3b36f933362f74b3676567c13abc'] + +builddependencies = [('CMake', '3.10.1')] + +sanity_check_paths = { + 'files': ['lib/mariadb/libmariadbclient.a', 'lib/mariadb/libmariadb.%s' % SHLIB_EXT], + 'dirs': ['include/mariadb'], +} + +modextrapaths = { + 'CPATH': ['include/mariadb'], + 'LD_LIBRARY_PATH': ['lib/mariadb'], + 'LIBRARY_PATH': ['lib/mariadb'], +} + +moduleclass = 'lib' From 2ef962925b7bc7a9ec314b44ee61421f7ceeb252 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 13 Feb 2019 08:16:57 +0100 Subject: [PATCH 0343/5331] adding easyconfigs: MetaPhlAn2-2.7.8-foss-2018b-Python-3.6.6.eb --- ...etaPhlAn2-2.7.8-foss-2018b-Python-3.6.6.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaPhlAn2/MetaPhlAn2-2.7.8-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/m/MetaPhlAn2/MetaPhlAn2-2.7.8-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MetaPhlAn2/MetaPhlAn2-2.7.8-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..ba832273025 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaPhlAn2/MetaPhlAn2-2.7.8-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'Tarball' + +name = 'MetaPhlAn2' +version = '2.7.8' +versionsuffix = '-Python-%(pyver)s' + +bitbucket_account = 'biobakery' +homepage = 'https://bitbucket.org/%(bitbucket_account)s/%(namelower)s/' +description = """MetaPhlAn is a computational tool for profiling the composition of microbial + communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing + data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now + possible to perform accurate strain-level microbial profiling.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['24cd29c8b1d475adbe6b354391ce455fcfe9ef2266b6fb6635dee2bdb6a3edd3'] + +dependencies = [ + ('Bowtie2', '2.3.4.2'), + ('Perl', '5.28.0'), + ('Python', '3.6.6'), +] + +# needed to create database during installation +# the database is used if --input_type is fastq, fasta, multifasta, or multifastq +# otherwise database creation will be tried on first use with one of the above options +# and likely fail because a normal user can't write in the software directory +postinstallcmds = ['%(installdir)s/%(namelower)s.py --install'] + +modextrapaths = { + 'PATH': '', + 'mpa_dir': '', +} + +sanity_check_paths = { + 'files': ['%(namelower)s.py', 'strainphlan.py'], + 'dirs': ['utils', 'strainphlan_src', 'strainphlan_tutorial'], +} + +sanity_check_commands = ['%(namelower)s.py -v'] + +moduleclass = 'bio' From 6edfaca2259d83dffe80664e2ddd5d2e6c93cd4e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Feb 2019 09:30:57 +0100 Subject: [PATCH 0344/5331] add liquidSVM extension to R 3.5.1 --- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 3 +++ easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index 2573f954659..ee8828958a2 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -2066,6 +2066,9 @@ exts_list = [ ('asnipe', '1.1.11', { 'checksums': ['982b9f34dbcf98136a8406b9ce4717faf155c7d5d923dcdf0dca6a9d53e27219'], }), + ('liquidSVM', '1.2.2', { + 'checksums': ['96f545e5878d2cce27f37185757945607b00fdeaa43258f0884a578be6c3688a'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index da852d607f8..7d71a230890 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -2064,6 +2064,9 @@ exts_list = [ ('asnipe', '1.1.11', { 'checksums': ['982b9f34dbcf98136a8406b9ce4717faf155c7d5d923dcdf0dca6a9d53e27219'], }), + ('liquidSVM', '1.2.2', { + 'checksums': ['96f545e5878d2cce27f37185757945607b00fdeaa43258f0884a578be6c3688a'], + }), ] moduleclass = 'lang' From 4775ecab52a99002560291c7ad326c7f0d954158 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Feb 2019 09:34:23 +0100 Subject: [PATCH 0345/5331] use pip to install CVXOPT 1.2.3 --- .../c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb index 8de4194ac15..087a32429ac 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb @@ -27,10 +27,15 @@ dependencies = [ ('GSL', '2.5'), ] -prebuildopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' -prebuildopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' +download_dep_fail = True +use_pip = True -installopts = ' && nosetests' +preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' +preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' + +installopts = ' --no-binary cvxopt' + +postinstallcmds = ['nosetests'] sanity_check_paths = { 'files': [], From 966d3aff053181383834e2867484162bce148497 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Feb 2019 09:44:49 +0100 Subject: [PATCH 0346/5331] stick to SuiteSparse 5.1.2 with 2018b generation of easyconfigs --- .../CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb | 2 +- ...uiteSparse-5.4.0-foss-2018b-METIS-5.1.0.eb | 25 ------------------- 2 files changed, 1 insertion(+), 26 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2018b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb index 087a32429ac..f68aa1a298e 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb @@ -23,7 +23,7 @@ checksums = [ dependencies = [ ('Python', '3.6.6'), - ('SuiteSparse', '5.4.0', '-METIS-5.1.0'), + ('SuiteSparse', '5.1.2', '-METIS-5.1.0'), ('GSL', '2.5'), ] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2018b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2018b-METIS-5.1.0.eb deleted file mode 100644 index 33a1038bfb2..00000000000 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2018b-METIS-5.1.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'SuiteSparse' -version = '5.4.0' -metis_ver = '5.1.0' -versionsuffix = '-METIS-%s' % metis_ver - -homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' -description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" - -toolchain = {'name': 'foss', 'version': '2018b'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] -sources = [SOURCE_TAR_GZ] -checksums = ['374dd136696c653e34ef3212dc8ab5b61d9a67a6791d5ec4841efb838e94dbd1'] - -builddependencies = [('CMake', '3.12.1')] - -dependencies = [('METIS', metis_ver)] - -parallel = 1 - -prebuildopts = "sed -i 's/-openmp/-fopenmp/g' SuiteSparse_config/SuiteSparse_config.mk && " -prebuildopts += "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse/lib:$LD_LIBRARY_PATH && " - -moduleclass = 'numlib' From 02a1e883d09562d515f7ea11586da253b4dc7966 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Feb 2019 10:40:34 +0100 Subject: [PATCH 0347/5331] {toolchain} intel/2019.02 (+ HPL test case) --- .../h/HPL/HPL-2.3-intel-2019.02.eb | 21 ++++++++++ .../i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb | 33 ++++++++++++++++ .../iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb | 18 +++++++++ .../ifort-2019.2.187-GCC-8.2.0-2.31.1.eb | 38 ++++++++++++++++++ ...ort-2019.2.187_no_mpi_mic_dependency.patch | 13 +++++++ .../easyconfigs/i/iimpi/iimpi-2019.02.eb | 20 ++++++++++ .../i/imkl/imkl-2019.2.187-iimpi-2019.02.eb | 39 +++++++++++++++++++ ...87-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb | 22 +++++++++++ .../easyconfigs/i/intel/intel-2019.02.eb | 24 ++++++++++++ 9 files changed, 228 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2019.02.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2019.2.187_no_mpi_mic_dependency.patch create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2019.02.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2019.02.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2019.02.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2019.02.eb new file mode 100644 index 00000000000..059334e75da --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2019.02.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2019.02'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..87b5da692d0 --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'icc' +version = '2019.2.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Intel C and C++ compilers" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15093/'] +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] +checksums = ['fc434a2e005af223f43d258c16f004134def726a8d2a225e830af85d553bee55'] + +gccver = '8.2.0' +binutilsver = '2.31.1' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..4df7dcbde6b --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iccifort' +version = '2019.2.187' +versionsuffix = '-GCC-8.2.0-2.31.1' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = "Intel C, C++ & Fortran compilers" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..ec71efeb29b --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'ifort' +version = '2019.2.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Intel Fortran compiler" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15094/'] +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] +patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2019_update2_composer_edition_for_fortran.tgz + '71e5c9bf055da9ccc50252064740febf506cdf9a560cefe88ba4ba18f84f885e', + 'dbc6496cb2adbf34e66b73d8d75da7dec2738c1026e736bb5bc8393e879f434f', # ifort_2019.2.187_no_mpi_mic_dependency.patch +] + +gccver = '8.2.0' +binutilsver = '2.31.1' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187_no_mpi_mic_dependency.patch b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187_no_mpi_mic_dependency.patch new file mode 100644 index 00000000000..a23d962a877 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187_no_mpi_mic_dependency.patch @@ -0,0 +1,13 @@ +don't install Intel MIC runtine components (mpi-mic-rt), cfr. https://github.com/easybuilders/easybuild-easyconfigs/pull/3793 +--- parallel_studio_xe_2019_update2_composer_edition_for_fortran/pset/mediaconfig.xml.orig 2019-02-13 09:15:51.376296916 +0100 +author: Kenneth Hoste (HPC-UGent) ++++ parallel_studio_xe_2019_update2_composer_edition_for_fortran/pset/mediaconfig.xml 2019-02-13 09:17:04.896021592 +0100 +@@ -1047,7 +1047,7 @@ + + ${COMPLIB_ROOT} + 1548933044877 +- ++ + Intel Fortran Compiler for Intel(R) 64 + Intel Fortran Compiler 19.0 Update 2 + (R) Fortran ((R) 64) diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2019.02.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2019.02.eb new file mode 100644 index 00000000000..b492c9b55d4 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2019.02.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2019.02' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2019.2.187' +suff = '-GCC-8.2.0-2.31.1' +dependencies = [ + ('icc', compver, suff), + ('ifort', compver, suff), + ('impi', compver, '', ('iccifort', '%s%s' % (compver, suff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb new file mode 100644 index 00000000000..b6886b31353 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.2.187-iimpi-2019.02.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2019.2.187' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2019.02'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15095/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['2bf004e6b5adb4f956993d6c20ea6ce289bb630314dd501db7f2dd5b9978ed1d'] + +dontcreateinstalldir = 'True' + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..75e3a61ab85 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2019.2.187-iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,22 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'impi' +version = '2019.2.187' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'iccifort', 'version': '2019.2.187-GCC-8.2.0-2.31.1'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15040/'] +sources = ['l_mpi_%(version)s.tgz'] +checksums = ['6a3305933b5ef9e3f7de969e394c91620f3fa4bb815a4f439577739d04778b20'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2019.02.eb b/easybuild/easyconfigs/i/intel/intel-2019.02.eb new file mode 100644 index 00000000000..d12e6866f2b --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2019.02.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2019.02' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2019.2.187' +gccver = '8.2.0' +binutilsver = '2.31.1' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', compver, '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', compver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From 2283bed62bfa881817a62d90fd42099478e39319 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 13 Feb 2019 10:52:27 +0100 Subject: [PATCH 0348/5331] adding easyconfigs: RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb, bx-python-0.8.2-foss-2018b-Python-3.6.6.eb, pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb --- ...bx-python-0.8.2-foss-2018b-Python-3.6.6.eb | 48 +++++++++++++++++++ ...pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb | 37 ++++++++++++++ .../RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb | 43 +++++++++++++++++ 3 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/r/RSeQC/RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..e1f614e8280 --- /dev/null +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'bx-python' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/bxlab/%(name)s' +description = """The bx-python project is a Python library and associated set of scripts to allow for rapid + implementation of genome scale analyses.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('LZO', '2.10'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " + +exts_download_dep_fail = True + +exts_list = [ + ('python-lzo', '1.12', { + 'modulename': 'lzo', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-lzo/'], + 'checksums': ['97a8e46825e8f1abd84c2a3372bc09adae9745a5be5d3af2692cd850dac35345'], + }), + (name, version, { + 'modulename': 'bx', + 'source_urls': ['https://pypi.python.org/packages/source/b/%(name)s/'], + 'checksums': ['faeb0c7c9fcb2f95c4fc1995af4f45287641deee43a01659bd30fe95c5d37386'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..51aaaa924c1 --- /dev/null +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonPackage' + +name = 'pyBigWig' +version = '0.3.13' +versionsuffix = '-Python-%(pyver)s' + +github_account = 'deeptools' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """A python extension, written in C, for quick access to bigBed files and access to and creation of + bigWig files.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['1e0114bb106b7b05613d8be753759b578e7a16b3cd03f21bedcdace13b2bea08'] + +dependencies = [('Python', '3.6.6')] + +use_pip = True + +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python lib/python%(pyshortver)s/site-packages/pyBigWigTest/test.py'] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +options = {'modulename': 'pyBigWig'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..bb38004db19 --- /dev/null +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'RSeQC' +version = '3.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://%(namelower)s.sourceforge.net/' +description = """RSeQC provides a number of useful modules that can + comprehensively evaluate high throughput sequence data especially RNA-seq + data. Some basic modules quickly inspect sequence quality, nucleotide + composition bias, PCR bias and GC bias, while RNA-seq specific modules + evaluate sequencing saturation, mapped reads distribution, coverage + uniformity, strand specificity, transcript level RNA integrity etc.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['a5c49d47915ad0c94d7b14968d82697d0b3c5ddbb18aaa186f2e1252478f0836'] + +dependencies = [ + ('Python', '3.6.6'), + ('Pysam', '0.15.1', versionsuffix), + ('bx-python', '0.8.2', versionsuffix), + ('pyBigWig', '0.3.13', versionsuffix), +] + +use_pip = True + +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', 'bin/split_paired_bam.py'], + 'dirs': ['lib'] +} + +options = {'modulename': 'qcmodule'} + +moduleclass = 'bio' From b5524770d6e43f6a579c9d0505a58d5e11daeede Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 13 Feb 2019 11:16:37 +0100 Subject: [PATCH 0349/5331] adding easyconfigs: imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb --- ...ced-learn-0.4.3-foss-2018b-Python-3.6.6.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..3f2d579c9b9 --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'imbalanced-learn' +version = '0.4.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5bd9e86e40ce4001a57426541d7c79b18143cbd181e3330c1a3e5c5c43287083'] + +dependencies = [ + ('Python', '3.6.6'), + ('scikit-learn', '0.20.2', versionsuffix), +] + +options = {'modulename': 'imblearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From bb522291593f9c591cd27e15b8e9114c9f7e4a08 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Wed, 13 Feb 2019 11:19:48 +0100 Subject: [PATCH 0350/5331] adding easyconfigs: SRA-Toolkit-2.9.4-centos_linux64.eb --- .../SRA-Toolkit-2.9.4-centos_linux64.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.4-centos_linux64.eb diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.4-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.4-centos_linux64.eb new file mode 100644 index 00000000000..febc37cc437 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.4-centos_linux64.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute +# Based on work by npklein +# updated to version 2.9.4 +# uploaded by J. Sassmannshausen + +easyblock = 'PackedBinary' + +name = 'SRA-Toolkit' +version = '2.9.4' +versionsuffix = '-centos_linux64' + +homepage = 'http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] +sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['3cce659729da72f476cf2a20adb1a44da39da69a2667205de3ab39ee13752b41'] + +sanity_check_paths = { + 'files': ['bin/abi-load', 'bin/fastq-dump', 'bin/sff-load', 'bin/vdb-dump'], + 'dirs': [] +} + +moduleclass = 'bio' From 0683130513478557fbe883e883b946b1eeafc2e9 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 13 Feb 2019 10:58:28 +0000 Subject: [PATCH 0351/5331] adding easyconfigs: PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb, PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb --- .../PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb | 223 +++++++++++++++++ ...Torch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 229 ++++++++++++++++++ 2 files changed, 452 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..653c5d789ed --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,223 @@ +easyblock = 'PythonPackage' + +name = 'PyTorch' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +pytorchdir = 'pytorch-%(version)s' +extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' +mklml_extract_cmd = "mkdir -p %s/%s && tar -C %s/%s --strip-components=1 -xzf %%s" + +source_urls = ['https://github.com/pytorch/pytorch/archive'] + +# PyTorch pulls in a bunch of submodules which don't have releases. +# We download the submodule revisions from their repos. +# determine commit of additional sources via https://github.com/pytorch/pytorch/tree/v1.0.1/third_party +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], + 'download_filename': '670b4d4aa46886cc66874e2a4dc846f5cfc2a285.tar.gz', + 'filename': 'gloo-20190201.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/gloo'), + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/googletest'), + }, + { + 'source_urls': ['https://github.com/pybind/pybind11/archive'], + 'download_filename': '5c8746ff135abb390bf95944be593e895a586a50.tar.gz', + 'filename': 'pybind11-20180911.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pybind11'), + }, + { + 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], + 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', + 'filename': 'clang-cindex-python3-20170330.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pybind11/tools/clang'), + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': '89fe1695edf9ee14c22f815f24bac45577a4f135.tar.gz', + 'filename': 'cpuinfo-20190117.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/cpuinfo'), + }, + { + 'source_urls': ['https://github.com/onnx/onnx/archive'], + 'download_filename': '42804705bdbf179d1a98394008417e1392013547.tar.gz', + 'filename': 'onnx-20181204.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/onnx'), + }, + { + 'source_urls': ['https://github.com/google/protobuf/archive'], + 'download_filename': '2761122b810fe8861004ae785cc3ab39f384d342.tar.gz', + 'filename': 'protobuf-20171113.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/protobuf'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], + 'download_filename': '13da0b4c21d17f94150713366420baaf1b5a46f4.tar.gz', + 'filename': 'pthreadpool-20181008.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pthreadpool'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], + 'download_filename': 'b742d1143724d646cd0f914646f1240eacf5bd73.tar.gz', + 'filename': 'FXdiv-20181016.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/FXdiv'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/psimd/archive'], + 'download_filename': '90a938f30ba414ada2f4b00674ee9631d7d85e19.tar.gz', + 'filename': 'psimd-20180906.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/psimd'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FP16/archive'], + 'download_filename': '34d4bf01bbf7376f2baa71b8fa148b18524d45cf.tar.gz', + 'filename': 'FP16-20181011.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/FP16'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/NNPACK/archive'], + 'download_filename': '1e005b0c2777f39972a4ac15bea03e0e315a3d92.tar.gz', + 'filename': 'NNPACK-20180903.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/NNPACK'), + }, + { + 'source_urls': ['https://github.com/shibatch/sleef/archive'], + 'download_filename': '6ff7a135a1e31979d1e1844a2e7171dfbd34f54f.tar.gz', + 'filename': 'sleef-20180509.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/sleef'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/PeachPy/archive'], + 'download_filename': '07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz', + 'filename': 'PeachPy-20180219.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/python-peachpy'), + }, + { + 'source_urls': ['https://github.com/pytorch/QNNPACK/archive'], + 'download_filename': 'ef05e87cef6b8e719989ce875b5e1c9fdb304c05.tar.gz', + 'filename': 'QNNPACK-20181205.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/QNNPACK'), + }, + { + 'source_urls': ['https://github.com/pytorch/fbgemm/archive'], + 'download_filename': '79333308f5e2fc242727879dcd3de3536b6ffc39.tar.gz', + 'filename': 'fbgemm-20190123.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/fbgemm'), + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': '505be96ab23056580a3a2315abba048f4428b04e.tar.gz', + 'filename': 'benchmark-20180606.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/benchmark'), + }, + { + 'source_urls': ['https://github.com/eigenteam/eigen-git-mirror/archive'], + 'download_filename': 'f59336cee358f92b959de6a0daf07c4ab2318022.tar.gz', + 'filename': 'eigen-20180908.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/eigen'), + }, + { + 'source_urls': ['https://github.com/google/gemmlowp/archive'], + 'download_filename': '8416bab644641a5c0a81ecf91a5cda804af0aee1.tar.gz', + 'filename': 'gemmlowp-20180828.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/gemmlowp/gemmlowp'), + }, + { + 'source_urls': ['https://github.com/NVIDIA/nccl/archive'], + 'download_filename': '3c6e25210bb1b544748937e5db74db0b9679b95e.tar.gz', + 'filename': 'nccl-20181109.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/nccl/nccl'), + }, + { + 'source_urls': ['https://github.com/NVlabs/cub/archive'], + 'download_filename': '285aeebaa34b0e8a7670867a2e66c1a52d998d6a.tar.gz', + 'filename': 'cub-20170829.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/cub'), + }, + { + 'source_urls': ['https://github.com/intel/ideep/archive'], + 'download_filename': '7b8f9d025a675522305a1c5d1328d83f11f205e8.tar.gz', + 'filename': 'ideep-20181224.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/ideep'), + }, + { + 'source_urls': ['https://github.com/intel/mkl-dnn/archive'], + 'download_filename': '0c3cb94999919d33e4875177fdef662bd9413dd4.tar.gz', + 'filename': 'mkl-dnn-20190131.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/ideep/mkl-dnn'), + }, + # mkl-dnn requires Intel MKL, so download minimal Intel MKL version + # actually using imkl as a dependency would be messy due to underlying icc/ifort compilers & impi MPI lib + { + 'source_urls': ['https://github.com/intel/mkl-dnn/releases/download/v0.17.3'], + 'filename': 'mklml_lnx_2019.0.1.20180928.tgz', + 'extract_cmd': mklml_extract_cmd % + (pytorchdir, 'third_party/ideep/mkl-dnn/external/mklml_lnx_2019.0.1.20180928', + pytorchdir, 'third_party/ideep/mkl-dnn/external/mklml_lnx_2019.0.1.20180928'), + }, +] +checksums = [ + '210561583378132d07287518710251bcf861f9b7d625eb67258ed2e9d567cea1', # v1.0.1.tar.gz + '0e98a4fdb6e27add72b4bb0e63a5ed20a9271139c3d0ccc2c15c502e3366bca3', # gloo-20190201.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + 'ffe077d0fccc34aa95c2aba7a3abadbdc2a480c44a238879381733d38322e921', # pybind11-20180911.tar.gz + '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz + 'b84c49b4bdc12b0e8f1bff365dcefd50e5a2a25eeef8c928aeb2dab9fda4d599', # cpuinfo-20190117.tar.gz + 'b9520d6ce9f8b9928bf517696ea62fd03308fd21dafdebfec7aeb8894b3813ab', # onnx-20181204.tar.gz + 'd293a86f4c82a31990b89be2b9787df045e3f6b86378e9950e5e1145d4a08e6a', # protobuf-20171113.tar.gz + '90ab4f60ae0e99c0172dd5201dccc6de6c8f384a21b3d959588f4c1e00beec0f', # pthreadpool-20181008.tar.gz + '07625551202a1f35fe5e826669ad495962b26f6a139290e90b321c5996f002ef', # FXdiv-20181016.tar.gz + 'afd27417c6df1c85f79a68361055dd3adc292174913c39c1f58b698b9cfd7926', # psimd-20180906.tar.gz + 'dacd927f345c40163532e65ed3ea796d190f4efdd125838401a35e8147e55313', # FP16-20181011.tar.gz + '02d278559609982f2dbd973f265caf674274ac7a61ddd867c4956176252d940e', # NNPACK-20180903.tar.gz + 'f822489cbbf3cd09db578ea7ac9af40a9d3184f8ff95cb98e8b33b71ed5d89f8', # sleef-20180509.tar.gz + '13100c3deed300bbf16f87d8af3539f432462bfef9d38f0c7e3e387dc2e88676', # PeachPy-20180219.tar.gz + 'dc0c9ca760bb1bf858dd1aebaf1471b8437c1b2ef9a9b6acaf302fa14b04194f', # QNNPACK-20181205.tar.gz + 'd2dabcd172db8fb91dfa75422a5eb6f55f55f22d047d9f1b02eb6a3be88a09cd', # fbgemm-20190123.tar.gz + '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz + 'fd9e9f0d6ef407a162f5f283c52d3c271efc1092377274abe1e30dff83dbc1a4', # eigen-20180908.tar.gz + 'e12e096e986221d96d55185e870397b3717b625d6c5d155fbd9a7be314bed06a', # gemmlowp-20180828.tar.gz + '72b4835362d8586e315bdf5c30eea99f2efcf14f19162f00ac0675e8b1b22e61', # nccl-20181109.tar.gz + '7224b03af4acbc54525105bb42e3ecd75c66a3a5b47e8a725ab008467c4109f9', # cub-20170829.tar.gz + 'c7418025bd57b3143e651433d0874a39629fce6cc96b43e3f8d5861a8ad23ffb', # ideep-20181224.tar.gz + 'f98d2c297353acfab1ecff2054bee65efd2367b4c621e762cf26f50e037a9728', # mkl-dnn-20190131.tar.gz + 'f00dc3b142a5be399bdeebd7e7ea369545a35d4fb84c86f98b6b048d72685295', # mklml_lnx_2019.0.1.20180928.tgz +] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '3.6.6'), + ('PyYAML', '3.13', versionsuffix), + ('hypothesis', '4.5.0', versionsuffix), + ('Ninja', '1.8.2'), +] + +# This environment is needed to prevent setup.py from invoking git to determine version. +prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' + +runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' +# skip test subsuites that include hanging/failing tests for now +runtest += '&& python test/run_test.py --exclude autograd cpp_extensions c10d torch --verbose' + +options = {'modulename': 'torch'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..ffa97254219 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,229 @@ +easyblock = 'PythonPackage' + +name = 'PyTorch' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +pytorchdir = 'pytorch-%(version)s' +extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' +mklml_extract_cmd = "mkdir -p %s/%s && tar -C %s/%s --strip-components=1 -xzf %%s" + +source_urls = ['https://github.com/pytorch/pytorch/archive'] +# PyTorch pulls in a bunch of submodules which don't have releases. +# We download the submodule revisions from their repos. +# determine commit of additional sources via https://github.com/pytorch/pytorch/tree/v1.0.1/third_party +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], + 'download_filename': '670b4d4aa46886cc66874e2a4dc846f5cfc2a285.tar.gz', + 'filename': 'gloo-20190201.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/gloo'), + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/googletest'), + }, + { + 'source_urls': ['https://github.com/pybind/pybind11/archive'], + 'download_filename': '5c8746ff135abb390bf95944be593e895a586a50.tar.gz', + 'filename': 'pybind11-20180911.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pybind11'), + }, + { + 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], + 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', + 'filename': 'clang-cindex-python3-20170330.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pybind11/tools/clang'), + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': '89fe1695edf9ee14c22f815f24bac45577a4f135.tar.gz', + 'filename': 'cpuinfo-20190117.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/cpuinfo'), + }, + { + 'source_urls': ['https://github.com/onnx/onnx/archive'], + 'download_filename': '42804705bdbf179d1a98394008417e1392013547.tar.gz', + 'filename': 'onnx-20181204.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/onnx'), + }, + { + 'source_urls': ['https://github.com/google/protobuf/archive'], + 'download_filename': '2761122b810fe8861004ae785cc3ab39f384d342.tar.gz', + 'filename': 'protobuf-20171113.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/protobuf'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], + 'download_filename': '13da0b4c21d17f94150713366420baaf1b5a46f4.tar.gz', + 'filename': 'pthreadpool-20181008.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pthreadpool'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], + 'download_filename': 'b742d1143724d646cd0f914646f1240eacf5bd73.tar.gz', + 'filename': 'FXdiv-20181016.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/FXdiv'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/psimd/archive'], + 'download_filename': '90a938f30ba414ada2f4b00674ee9631d7d85e19.tar.gz', + 'filename': 'psimd-20180906.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/psimd'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FP16/archive'], + 'download_filename': '34d4bf01bbf7376f2baa71b8fa148b18524d45cf.tar.gz', + 'filename': 'FP16-20181011.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/FP16'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/NNPACK/archive'], + 'download_filename': '1e005b0c2777f39972a4ac15bea03e0e315a3d92.tar.gz', + 'filename': 'NNPACK-20180903.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/NNPACK'), + }, + { + 'source_urls': ['https://github.com/shibatch/sleef/archive'], + 'download_filename': '6ff7a135a1e31979d1e1844a2e7171dfbd34f54f.tar.gz', + 'filename': 'sleef-20180509.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/sleef'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/PeachPy/archive'], + 'download_filename': '07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz', + 'filename': 'PeachPy-20180219.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/python-peachpy'), + }, + { + 'source_urls': ['https://github.com/pytorch/QNNPACK/archive'], + 'download_filename': 'ef05e87cef6b8e719989ce875b5e1c9fdb304c05.tar.gz', + 'filename': 'QNNPACK-20181205.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/QNNPACK'), + }, + { + 'source_urls': ['https://github.com/pytorch/fbgemm/archive'], + 'download_filename': '79333308f5e2fc242727879dcd3de3536b6ffc39.tar.gz', + 'filename': 'fbgemm-20190123.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/fbgemm'), + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': '505be96ab23056580a3a2315abba048f4428b04e.tar.gz', + 'filename': 'benchmark-20180606.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/benchmark'), + }, + { + 'source_urls': ['https://github.com/eigenteam/eigen-git-mirror/archive'], + 'download_filename': 'f59336cee358f92b959de6a0daf07c4ab2318022.tar.gz', + 'filename': 'eigen-20180908.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/eigen'), + }, + { + 'source_urls': ['https://github.com/google/gemmlowp/archive'], + 'download_filename': '8416bab644641a5c0a81ecf91a5cda804af0aee1.tar.gz', + 'filename': 'gemmlowp-20180828.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/gemmlowp/gemmlowp'), + }, + { + 'source_urls': ['https://github.com/NVIDIA/nccl/archive'], + 'download_filename': '3c6e25210bb1b544748937e5db74db0b9679b95e.tar.gz', + 'filename': 'nccl-20181109.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/nccl/nccl'), + }, + { + 'source_urls': ['https://github.com/NVlabs/cub/archive'], + 'download_filename': '285aeebaa34b0e8a7670867a2e66c1a52d998d6a.tar.gz', + 'filename': 'cub-20170829.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/cub'), + }, + { + 'source_urls': ['https://github.com/intel/ideep/archive'], + 'download_filename': '7b8f9d025a675522305a1c5d1328d83f11f205e8.tar.gz', + 'filename': 'ideep-20181224.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/ideep'), + }, + { + 'source_urls': ['https://github.com/intel/mkl-dnn/archive'], + 'download_filename': '0c3cb94999919d33e4875177fdef662bd9413dd4.tar.gz', + 'filename': 'mkl-dnn-20190131.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/ideep/mkl-dnn'), + }, + # mkl-dnn requires Intel MKL, so download minimal Intel MKL version + # actually using imkl as a dependency would be messy due to underlying icc/ifort compilers & impi MPI lib + { + 'source_urls': ['https://github.com/intel/mkl-dnn/releases/download/v0.17.3'], + 'filename': 'mklml_lnx_2019.0.1.20180928.tgz', + 'extract_cmd': mklml_extract_cmd % + (pytorchdir, 'third_party/ideep/mkl-dnn/external/mklml_lnx_2019.0.1.20180928', + pytorchdir, 'third_party/ideep/mkl-dnn/external/mklml_lnx_2019.0.1.20180928'), + }, +] +checksums = [ + '210561583378132d07287518710251bcf861f9b7d625eb67258ed2e9d567cea1', # v1.0.1.tar.gz + '0e98a4fdb6e27add72b4bb0e63a5ed20a9271139c3d0ccc2c15c502e3366bca3', # gloo-20190201.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + 'ffe077d0fccc34aa95c2aba7a3abadbdc2a480c44a238879381733d38322e921', # pybind11-20180911.tar.gz + '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz + 'b84c49b4bdc12b0e8f1bff365dcefd50e5a2a25eeef8c928aeb2dab9fda4d599', # cpuinfo-20190117.tar.gz + 'b9520d6ce9f8b9928bf517696ea62fd03308fd21dafdebfec7aeb8894b3813ab', # onnx-20181204.tar.gz + 'd293a86f4c82a31990b89be2b9787df045e3f6b86378e9950e5e1145d4a08e6a', # protobuf-20171113.tar.gz + '90ab4f60ae0e99c0172dd5201dccc6de6c8f384a21b3d959588f4c1e00beec0f', # pthreadpool-20181008.tar.gz + '07625551202a1f35fe5e826669ad495962b26f6a139290e90b321c5996f002ef', # FXdiv-20181016.tar.gz + 'afd27417c6df1c85f79a68361055dd3adc292174913c39c1f58b698b9cfd7926', # psimd-20180906.tar.gz + 'dacd927f345c40163532e65ed3ea796d190f4efdd125838401a35e8147e55313', # FP16-20181011.tar.gz + '02d278559609982f2dbd973f265caf674274ac7a61ddd867c4956176252d940e', # NNPACK-20180903.tar.gz + 'f822489cbbf3cd09db578ea7ac9af40a9d3184f8ff95cb98e8b33b71ed5d89f8', # sleef-20180509.tar.gz + '13100c3deed300bbf16f87d8af3539f432462bfef9d38f0c7e3e387dc2e88676', # PeachPy-20180219.tar.gz + 'dc0c9ca760bb1bf858dd1aebaf1471b8437c1b2ef9a9b6acaf302fa14b04194f', # QNNPACK-20181205.tar.gz + 'd2dabcd172db8fb91dfa75422a5eb6f55f55f22d047d9f1b02eb6a3be88a09cd', # fbgemm-20190123.tar.gz + '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz + 'fd9e9f0d6ef407a162f5f283c52d3c271efc1092377274abe1e30dff83dbc1a4', # eigen-20180908.tar.gz + 'e12e096e986221d96d55185e870397b3717b625d6c5d155fbd9a7be314bed06a', # gemmlowp-20180828.tar.gz + '72b4835362d8586e315bdf5c30eea99f2efcf14f19162f00ac0675e8b1b22e61', # nccl-20181109.tar.gz + '7224b03af4acbc54525105bb42e3ecd75c66a3a5b47e8a725ab008467c4109f9', # cub-20170829.tar.gz + 'c7418025bd57b3143e651433d0874a39629fce6cc96b43e3f8d5861a8ad23ffb', # ideep-20181224.tar.gz + 'f98d2c297353acfab1ecff2054bee65efd2367b4c621e762cf26f50e037a9728', # mkl-dnn-20190131.tar.gz + 'f00dc3b142a5be399bdeebd7e7ea369545a35d4fb84c86f98b6b048d72685295', # mklml_lnx_2019.0.1.20180928.tgz +] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '3.6.6'), + ('PyYAML', '3.13', versionsuffix), + ('hypothesis', '4.5.0', versionsuffix), + ('cuDNN', '7.1.4.18'), + ('Ninja', '1.8.2'), +] + +# This environment is needed to prevent setup.py from invoking git to determine version. +prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' + +# you can choice here: either give a list of CUDA cc version or tell it All +# by default it does autodetect of the GPU on the local machine +# https://en.wikipedia.org/wiki/CUDA#GPUs_supported +# register error with 5.2, 5.3, 6.2 +prebuildopts += ' TORCH_CUDA_ARCH_LIST="3.0 3.2 3.5 3.7 5.0 6.0 6.1 7.0 7.2"' + +runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' +# skip test subsuites that include hanging/failing tests for now +runtest += '&& python test/run_test.py --exclude autograd cpp_extensions c10d torch --verbose' + +options = {'modulename': 'torch'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' From d1538735f16971cc160b32a9af5f0423cbf49248 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 13 Feb 2019 12:09:07 +0100 Subject: [PATCH 0352/5331] change version of scikit-learn --- .../imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb index 3f2d579c9b9..fe59988cbf4 100644 --- a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb @@ -16,7 +16,7 @@ checksums = ['5bd9e86e40ce4001a57426541d7c79b18143cbd181e3330c1a3e5c5c43287083'] dependencies = [ ('Python', '3.6.6'), - ('scikit-learn', '0.20.2', versionsuffix), + ('scikit-learn', '0.20.0', versionsuffix), ] options = {'modulename': 'imblearn'} From 99701e3eb29da60794aba73e96aafe474eecf283 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 13 Feb 2019 12:20:32 +0100 Subject: [PATCH 0353/5331] add note for Click locale. change Click extension name --- .../m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb index c071cb07206..57aad2712b6 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-foss-2018b-Python-3.6.6.eb @@ -5,6 +5,9 @@ # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + easyblock = 'PythonBundle' name = 'MultiQC' @@ -33,8 +36,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), - ('click', '7.0', { - 'source_tmpl': 'Click-%(version)s.tar.gz', + ('Click', '7.0', { 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], }), From af12621009fcbdf96eea9a29f0d47a32436c611f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 13 Feb 2019 12:26:35 +0000 Subject: [PATCH 0354/5331] adding missing dependencies --- ...ypothesis-4.5.0-foss-2018b-Python-3.6.6.eb | 45 ++++ ...hesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb | 45 ++++ .../n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb | 26 ++ ...PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb | 28 +++ .../p/Python/Python-3.6.6-fosscuda-2018b.eb | 231 ++++++++++++++++++ 5 files changed, 375 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..f19717fa4c1 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,45 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'Bundle' + +name = 'hypothesis' +version = '4.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), +] + + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('attrs', '18.2.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], + 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/h/hypothesis/'], + 'checksums': ['2187928e96bab144b89c6c19d08d61dc247bb1623e58e31bec1da7f71381fa9e'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..4020f1b51ad --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,45 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'Bundle' + +name = 'hypothesis' +version = '4.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), +] + + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('attrs', '18.2.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], + 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/h/hypothesis/'], + 'checksums': ['2187928e96bab144b89c6c19d08d61dc247bb1623e58e31bec1da7f71381fa9e'], + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb new file mode 100644 index 00000000000..8cce11f2088 --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb @@ -0,0 +1,26 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.8.2' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['86b8700c3d0880c2b44c2ff67ce42774aaf8c28cbf57725cb881569288c1c6f4'] + +builddependencies = [('Python', '3.6.6')] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..33906e08e06 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'] + +dependencies = [ + ('Python', '3.6.6'), + ('libyaml', '0.2.1'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb new file mode 100644 index 00000000000..8a8e6ea997d --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb @@ -0,0 +1,231 @@ +name = 'Python' +version = '3.6.6' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['7d56dadf6c7d92a238702389e80cfe66fbfae73e584189ed6f89c75bbf3eda58'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.1'), + ('SQLite', '3.24.0'), + ('XZ', '5.2.4'), + ('GMP', '6.1.2'), # required for pycrypto + ('libffi', '3.2.1'), # required for cryptography + # OS dependency should be preferred if the OS version is more recent then this version, + # it's nice to have an up to date OpenSSL for security reasons; + # ('OpenSSL', '1.1.0h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +exts_download_dep_fail = True + +# workaround for "undefined symbol: __stack_chk_guard" +# see also https://software.intel.com/en-us/forums/intel-c-compiler/topic/610514 +buildopts = 'LDFLAGS="$LDFLAGS -lssp"' + +# order is important! +# package versions updated August 15th 2018 +exts_list = [ + ('setuptools', '40.0.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['012adb8e25fbfd64c652e99e7bab58799a3aaf05d39ab38561f69190a909015f'], + }), + ('pip', '18.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + 'checksums': ['a0e11645ee37c90b40c46d607070c4fd583e2cd46231b1c06e389c5e814eed76'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('numpy', '1.15.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + 'checksums': ['f28e73cf18d37a413f7d5de35d024e6b98f14566a10d82100f9dc491a7d449f9'], + }), + ('scipy', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('mpi4py', '3.0.0', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], + 'checksums': [ + '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz + # paycheck-1.0.2_setup-open-README-utf8.patch + 'ceb7f08aebf016cdcd94ae41c1c76c8c120907f85cbfce240d3a112afb264d79', + ], + }), + ('pbr', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + 'checksums': ['1b8be50d938c9bb75d0eaf7eda111eec1bf6dc88a62a6412e33bf077457e0f45'], + }), + ('Cython', '0.28.5', { + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'checksums': ['b64575241f64f6ec005a4d4137339fb0ba5e156e826db2fdb5f458060d9979e0'], + }), + ('six', '1.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], + }), + ('python-dateutil', '2.7.3', { + 'modulename': 'dateutil', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], + }), + ('deap', '1.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], + }), + ('decorator', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], + }), + ('liac-arff', '2.3', { + 'modulename': 'arff', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'checksums': ['21b1b17c082cacd7b554bf9a42f6de61d2bf02feef6eb31ec36b5486c31b2ae9'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], + }), + ('pycparser', '2.18', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], + 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], + }), + ('cffi', '1.11.5', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), + ('asn1crypto', '0.24.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], + 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], + }), + ('idna', '2.7', { + 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], + 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], + }), + ('cryptography', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6'], + }), + ('pyasn1', '0.4.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['f58f2a3d12fd754aa123e9fa74fb7345333000a035f3921dbdaa08597aa53137'], + }), + ('PyNaCl', '1.2.1', { + 'modulename': 'nacl', + 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], + 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], + }), + ('bcrypt', '3.1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], + 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], + }), + ('paramiko', '2.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], + }), + ('pyparsing', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], + }), + ('netifaces', '0.10.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], + 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], + 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], + 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], + }), + ('pytz', '2018.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + 'checksums': ['ffb9ef1de172603304d9d2819af6f5ece76f2e85ec10692a524dd876e72bf277'], + }), + ('pandas', '0.23.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + 'checksums': ['5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], + 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], + }), + ('virtualenv', '16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], + 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], + }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], + 'checksums': ['e9f04885cf11704669f3a731ea6ac00bbc7dea16137aa4394ef7c272cdb9d008'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('certifi', '2018.8.13', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['4c1d68a1408dd090d2f3a869aa94c3947cc1d967821d1ed303208c9f41f0f2f4'], + }), + ('urllib3', '1.23', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], + }), + ('requests', '2.19.1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], + }), + ('xlrd', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], + 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], + }), + ('py_expression_eval', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], + }), + ('mpmath', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], + 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], + }), + ('tabulate', '0.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], + 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], + }), +] + +moduleclass = 'lang' From 72d4f09b489f42014e07167b9e0450bfd967c26b Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Feb 2019 06:27:18 -0600 Subject: [PATCH 0355/5331] Fix outdated source URL --- .../MariaDB-connector-c-2.3.4-foss-2017b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-foss-2017b.eb b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-foss-2017b.eb index 507fca0c1e7..54674ca8c86 100644 --- a/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-foss-2017b.eb +++ b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-2.3.4-foss-2017b.eb @@ -8,9 +8,9 @@ description = "MariaDB Connector/C is used to connect applications developed in toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['https://downloads.mariadb.org/f/connector-c-%(version)s'] -sources = ['mariadb-connector-c-%(version)s-src.tar.gz'] -checksums = ['8beb0513da8a24ed2cb47836564c8b57045c3b36f933362f74b3676567c13abc'] +source_urls = ['https://github.com/MariaDB/mariadb-connector-c/archive/'] +sources = ['v_%(version)s.tar.gz'] +checksums = ['0e7e65814a859f9f2120f17155b4eaa7bb7c3a368f63dfb924706ef5b324c552'] builddependencies = [('CMake', '3.10.1')] From 2d4344cd0efccbdbb1fdd884f4209e12f9403919 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Feb 2019 06:43:18 -0600 Subject: [PATCH 0356/5331] adding easyconfigs: wheel-0.30.0-fosscuda-2017b-Python-2.7.14.eb, wheel-0.30.0-fosscuda-2017b-Python-3.6.3.eb, wheel-0.30.0-intelcuda-2017b-Python-2.7.14.eb, wheel-0.30.0-intelcuda-2017b-Python-3.6.3.eb --- ...eel-0.30.0-fosscuda-2017b-Python-2.7.14.eb | 26 +++++++++++++++++++ ...heel-0.30.0-fosscuda-2017b-Python-3.6.3.eb | 26 +++++++++++++++++++ ...el-0.30.0-intelcuda-2017b-Python-2.7.14.eb | 26 +++++++++++++++++++ ...eel-0.30.0-intelcuda-2017b-Python-3.6.3.eb | 26 +++++++++++++++++++ 4 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..dbdf2b5273e --- /dev/null +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'wheel' +version = '0.30.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/wheel' +description = """A built-package format for Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] + +dependencies = [('Python', '2.7.14')] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/wheel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..22b2b003051 --- /dev/null +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'wheel' +version = '0.30.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/wheel' +description = """A built-package format for Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] + +dependencies = [('Python', '3.6.3')] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/wheel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..d6564ddf387 --- /dev/null +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-2.7.14.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'wheel' +version = '0.30.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/wheel' +description = """A built-package format for Python.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] + +dependencies = [('Python', '2.7.14')] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/wheel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..fd45223ab46 --- /dev/null +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-intelcuda-2017b-Python-3.6.3.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'wheel' +version = '0.30.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/wheel' +description = """A built-package format for Python.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] + +dependencies = [('Python', '3.6.3')] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/wheel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From fa1460df5ed614d887cb10c1a0906c65c8bcaa8b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 13 Feb 2019 13:44:51 +0100 Subject: [PATCH 0357/5331] adding easyconfigs: PEAR-0.9.11-foss-2018b.eb --- .../p/PEAR/PEAR-0.9.11-foss-2018b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-foss-2018b.eb diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-foss-2018b.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-foss-2018b.eb new file mode 100644 index 00000000000..38188f1670d --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-foss-2018b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'PEAR' +version = '0.9.11' + +homepage = 'https://cme.h-its.org/exelixis/web/software/%(namelower)s/' +description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. + It is fully parallelized and can run with as low as just a few kilobytes of memory.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +# Needs manual download via web-form, +# https://www.h-its.org/en/research/sco/software/#NextGenerationSequencingSequenceAnalysis +# source_urls = ['https://cme.h-its.org/exelixis/web/software/pear/files/'] +sources = ['%(namelower)s-src-%(version)s.tar.gz'] +checksums = ['94f4a1835cd75ec6fab83405c2545ddba6b6bb1644579222e9cc2ad57a59d654'] + +builddependencies = [ + ('Autotools', '20180311'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), +] + +preconfigopts = 'autoreconf && ' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 9fd9e61b5f4bac38311026d0d5ddb30944e0859e Mon Sep 17 00:00:00 2001 From: dugan Date: Wed, 13 Feb 2019 13:39:50 +0000 Subject: [PATCH 0358/5331] adding easyconfigs: mkl-dnn-0.16-intel-2018b.eb --- .../m/mkl-dnn/mkl-dnn-0.16-intel-2018b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/mkl-dnn/mkl-dnn-0.16-intel-2018b.eb diff --git a/easybuild/easyconfigs/m/mkl-dnn/mkl-dnn-0.16-intel-2018b.eb b/easybuild/easyconfigs/m/mkl-dnn/mkl-dnn-0.16-intel-2018b.eb new file mode 100644 index 00000000000..814a24f5f51 --- /dev/null +++ b/easybuild/easyconfigs/m/mkl-dnn/mkl-dnn-0.16-intel-2018b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'mkl-dnn' +version = '0.16' + +homepage = 'https://01.org/mkl-dnn' +description = "Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN)" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/01org/mkl-dnn/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7557f820d6801dbe7741627199c0165fe9e651245b9c1c744d615f576da1098a'] + +builddependencies = [('CMake', '3.12.1')] + +separate_build_dir = True + +configopts = "-DFAIL_WITHOUT_MKL=1" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['include/mkldnn.h', 'include/mkldnn.hpp', 'include/mkldnn_types.h', 'lib/libmkldnn.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 0f1cab52374f7295c3d9d5e988e486073756c57c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 13 Feb 2019 15:08:37 +0100 Subject: [PATCH 0359/5331] adding easyconfigs: nodejs-10.15.1-foss-2018b.eb --- .../n/nodejs/nodejs-10.15.1-foss-2018b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-10.15.1-foss-2018b.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-10.15.1-foss-2018b.eb b/easybuild/easyconfigs/n/nodejs/nodejs-10.15.1-foss-2018b.eb new file mode 100644 index 00000000000..f97b3108f05 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-10.15.1-foss-2018b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '10.15.1' + +homepage = 'http://%(name)s.org' + +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'lowopt': True} + +sources = ['node-v%(version)s.tar.gz'] +source_urls = ['http://%(name)s.org/dist/v%(version)s/'] +checksums = ['5202f6f6bfda16554c8121ea78e4cffee52e2707e1136c88f3c40b0c2af8100f'] + +# Python is required (only) as build dependency +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm'], + 'dirs': ['lib/node_modules', 'include/node'] +} + +moduleclass = 'lang' From f3f4bcc1165dc6eb1afbd234fb48ba6907c2b544 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Feb 2019 09:10:25 -0600 Subject: [PATCH 0360/5331] adding easyconfigs: PHYLIP-3.697-GCC-6.4.0-2.28.eb, PHYLIP-3.697-iccifort-2017.4.196-GCC-6.4.0-2.28.eb --- .../p/PHYLIP/PHYLIP-3.697-GCC-6.4.0-2.28.eb | 24 +++++++++++++++++++ ....697-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-iccifort-2017.4.196-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..bc2fc2ac4cb --- /dev/null +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-6.4.0-2.28.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'PHYLIP' +version = '3.697' + +homepage = 'http://evolution.genetics.washington.edu/phylip' +description = "PHYLIP is a free package of programs for inferring phylogenies." + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = ['http://evolution.gs.washington.edu/phylip/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9a26d8b08b8afea7f708509ef41df484003101eaf4beceb5cf7851eb940510c1'] + +buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' + +files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.so', 'src/libdrawtree.so'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..78062c0a529 --- /dev/null +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'PHYLIP' +version = '3.697' + +homepage = 'http://evolution.genetics.washington.edu/phylip' +description = "PHYLIP is a free package of programs for inferring phylogenies." + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +source_urls = ['http://evolution.gs.washington.edu/phylip/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9a26d8b08b8afea7f708509ef41df484003101eaf4beceb5cf7851eb940510c1'] + +buildopts = '-Csrc -fMakefile.unx all && make -Csrc -fMakefile.unx install' + +files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.so', 'src/libdrawtree.so'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libdrawgram.so', 'lib/libdrawtree.so'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' From b99c234c641f151144c016877de1b7c167e0cfd4 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Feb 2019 09:24:35 -0600 Subject: [PATCH 0361/5331] adding easyconfigs: MUSCLE-3.8.31-foss-2017b.eb, MUSCLE-3.8.31-intel-2017b.eb --- .../m/MUSCLE/MUSCLE-3.8.31-foss-2017b.eb | 31 ++++++++++++++++ .../m/MUSCLE/MUSCLE-3.8.31-intel-2017b.eb | 36 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2017b.eb create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2017b.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2017b.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2017b.eb new file mode 100644 index 00000000000..da34176c6a4 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-foss-2017b.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'http://drive5.com/muscle/' +description = """ MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + 'e108d1cc2d394236f839facc1304ff96c0e11f7fdd6d2444761808ec860cd58a', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2017b.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2017b.eb new file mode 100644 index 00000000000..eebb386fdbf --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2017b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'http://drive5.com/muscle/' +description = """ MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + 'e108d1cc2d394236f839facc1304ff96c0e11f7fdd6d2444761808ec860cd58a', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' From 7bab17b52f7084c85651b9fff4596ecc7c8ba79e Mon Sep 17 00:00:00 2001 From: dugan Date: Wed, 13 Feb 2019 15:42:52 +0000 Subject: [PATCH 0362/5331] adding easyconfigs: Pillow-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb --- ...low-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..76599d0f98b --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '5.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['v%(version)s.post0.tar.gz'] +checksums = ['0086cea17590587e8041fe35a2c0c8680975198d798c2b39cdf277354b3b16c8'] + +dependencies = [ + ('Python', '3.6.6'), + ('libjpeg-turbo', '2.0.0'), + ('libpng', '1.6.34'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.9'), + ('freetype', '2.9.1') +] + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' From 1f1e953ce073aef6f582fcd1830d37a7935ac195 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Feb 2019 10:33:19 -0600 Subject: [PATCH 0363/5331] adding easyconfigs: TensorFlow-1.8.0-fosscuda-2017b-Python-2.7.14.eb, TensorFlow-1.8.0-fosscuda-2017b-Python-3.6.3.eb --- ...Flow-1.8.0-fosscuda-2017b-Python-2.7.14.eb | 53 +++++++++++++++++++ ...rFlow-1.8.0-fosscuda-2017b-Python-3.6.3.eb | 53 +++++++++++++++++++ 2 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-fosscuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..8b35c4e70f4 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,53 @@ +name = 'TensorFlow' +version = '1.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = ['https://github.com/tensorflow/tensorflow/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'TensorFlow-1.5.0_swig-env.patch', + 'TensorFlow-%(version)s_remove-msse-hardcoding.patch', + 'TensorFlow-%(version)s_lrt-flag.patch', + 'TensorFlow-1.6.0_use_64b_alignment.patch', + 'TensorFlow-1.8.0_dont_expand_cuda_cudnn_path.patch', + 'TensorFlow-%(version)s_no_grpc.patch', + 'TensorFlow-%(version)s_no_boringssl.patch', + 'TensorFlow-%(version)s_use_mklddn_0.14.patch', + 'TensorFlow-%(version)s_GetVersion_tuple_2_struct.patch', +] +checksums = [ + '47646952590fd213b747247e6870d89bb4a368a95ae3561513d6c76e44f92a75', # v1.8.0.tar.gz + '53807290f1acb6a0f2a84f1a0ad9f917ee131c304b3e08679f3cbd335b22c7ef', # TensorFlow-1.5.0_swig-env.patch + '4d043bba84d19aa38e402ef4ddaa89df936ae792f82693a49ce8ae4a1d091f6d', # TensorFlow-1.8.0_remove-msse-hardcoding.patch + '3c499788266800c71fa9874d411df79f7331320b3a86bc7c79c74763ae04c143', # TensorFlow-1.8.0_lrt-flag.patch + 'bcff66b5cc7a98e2ae894df6940aac5e3dcec3700773d24a6c3a5a69128ef66f', # TensorFlow-1.6.0_use_64b_alignment.patch + # TensorFlow-1.8.0_dont_expand_cuda_cudnn_path.patch + '37ba1f77f42252b7484b32b8309f9acf1f910612623581a98fd39c9f94e9b285', + '7cb51ce3b4619320cb1c6ef4ff1d4e1afcc5b41254c7031fccf51e3e7ce34844', # TensorFlow-1.8.0_no_grpc.patch + 'ca2338e189496711bc8798070d63255c3ff77ed616d1d2775abbef6f984db7ad', # TensorFlow-1.8.0_no_boringssl.patch + '8303273a037f6f90f496783b67bde66d0f5cc826c61e5ad6d7e37290db029644', # TensorFlow-1.8.0_use_mklddn_0.14.patch + # TensorFlow-1.8.0_GetVersion_tuple_2_struct.patch + '6ab6ca0179265a20892b1f03b0fa13d2f197254b8a941c2e0050824491b9a678', + +] + +builddependencies = [ + ('Bazel', '0.10.0'), + ('wheel', '0.30.0', versionsuffix), +] + +dependencies = [ + ('Python', '2.7.14'), + ('cuDNN', '7.0.5.15'), +] + +preconfigopts = 'export CC_OPT_FLAGS="$CC_OPT_FLAGS -mno-avx512f" && ' + +cuda_compute_capabilities = ['3.0', '3.2', '3.5', '3.7', '5.0', '5.2', '6.0', '6.1', '7.0'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..48eb8f91152 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,53 @@ +name = 'TensorFlow' +version = '1.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = ['https://github.com/tensorflow/tensorflow/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'TensorFlow-1.5.0_swig-env.patch', + 'TensorFlow-%(version)s_remove-msse-hardcoding.patch', + 'TensorFlow-%(version)s_lrt-flag.patch', + 'TensorFlow-1.6.0_use_64b_alignment.patch', + 'TensorFlow-1.8.0_dont_expand_cuda_cudnn_path.patch', + 'TensorFlow-%(version)s_no_grpc.patch', + 'TensorFlow-%(version)s_no_boringssl.patch', + 'TensorFlow-%(version)s_use_mklddn_0.14.patch', + 'TensorFlow-%(version)s_GetVersion_tuple_2_struct.patch', +] +checksums = [ + '47646952590fd213b747247e6870d89bb4a368a95ae3561513d6c76e44f92a75', # v1.8.0.tar.gz + '53807290f1acb6a0f2a84f1a0ad9f917ee131c304b3e08679f3cbd335b22c7ef', # TensorFlow-1.5.0_swig-env.patch + '4d043bba84d19aa38e402ef4ddaa89df936ae792f82693a49ce8ae4a1d091f6d', # TensorFlow-1.8.0_remove-msse-hardcoding.patch + '3c499788266800c71fa9874d411df79f7331320b3a86bc7c79c74763ae04c143', # TensorFlow-1.8.0_lrt-flag.patch + 'bcff66b5cc7a98e2ae894df6940aac5e3dcec3700773d24a6c3a5a69128ef66f', # TensorFlow-1.6.0_use_64b_alignment.patch + # TensorFlow-1.8.0_dont_expand_cuda_cudnn_path.patch + '37ba1f77f42252b7484b32b8309f9acf1f910612623581a98fd39c9f94e9b285', + '7cb51ce3b4619320cb1c6ef4ff1d4e1afcc5b41254c7031fccf51e3e7ce34844', # TensorFlow-1.8.0_no_grpc.patch + 'ca2338e189496711bc8798070d63255c3ff77ed616d1d2775abbef6f984db7ad', # TensorFlow-1.8.0_no_boringssl.patch + '8303273a037f6f90f496783b67bde66d0f5cc826c61e5ad6d7e37290db029644', # TensorFlow-1.8.0_use_mklddn_0.14.patch + # TensorFlow-1.8.0_GetVersion_tuple_2_struct.patch + '6ab6ca0179265a20892b1f03b0fa13d2f197254b8a941c2e0050824491b9a678', + +] + +builddependencies = [ + ('Bazel', '0.10.0'), + ('wheel', '0.30.0', versionsuffix), +] + +dependencies = [ + ('Python', '3.6.3'), + ('cuDNN', '7.0.5.15'), +] + +preconfigopts = 'export CC_OPT_FLAGS="$CC_OPT_FLAGS -mno-avx512f" && ' + +cuda_compute_capabilities = ['3.0', '3.2', '3.5', '3.7', '5.0', '5.2', '6.0', '6.1', '7.0'] + +moduleclass = 'lib' From 56d41f2bc8b123b125d38101cce5216164d26808 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Feb 2019 10:52:56 -0600 Subject: [PATCH 0364/5331] adding easyconfigs: SNPhylo-20160204-foss-2017b-Python-2.7.14-R-3.4.3.eb, SNPhylo-20160204-intel-2017b-Python-2.7.14-R-3.4.3.eb --- ...160204-foss-2017b-Python-2.7.14-R-3.4.3.eb | 23 +++++++++++++++++++ ...60204-intel-2017b-Python-2.7.14-R-3.4.3.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNPhylo/SNPhylo-20160204-foss-2017b-Python-2.7.14-R-3.4.3.eb create mode 100644 easybuild/easyconfigs/s/SNPhylo/SNPhylo-20160204-intel-2017b-Python-2.7.14-R-3.4.3.eb diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20160204-foss-2017b-Python-2.7.14-R-3.4.3.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20160204-foss-2017b-Python-2.7.14-R-3.4.3.eb new file mode 100644 index 00000000000..a177f310e2d --- /dev/null +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20160204-foss-2017b-Python-2.7.14-R-3.4.3.eb @@ -0,0 +1,23 @@ +name = 'SNPhylo' +version = '20160204' +versionsuffix = '-Python-%(pyver)s-R-%(rver)s' + +homepage = 'http://chibba.pgml.uga.edu/snphylo/' +description = """SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +# download from http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz and rename +# see http://chibba.pgml.uga.edu/snphylo/ for version +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d9e144021c83dbef97bebf743b92109ad0afcfe70f37c244059b43f11b8a50da'] + +dependencies = [ + ('R', '3.4.3', '-X11-20171023'), + ('R-bundle-Bioconductor', '3.6', '-R-%(rver)s'), + ('Python', '2.7.14'), + ('MUSCLE', '3.8.31'), + ('PHYLIP', '3.697'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20160204-intel-2017b-Python-2.7.14-R-3.4.3.eb b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20160204-intel-2017b-Python-2.7.14-R-3.4.3.eb new file mode 100644 index 00000000000..e8bab0c1fe0 --- /dev/null +++ b/easybuild/easyconfigs/s/SNPhylo/SNPhylo-20160204-intel-2017b-Python-2.7.14-R-3.4.3.eb @@ -0,0 +1,23 @@ +name = 'SNPhylo' +version = '20160204' +versionsuffix = '-Python-%(pyver)s-R-%(rver)s' + +homepage = 'http://chibba.pgml.uga.edu/snphylo/' +description = """SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +# download from http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz and rename +# see http://chibba.pgml.uga.edu/snphylo/ for version +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d9e144021c83dbef97bebf743b92109ad0afcfe70f37c244059b43f11b8a50da'] + +dependencies = [ + ('R', '3.4.3', '-X11-20171023'), + ('R-bundle-Bioconductor', '3.6', '-R-%(rver)s'), + ('Python', '2.7.14'), + ('MUSCLE', '3.8.31'), + ('PHYLIP', '3.697'), +] + +moduleclass = 'bio' From 9260b53dbcd7f88ae84acef38282125d84a38e1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Feb 2019 17:55:49 +0100 Subject: [PATCH 0365/5331] {lib}[intel/2018b] scikit-optimize v0.5.2 w/ Python 3.6.6 --- ...optimize-0.5.2-intel-2018b-Python-3.6.6.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.5.2-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.5.2-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.5.2-intel-2018b-Python-3.6.6.eb new file mode 100755 index 00000000000..eeb8892d7d5 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.5.2-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-optimize' +version = '0.5.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://scikit-optimize.github.io' +description = """Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive + and noisy black-box functions.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1d7657a4b8ef9aa6d81e49b369c677c584e83269f11710557741d3b3f8fa0a75'] + +dependencies = [ + ('Python', '3.6.6'), + ('PyYAML', '3.13', versionsuffix), + ('scikit-learn', '0.20.0', versionsuffix), + ('matplotlib', '3.0.0', versionsuffix), +] + +options = {'modulename': 'skopt'} + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From a12bac04499a852f22fc80c8835a892db5bd7e58 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Feb 2019 18:19:06 +0100 Subject: [PATCH 0366/5331] {chem}[intel/2018b] OpenBabel v2.4.1 w/ Python 2.7.15 & 3.6.6 --- ...enBabel-2.4.1-intel-2018b-Python-2.7.15.eb | 37 ++++++++++++++ ...penBabel-2.4.1-intel-2018b-Python-3.6.6.eb | 39 +++++++++++++++ .../OpenBabel-2.4.1_fix-Python-3.patch | 49 +++++++++++++++++++ 3 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1_fix-Python-3.patch diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..303e55408ce --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,37 @@ +name = 'OpenBabel' +version = '2.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'OpenBabel-2.3.2-use-xHost.patch', + 'OpenBabel-%(version)s-fix-link-path-tests.patch', +] +checksums = [ + '204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc', # openbabel-2.4.1.tar.gz + '0db85c64f53862dce05ada9091a35d7b4c5c29a44aef76e0cb41cd679441a446', # OpenBabel-2.3.2-use-xHost.patch + 'a6a1f687fc22e20a83b4f8c5e89e32e3eebefb1bb9440c9ca3848d23120bc458', # OpenBabel-2.4.1-fix-link-path-tests.patch +] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '2.7.15'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.8'), + ('Eigen', '3.3.4', '', True), +] + +runtest = 'test' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..fe1c852d320 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,39 @@ +name = 'OpenBabel' +version = '2.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'OpenBabel-2.3.2-use-xHost.patch', + 'OpenBabel-%(version)s-fix-link-path-tests.patch', + 'OpenBabel-%(version)s_fix-Python-3.patch', +] +checksums = [ + '204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc', # openbabel-2.4.1.tar.gz + '0db85c64f53862dce05ada9091a35d7b4c5c29a44aef76e0cb41cd679441a446', # OpenBabel-2.3.2-use-xHost.patch + 'a6a1f687fc22e20a83b4f8c5e89e32e3eebefb1bb9440c9ca3848d23120bc458', # OpenBabel-2.4.1-fix-link-path-tests.patch + '270ab3770839b4163c906ed88366157d8823b7038863d1b3affec04cd0b788bf', # OpenBabel-2.4.1_fix-Python-3.patch +] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '3.6.6'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.8'), + ('Eigen', '3.3.4', '', True), +] + +runtest = 'test' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1_fix-Python-3.patch b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1_fix-Python-3.patch new file mode 100644 index 00000000000..a1d96e2b2c4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1_fix-Python-3.patch @@ -0,0 +1,49 @@ +fix issues causing test failures with Python 3.6 +partially inspired by https://bugs.archlinux.org/task/52409 +author: Kenneth Hoste (HPC-UGent) +--- openbabel-2.4.1/scripts/python/openbabel.py.orig 2019-02-13 17:59:40.515899728 +0100 ++++ openbabel-2.4.1/scripts/python/openbabel.py 2019-02-13 18:00:22.775794400 +0100 +@@ -3,7 +3,11 @@ + try: + import dl + except ImportError: +- import DLFCN as dl ++ try: ++ import DLFCN as dl ++ except ImportError: ++ # fallback for Python 3.x ++ import os as dl + sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL) + # This file was automatically generated by SWIG (http://www.swig.org). + # Version 3.0.10 +--- openbabel-2.4.1/test/testpdbformat.py.orig 2016-03-02 22:09:51.000000000 +0100 ++++ openbabel-2.4.1/test/testpdbformat.py 2019-02-13 17:50:27.917372676 +0100 +@@ -24,12 +24,12 @@ + + def testInsertionCodes(self): + """ +- Testing a PDB entry with insertion codes to distinguish residues +- upon conversion to FASTA. ++ Testing a PDB entry with insertion codes to distinguish residues ++ upon conversion to FASTA. + """ + self.canFindExecutable("babel") + +- self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N ++ self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N + ATOM 407 CA VAL L 29 57.124 18.088 47.170 1.00 0.00 C + ATOM 408 C VAL L 29 55.739 17.571 47.538 1.00 0.00 C + ATOM 409 O VAL L 29 55.535 16.362 47.550 1.00 0.00 O +@@ -100,9 +100,9 @@ + ATOM 474 HE2 TYR L 32 48.145 19.172 44.648 1.00 0.00 H + ATOM 475 HH TYR L 32 46.462 17.658 44.280 1.00 0.00 H + """ +- output, error = run_exec(self.entryPDBwithInsertioncodes, +- "babel -ipdb -ofasta") +- self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY") ++ output, error = run_exec(self.entryPDBwithInsertioncodes, ++ "babel -ipdb -ofasta") ++ self.assertEqual(output.rstrip().rsplit("\n",1)[1], "VSSSY") + + if __name__ == "__main__": + testsuite = [] From ee8819a544dacabab4f56cdaf2f7ff8fd75d7961 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 13 Feb 2019 13:21:20 -0600 Subject: [PATCH 0367/5331] adding easyconfigs: lftp-4.8.4-GCCcore-6.4.0.eb --- .../l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..c77aa8444d0 --- /dev/null +++ b/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'lftp' +version = '4.8.4' + +homepage = 'http://lftp.yar.ru' +description = """LFTP is a sophisticated ftp/http client, and a file transfer program supporting + a number of network protocols. Like BASH, it has job control and uses the readline library for + input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. + It was designed with reliability in mind.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = { 'http://lftp.yar.ru/ftp/'} +sources = [SOURCE_TAR_GZ] +checksums = ['19f3a4236558fbdb88eec01bc9d693c51b122d23487b6bedad4cc67ae6825fc2'] + +builddependencies = { + ('binutils', '2.28'), + ('libreadline', '7.0'), + ('zlib', '1.2.11') +} + +# for this version of lftp the gnutls library is optional +configopts = "--with-readline=$EBROOTLIBREADLINE --without-gnutls" + +sanity_check_paths = { + 'files': ['bin/lftp'], + 'dirs': [] +} + +moduleclass = 'tools' From 4536daece81a4a24c18533891a26a37ab0f84f1a Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 13 Feb 2019 15:54:10 -0600 Subject: [PATCH 0368/5331] correct style problem captured by Travis test --- easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb index c77aa8444d0..2fac5e6db89 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb @@ -12,13 +12,13 @@ description = """LFTP is a sophisticated ftp/http client, and a file transfer pr toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = { 'http://lftp.yar.ru/ftp/'} +source_urls = {'http://lftp.yar.ru/ftp/'} sources = [SOURCE_TAR_GZ] checksums = ['19f3a4236558fbdb88eec01bc9d693c51b122d23487b6bedad4cc67ae6825fc2'] builddependencies = { ('binutils', '2.28'), - ('libreadline', '7.0'), + ('libreadline', '7.0'), ('zlib', '1.2.11') } From 6d30f39547422bc61933e2ee762f8f321dc27427 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Feb 2019 17:27:27 -0600 Subject: [PATCH 0369/5331] adding easyconfigs: TensorFlow-1.8.0-foss-2017b-Python-2.7.14.eb, TensorFlow-1.8.0-foss-2017b-Python-3.6.3.eb --- ...nsorFlow-1.8.0-foss-2017b-Python-2.7.14.eb | 35 +++++++++++++++++++ ...ensorFlow-1.8.0-foss-2017b-Python-3.6.3.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-foss-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..e6ed9dad8bc --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,35 @@ +name = 'TensorFlow' +version = '1.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/tensorflow/tensorflow/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'TensorFlow-1.5.0_swig-env.patch', + 'TensorFlow-%(version)s_remove-msse-hardcoding.patch', + 'TensorFlow-1.8.0_lrt-flag.patch', + 'TensorFlow-1.6.0_use_64b_alignment.patch', +] +checksums = [ + '47646952590fd213b747247e6870d89bb4a368a95ae3561513d6c76e44f92a75', # v1.8.0.tar.gz + '53807290f1acb6a0f2a84f1a0ad9f917ee131c304b3e08679f3cbd335b22c7ef', # TensorFlow-1.5.0_swig-env.patch + '4d043bba84d19aa38e402ef4ddaa89df936ae792f82693a49ce8ae4a1d091f6d', # TensorFlow-1.8.0_remove-msse-hardcoding.patch + '3c499788266800c71fa9874d411df79f7331320b3a86bc7c79c74763ae04c143', # TensorFlow-1.8.0_lrt-flag.patch + 'bcff66b5cc7a98e2ae894df6940aac5e3dcec3700773d24a6c3a5a69128ef66f', # TensorFlow-1.6.0_use_64b_alignment.patch +] + +builddependencies = [ + ('Bazel', '0.10.0'), + ('wheel', '0.30.0', versionsuffix), +] + +dependencies = [('Python', '2.7.14')] + +preconfigopts = 'export CC_OPT_FLAGS="$CC_OPT_FLAGS -mno-avx512f" && ' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..24c219275d3 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.8.0-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,35 @@ +name = 'TensorFlow' +version = '1.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/tensorflow/tensorflow/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'TensorFlow-1.5.0_swig-env.patch', + 'TensorFlow-%(version)s_remove-msse-hardcoding.patch', + 'TensorFlow-1.8.0_lrt-flag.patch', + 'TensorFlow-1.6.0_use_64b_alignment.patch', +] +checksums = [ + '47646952590fd213b747247e6870d89bb4a368a95ae3561513d6c76e44f92a75', # v1.8.0.tar.gz + '53807290f1acb6a0f2a84f1a0ad9f917ee131c304b3e08679f3cbd335b22c7ef', # TensorFlow-1.5.0_swig-env.patch + '4d043bba84d19aa38e402ef4ddaa89df936ae792f82693a49ce8ae4a1d091f6d', # TensorFlow-1.8.0_remove-msse-hardcoding.patch + '3c499788266800c71fa9874d411df79f7331320b3a86bc7c79c74763ae04c143', # TensorFlow-1.8.0_lrt-flag.patch + 'bcff66b5cc7a98e2ae894df6940aac5e3dcec3700773d24a6c3a5a69128ef66f', # TensorFlow-1.6.0_use_64b_alignment.patch +] + +builddependencies = [ + ('Bazel', '0.10.0'), + ('wheel', '0.30.0', versionsuffix), +] + +dependencies = [('Python', '3.6.3')] + +preconfigopts = 'export CC_OPT_FLAGS="$CC_OPT_FLAGS -mno-avx512f" && ' + +moduleclass = 'lib' From d97c2a4d03ab38dd8c33c63e1a285664c15fcf46 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Feb 2019 17:28:33 -0600 Subject: [PATCH 0370/5331] Add dependency --- .../wheel-0.30.0-foss-2017b-Python-2.7.14.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..99ca22f0fbc --- /dev/null +++ b/easybuild/easyconfigs/w/wheel/wheel-0.30.0-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'wheel' +version = '0.30.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/wheel' +description = """A built-package format for Python.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9515fe0a94e823fd90b08d22de45d7bde57c90edce705b22f5e1ecf7e1b653c8'] + +dependencies = [('Python', '2.7.14')] + +sanity_check_paths = { + 'files': ['bin/wheel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From ed6b6b06997643e2f50076a24eb9a8ebeb0d6947 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Feb 2019 08:50:40 +0100 Subject: [PATCH 0371/5331] minor style fixes in TensorRT easyconfig + add comment to motivate not using 'pip' for protobuf-python --- .../TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb index b9ae131ade4..c1b6e3035f0 100644 --- a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb @@ -23,12 +23,12 @@ dependencies = [ exts_list = [ ('protobuf-python', '3.6.1', { - 'modulename': 'google.protobuf', - 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], - 'start_dir': 'python', - 'use_pip': False, + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + 'use_pip': False, # installation using pip fails + 'start_dir': 'python', + 'modulename': 'google.protobuf', }), ] From aa409ac1f26214951b97f20dfcf9a356c0552ef8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 14 Feb 2019 12:06:23 +0200 Subject: [PATCH 0372/5331] Update TensorFlow easyconfig for Python 2.7.15 and 3.6.6 with better style. Update TensorRT to use the new tensorrt easyblock. --- ...low-1.12.0-fosscuda-2018b-Python-2.7.15.eb | 2 +- ...Flow-1.12.0-fosscuda-2018b-Python-3.6.6.eb | 26 ++++++++--------- ...RT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb | 29 ++++--------------- 3 files changed, 19 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb index abe1d57b79c..2193fb911ca 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb @@ -32,8 +32,8 @@ exts_list = [ 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + 'use_pip': False, # installation using pip fails 'start_dir': 'python', - 'use_pip': False, 'modulename': 'google.protobuf', }), ('absl-py', '0.6.1', { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb index 8d8a8598e4a..398047b5848 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb @@ -28,17 +28,17 @@ use_pip = True exts_list = [ ('protobuf-python', '3.6.1', { - 'modulename': 'google.protobuf', - 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], - 'start_dir': 'python', - 'use_pip': False, + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + 'use_pip': False, # installation using pip fails + 'start_dir': 'python', + 'modulename': 'google.protobuf', }), ('absl-py', '0.6.1', { - 'modulename': 'absl', 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], 'checksums': ['87519e3b91a3d573664c6e2ee33df582bb68dca6642ae3cf3a4361b1c0a4e9d6'], + 'modulename': 'absl', }), ('astor', '0.7.1', { 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], @@ -49,17 +49,17 @@ exts_list = [ 'checksums': ['7068908321ecd2774f145193c4b34a11305bd104b4551b09273dfd1d6a374930'], }), ('grpcio', '1.16.0', { - 'modulename': 'grpc', 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], 'checksums': ['0cc5f2d3ee21c642d8982f197c83053fd3a8cbcd6a60240d8c87c6c256b10d57'], + 'modulename': 'grpc', }), ('Markdown', '3.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], }), ('tensorboard', version, { - 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'unpack_sources': False, 'checksums': ['ca275a7e39797946930d7d4460999369b73968e8191f2256e23bfb7924004d59'], }), @@ -72,26 +72,26 @@ exts_list = [ 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], }), ('Keras-Applications', '1.0.6', { - 'modulename': 'keras_applications', - 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['a03af60ddc9c5afdae4d5c9a8dd4ca857550e0b793733a5072e0725829b87017'], + 'modulename': 'keras_applications', }), ('Keras-Preprocessing', '1.0.5', { - 'modulename': 'keras_preprocessing', - 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['ef2e482c4336fcf7180244d06f4374939099daa3183816e82aee7755af35b754'], + 'modulename': 'keras_preprocessing', }), (name, version, { + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', 'patches': [ 'TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.12.0_lrt-flag.patch', 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch' ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'checksums': [ '3c87b81e37d4ed7f3da6200474fa5e656ffd20d8811068572f43610cae97ca92', # v1.12.0.tar.gz 'aa53c7f6d42b4a9e91e0ba639d79f69a7db3c0a88c3b8e43d332479b6368391a', # TensorFlow-1.11.0_swig-env.patch diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb index 12c69a81e81..c1b6e3035f0 100644 --- a/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-4.0.1.6-fosscuda-2018b-Python-2.7.15.eb @@ -1,5 +1,3 @@ -easyblock = 'Binary' - name = 'TensorRT' version = '4.0.1.6' versionsuffix = '-Python-%(pyver)s' @@ -7,11 +5,13 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://developer.nvidia.com/tensorrt' description = """NVIDIA TensorRT is a platform for high-performance deep learning inference""" +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +# Requires manual download from +# https://developer.nvidia.com/nvidia-tensorrt-4x-download sources = ['%(name)s-%(version)s.Ubuntu-16.04.4.x86_64-gnu.cuda-9.2.cudnn7.1.tar.gz'] checksums = ['fc5fd2ba86225ed62e60870cc24896107770a59829363fcb49229c82bb1f4fb5'] -toolchain = {'name': 'fosscuda', 'version': '2018b'} - builddependencies = [ ('protobuf', '3.6.1'), ] @@ -21,34 +21,15 @@ dependencies = [ ('cuDNN', '7.1.4.18'), ] -extract_sources = True -keepsymlinks = True - -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} - exts_list = [ ('protobuf-python', '3.6.1', { 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + 'use_pip': False, # installation using pip fails 'start_dir': 'python', - 'use_pip': False, 'modulename': 'google.protobuf', }), ] -postinstallcmds = [ - 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/python/%s ' - % 'tensorrt-4.0.1.6-cp27-cp27mu-linux_x86_64.whl', - 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/uff/%s ' % 'uff-0.4.0-py2.py3-none-any.whl', - 'pip install --no-deps --prefix=%%(installdir)s %%(installdir)s/graphsurgeon/%s ' - % 'graphsurgeon-0.2.0-py2.py3-none-any.whl', -] - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lib' From 5e3d495bc87dff17d7a14dd47d85684c5e7dc186 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Thu, 14 Feb 2019 13:25:25 +0100 Subject: [PATCH 0373/5331] adding easyconfigs: STAR-2.4.2a-foss-2018b.eb --- .../s/STAR/STAR-2.4.2a-foss-2018b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.4.2a-foss-2018b.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.4.2a-foss-2018b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.4.2a-foss-2018b.eb new file mode 100644 index 00000000000..a0093cd7a82 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.4.2a-foss-2018b.eb @@ -0,0 +1,40 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.4.2a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['ac166d190c0fd34bf3418a5640050b0e7734d279813e02daa013d0924fb579b0'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES', 'LICENSE', 'README', 'RELEASEnotes', + 'STAR-Fusion', 'STAR-Fusion-0.1.1', 'doc', 'extras', +] + +sanity_check_paths = { + 'files': ['bin/STAR', 'bin/STARlong'], + 'dirs': [], +} + +moduleclass = 'bio' From 9a443d9cc5b95db9699a6c5276bf0e2ef6eb84d9 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 14 Feb 2019 08:31:50 -0600 Subject: [PATCH 0374/5331] Added remove define DATE patch --- .../b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb | 6 +- .../Bazel-0.10.0_remove_define_DATE.patch | 189 ++++++++++++++++++ 2 files changed, 194 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-0.10.0_remove_define_DATE.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb index 9fdf4e5cdea..76b9371ed08 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb @@ -9,7 +9,11 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] -checksums = ['47e0798caaac4df499bce5fe554a914abd884a855a27085a4473de1d737d9548'] +patches = ['Bazel-%(version)s_remove_define_DATE.patch'] +checksums = [ + '47e0798caaac4df499bce5fe554a914abd884a855a27085a4473de1d737d9548', # bazel-0.10.0-dist.zip + '9df36185e877db7f7dde273d0f8074f6fb33b2d4bb818ad8bfe744e958eeb896', # Bazel-0.10.0_remove_define_DATE.patch +] builddependencies = [('binutils', '2.28')] dependencies = [('Java', '1.8.0_162', '', True)] diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0_remove_define_DATE.patch b/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0_remove_define_DATE.patch new file mode 100644 index 00000000000..48fb8593773 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0_remove_define_DATE.patch @@ -0,0 +1,189 @@ +Remove defined of __{DATE,TIMESTAMP,TIME}__ +Intel groks on using these on cmd line. + +Davide Vanzo, 20190213 +diff -ru bazel.orig/src/test/java/com/google/devtools/build/lib/analysis/mock/MOCK_CROSSTOOL bazel/src/test/java/com/google/devtools/build/lib/analysis/mock/MOCK_CROSSTOOL +--- bazel.orig/src/test/java/com/google/devtools/build/lib/analysis/mock/MOCK_CROSSTOOL 1980-01-01 00:00:00.000000000 -0600 ++++ bazel/src/test/java/com/google/devtools/build/lib/analysis/mock/MOCK_CROSSTOOL 2019-02-13 14:37:29.799413169 -0600 +@@ -87,9 +87,6 @@ + # Make C++ compilation deterministic. Use linkstamping instead of these + # compiler symbols. + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + + # Security hardening on by default. + # Conservative choice; -D_FORTIFY_SOURCE=2 may be unsafe in some cases. +diff -ru bazel.orig/src/test/shell/bazel/testdata/bazel_toolchain_test_data/tools/arm_compiler/CROSSTOOL bazel/src/test/shell/bazel/testdata/bazel_toolchain_test_data/tools/arm_compiler/CROSSTOOL +--- bazel.orig/src/test/shell/bazel/testdata/bazel_toolchain_test_data/tools/arm_compiler/CROSSTOOL 1980-01-01 00:00:00.000000000 -0600 ++++ bazel/src/test/shell/bazel/testdata/bazel_toolchain_test_data/tools/arm_compiler/CROSSTOOL 2019-02-13 14:41:00.643419003 -0600 +@@ -99,9 +99,6 @@ + # Make C++ compilation deterministic. Use linkstamping instead of these + # compiler symbols. + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + + # Security hardening on by default. + # Conservative choice; -D_FORTIFY_SOURCE=2 may be unsafe in some cases. +@@ -202,9 +199,6 @@ + target_system_name: "local" + unfiltered_cxx_flag: "-fno-canonical-system-headers" + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + tool_path {name: "ar" path: "/usr/bin/ar" } + tool_path {name: "cpp" path: "/usr/bin/cpp" } + tool_path {name: "dwp" path: "/usr/bin/dwp" } +diff -ru bazel.orig/tools/cpp/CROSSTOOL bazel/tools/cpp/CROSSTOOL +--- bazel.orig/tools/cpp/CROSSTOOL 1980-01-01 00:00:00.000000000 -0600 ++++ bazel/tools/cpp/CROSSTOOL 2019-02-13 14:42:51.283422065 -0600 +@@ -141,9 +141,6 @@ + # Make C++ compilation deterministic. Use linkstamping instead of these + # compiler symbols. + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + + # Security hardening on by default. + # Conservative choice; -D_FORTIFY_SOURCE=2 may be unsafe in some cases. +@@ -247,9 +244,6 @@ + # Make C++ compilation deterministic. Use linkstamping instead of these + # compiler symbols. + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + + # Security hardening on by default. + # Conservative choice; -D_FORTIFY_SOURCE=2 may be unsafe in some cases. +@@ -352,9 +346,6 @@ + # Make C++ compilation deterministic. Use linkstamping instead of these + # compiler symbols. + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + + # Security hardening on by default. + # Conservative choice; -D_FORTIFY_SOURCE=2 may be unsafe in some cases. +diff -ru bazel.orig/tools/cpp/unix_cc_configure.bzl bazel/tools/cpp/unix_cc_configure.bzl +--- bazel.orig/tools/cpp/unix_cc_configure.bzl 1980-01-01 00:00:00.000000000 -0600 ++++ bazel/tools/cpp/unix_cc_configure.bzl 2019-02-13 14:43:29.863423132 -0600 +@@ -249,9 +249,6 @@ + # Make C++ compilation deterministic. Use linkstamping instead of these + # compiler symbols. + "-Wno-builtin-macro-redefined", +- "-D__DATE__=\\\"redacted\\\"", +- "-D__TIMESTAMP__=\\\"redacted\\\"", +- "-D__TIME__=\\\"redacted\\\"" + ], + "compiler_flag": [ + # Security hardening requires optimization. +diff -ru bazel.orig/tools/osx/crosstool/CROSSTOOL.tpl bazel/tools/osx/crosstool/CROSSTOOL.tpl +--- bazel.orig/tools/osx/crosstool/CROSSTOOL.tpl 1980-01-01 00:00:00.000000000 -0600 ++++ bazel/tools/osx/crosstool/CROSSTOOL.tpl 2019-02-13 14:44:55.715425508 -0600 +@@ -153,9 +153,6 @@ + builtin_sysroot: "" + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + default_python_version: "python2.7" + feature { + name: "fastbuild" +@@ -1754,9 +1751,6 @@ + builtin_sysroot: "" + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + unfiltered_cxx_flag: "-target" + unfiltered_cxx_flag: "x86_64-apple-ios" + default_python_version: "python2.7" +@@ -3373,9 +3367,6 @@ + builtin_sysroot: "" + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + unfiltered_cxx_flag: "-target" + unfiltered_cxx_flag: "i386-apple-watchos" + default_python_version: "python2.7" +@@ -4995,9 +4986,6 @@ + builtin_sysroot: "" + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + unfiltered_cxx_flag: "-target" + unfiltered_cxx_flag: "x86_64-apple-tvos" + default_python_version: "python2.7" +@@ -6644,9 +6632,6 @@ + builtin_sysroot: "" + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + unfiltered_cxx_flag: "-target" + unfiltered_cxx_flag: "i386-apple-ios" + default_python_version: "python2.7" +@@ -8263,9 +8248,6 @@ + builtin_sysroot: "" + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + unfiltered_cxx_flag: "-target" + unfiltered_cxx_flag: "armv7-apple-ios" + default_python_version: "python2.7" +@@ -9870,9 +9852,6 @@ + builtin_sysroot: "" + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + unfiltered_cxx_flag: "-target" + unfiltered_cxx_flag: "armv7k-apple-watchos" + default_python_version: "python2.7" +@@ -11480,9 +11459,6 @@ + builtin_sysroot: "" + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + unfiltered_cxx_flag: "-target" + unfiltered_cxx_flag: "arm64-apple-tvos" + default_python_version: "python2.7" +@@ -13117,9 +13093,6 @@ + builtin_sysroot: "" + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + unfiltered_cxx_flag: "-target" + unfiltered_cxx_flag: "arm64-apple-ios" + default_python_version: "python2.7" +@@ -14724,9 +14697,6 @@ + builtin_sysroot: "" + unfiltered_cxx_flag: "-no-canonical-prefixes" + unfiltered_cxx_flag: "-Wno-builtin-macro-redefined" +- unfiltered_cxx_flag: "-D__DATE__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIMESTAMP__=\"redacted\"" +- unfiltered_cxx_flag: "-D__TIME__=\"redacted\"" + supports_normalizing_ar: false + supports_start_end_lib: false + default_python_version: "python2.7" From 8c732ed5057fd46c95b4f237b707ac5bb8729a5b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 14 Feb 2019 16:48:35 +0200 Subject: [PATCH 0375/5331] Add missing ujson to Python/3.6.6 for fosscuda/2018b --- easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb index 8331c2b7550..33c7eebb598 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb @@ -230,6 +230,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), ] moduleclass = 'lang' From 3cb28ddcadcc147aa8bd2709ef2e7342c3c5c137 Mon Sep 17 00:00:00 2001 From: murfreesboro Date: Thu, 14 Feb 2019 14:18:01 -0600 Subject: [PATCH 0376/5331] correct source_urls --- easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb index 2fac5e6db89..e772d6e59f6 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb @@ -12,7 +12,7 @@ description = """LFTP is a sophisticated ftp/http client, and a file transfer pr toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = {'http://lftp.yar.ru/ftp/'} +source_urls = ['http://lftp.yar.ru/ftp/'] sources = [SOURCE_TAR_GZ] checksums = ['19f3a4236558fbdb88eec01bc9d693c51b122d23487b6bedad4cc67ae6825fc2'] From 446fe2f46e40e20622e55e8f837587379096c2f2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 15 Feb 2019 08:35:03 +0100 Subject: [PATCH 0377/5331] Update Amber-16-AT-17-use_fftw_from_mkl_or_external.patch to use FFTW before MKL if found. Update checksums accordingly. --- ...-16-AT-17-use_fftw_from_mkl_or_external.patch | 16 ++++++++-------- ...-foss-2018b-AmberTools-17-patchlevel-10-15.eb | 2 +- ...scuda-2018b-AmberTools-17-patchlevel-10-15.eb | 2 +- ...intel-2018b-AmberTools-17-patchlevel-10-15.eb | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17-use_fftw_from_mkl_or_external.patch b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17-use_fftw_from_mkl_or_external.patch index f3dc368d1c1..8b415d0be79 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17-use_fftw_from_mkl_or_external.patch +++ b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17-use_fftw_from_mkl_or_external.patch @@ -56,14 +56,7 @@ diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure - echo " FFTW configure failed! Check the fftw3_config.log file" - echo " in the $AMBERHOME/AmberTools/src directory." - exit 1 -+ if [ -n "$MKL_HOME" ]; then -+ echo -+ echo "Using FFTW3 from MKL" -+ echo -+ flibs_fftw3="-lfftw3xf_intel $flibs_mkl" -+ fftw3="" -+ fppflags="$fppflags -I$FFT_INC_DIR" -+ elif [ -n "$EBROOTFFTW" ]; then ++ if [ -n "$EBROOTFFTW" ]; then + echo + echo "Using external FFTW3" + echo @@ -73,6 +66,13 @@ diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure + fi + flibs_fftw3="-L$FFT_LIB_DIR $flibs_fftw3" + fftw3="" ++ fppflags="$fppflags -I$FFT_INC_DIR" ++ elif [ -n "$MKL_HOME" ]; then ++ echo ++ echo "Using FFTW3 from MKL" ++ echo ++ flibs_fftw3="-lfftw3xf_intel $flibs_mkl" ++ fftw3="" + fppflags="$fppflags -I$FFT_INC_DIR" else - echo " fftw-3.3 configure succeeded." diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb index e0689c75ae1..9652793d703 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2018b-AmberTools-17-patchlevel-10-15.eb @@ -47,7 +47,7 @@ checksums = [ '43e79b40388caa2bc14f80acbe72e520b245459dde519d528c07928909dd3c08', '35fc82573ede194d11090f1df8fdef36d681bf78d2107a495e57a7f1d5ca0b69', # Amber-16-AT-17-fix_mkl_include_path.patch # Amber-16-AT-17-use_fftw_from_mkl_or_external.patch - '645f4ec6aacfc316c97f936d6549d91d1664b915ab7311c00c5c4591787753af', + 'dc42817ae02ba605a9a74044a0775e9be43fe9d5c8160977da01d68c533b9464', # Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch '8a377c87f95756bb072664a77d417eec66912872c4c02e354f4068104ee2a51c', # Amber-16-AT-17-fix_sander_link_with_external_fftw.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb index 04ec2b956a5..0cb92f12185 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2018b-AmberTools-17-patchlevel-10-15.eb @@ -49,7 +49,7 @@ checksums = [ '43e79b40388caa2bc14f80acbe72e520b245459dde519d528c07928909dd3c08', '35fc82573ede194d11090f1df8fdef36d681bf78d2107a495e57a7f1d5ca0b69', # Amber-16-AT-17-fix_mkl_include_path.patch # Amber-16-AT-17-use_fftw_from_mkl_or_external.patch - '645f4ec6aacfc316c97f936d6549d91d1664b915ab7311c00c5c4591787753af', + 'dc42817ae02ba605a9a74044a0775e9be43fe9d5c8160977da01d68c533b9464', # Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch '8a377c87f95756bb072664a77d417eec66912872c4c02e354f4068104ee2a51c', # Amber-16-AT-17-fix_sander_link_with_external_fftw.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb index c5e5edbd333..977bcc74898 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2018b-AmberTools-17-patchlevel-10-15.eb @@ -46,7 +46,7 @@ checksums = [ '43e79b40388caa2bc14f80acbe72e520b245459dde519d528c07928909dd3c08', '35fc82573ede194d11090f1df8fdef36d681bf78d2107a495e57a7f1d5ca0b69', # Amber-16-AT-17-fix_mkl_include_path.patch # Amber-16-AT-17-use_fftw_from_mkl_or_external.patch - '645f4ec6aacfc316c97f936d6549d91d1664b915ab7311c00c5c4591787753af', + 'dc42817ae02ba605a9a74044a0775e9be43fe9d5c8160977da01d68c533b9464', # Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch '8a377c87f95756bb072664a77d417eec66912872c4c02e354f4068104ee2a51c', # Amber-16-AT-17-fix_sander_link_with_external_fftw.patch From 869d268fdd4e0c3b8f221f55b5b8610e7ed4edb2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 15 Feb 2019 11:59:06 +0200 Subject: [PATCH 0378/5331] adding easyconfigs: libcerf-1.11-GCCcore-7.3.0.eb --- .../l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..abbe58bfa0a --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '1.11' + +homepage = 'http://apps.jcns.fz-juelich.de/doku/sc/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', +] +sources = [SOURCE_TGZ] +checksums = ['70101cac4a0d7863322d4d06cf95c507a9cfd64fc99ad1b31a8425204cfd9672'] + +builddependencies = [ + ('binutils', '2.30'), + ('CMake', '3.12.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From 87bf11fbc71c787a9c277afdb2aa00bc71396079 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 15 Feb 2019 10:59:44 +0100 Subject: [PATCH 0379/5331] adding easyconfigs: bokeh-1.0.4-foss-2018b-Python-3.6.6.eb --- .../bokeh-1.0.4-foss-2018b-Python-3.6.6.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..fbfb07f1342 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '1.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('PyYAML', '3.13', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('tornado', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], + 'checksums': ['ceeb6a75afc1b2de00c2b8b6da121dec3fb77031326897b80d4375a70e96aebf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 56b1a9d64eb071f421ad7efbaf5fbee84bed2268 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 15 Feb 2019 12:14:35 +0200 Subject: [PATCH 0380/5331] adding easyconfigs: libcerf-1.11-GCCcore-8.2.0.eb --- .../l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..33f40878949 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '1.11' + +homepage = 'http://apps.jcns.fz-juelich.de/doku/sc/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://apps.jcns.fz-juelich.de/src/libcerf/', + 'http://apps.jcns.fz-juelich.de/src/libcerf/old', +] +sources = [SOURCE_TGZ] +checksums = ['70101cac4a0d7863322d4d06cf95c507a9cfd64fc99ad1b31a8425204cfd9672'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From fb5f6742b38badd4216a5d6c9cbde225dc2dcf0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Feb 2019 14:41:14 +0100 Subject: [PATCH 0381/5331] adding easyconfigs: Clang-7.0.1-GCC-7.3.0-2.30.eb --- .../c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..3c9effc3622 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '7.0.1' + +homepage = 'http://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'cfe-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', +] +checksums = [ + 'a38dfc4db47102ec79dcc2aa61e93722c5f6f06f0a961073bd84b78fb949419b', # llvm-7.0.1.src.tar.xz + 'a45b62dde5d7d5fdcdfa876b0af92f164d434b06e9e89b5d0b1cbc65dfe3f418', # cfe-7.0.1.src.tar.xz + '782edfc119ee172f169c91dd79f2c964fb6b248bd9b73523149030ed505bbe18', # compiler-rt-7.0.1.src.tar.xz + '1bf146842a09336b9c88d2d76c2d117484e5fad78786821718653d1a9d57fb71', # polly-7.0.1.src.tar.xz + 'bf16b78a678da67d68405214ec7ee59d86a15f599855806192a75dcfca9b0d0c', # openmp-7.0.1.src.tar.xz +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +builddependencies = [ + ('CMake', '3.12.1'), + ('Python', '2.7.15', '-bare'), + ('libxml2', '2.9.8'), +] + +assertions = True +usepolly = True +skip_all_tests = True + +moduleclass = 'compiler' From 1a5672c25864964377507a6517e56ab09cc655cf Mon Sep 17 00:00:00 2001 From: h_zimm01 Date: Fri, 15 Feb 2019 14:59:33 +0100 Subject: [PATCH 0382/5331] adding easyconfigs: Go-1.11.5.eb --- easybuild/easyconfigs/g/Go/Go-1.11.5.eb | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.11.5.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.11.5.eb b/easybuild/easyconfigs/g/Go/Go-1.11.5.eb new file mode 100644 index 00000000000..90c7d94cf1a --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.11.5.eb @@ -0,0 +1,23 @@ +easyblock = 'Tarball' + +name = 'Go' +version = '1.11.5' + +homepage = 'http://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://storage.googleapis.com/golang/'] +sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] +checksums = ['ff54aafedff961eb94792487e827515da683d61a5f9482f668008832631e5d25'] + +sanity_check_paths = { + 'files': ['go/bin/go', 'go/bin/gofmt'], + 'dirs': ['go/api', 'go/doc', 'go/lib', 'go/pkg'], +} + +modextravars = {'GOROOT': '%(installdir)s/go'} +modextrapaths = {'PATH': ['go/bin']} +moduleclass = 'compiler' From be4fe9bd80e17d71b60df8710b9258818a9723fa Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 15 Feb 2019 16:17:33 +0200 Subject: [PATCH 0383/5331] Mesa depends on libunwind when building with GCC. --- .../libunwind-1.2.1-GCCcore-7.3.0.eb | 33 +++++++++++++++++++ .../m/Mesa/Mesa-18.1.1-foss-2018b.eb | 1 + 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..c01773d5893 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.2.1' + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3f3ecb90e28cbe53fba7a4a27ccce7aad188d3210bb1964a923a731a27a75acb'] + +builddependencies = [('binutils', '2.30')] + +dependencies = [ + ('XZ', '5.2.4'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb index eb6e1817da2..4a5428f2a85 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018b.eb @@ -50,6 +50,7 @@ dependencies = [ ('libdrm', '2.4.92'), ('LLVM', '6.0.0'), ('X11', '20180604'), + ('libunwind', '1.2.1'), ] # GLU is not part anymore of Mesa package! From c59127baa8ae2960898767f1bab2f4fdbec90849 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 15 Feb 2019 17:43:55 +0200 Subject: [PATCH 0384/5331] adding easyconfigs: SMARTdenovo-20180219-foss-2018b.eb and patches: SMARTdenovo-20180219_fix_build_flags_and_install.patch, SMARTdenovo-20180219_use_env_perl_for_startup.patch --- .../SMARTdenovo-20180219-foss-2018b.eb | 61 +++++++++++ ...20180219_fix_build_flags_and_install.patch | 39 +++++++ ...vo-20180219_use_env_perl_for_startup.patch | 103 ++++++++++++++++++ 3 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb create mode 100644 easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219_fix_build_flags_and_install.patch create mode 100644 easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219_use_env_perl_for_startup.patch diff --git a/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb new file mode 100644 index 00000000000..342dc16e189 --- /dev/null +++ b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb @@ -0,0 +1,61 @@ +easyblock = "ConfigureMake" + +name = 'SMARTdenovo' +version = '20180219' + +homepage = 'https://github.com/ruanjue/smartdenovo' +description = """SMARTdenovo is a de novo assembler for PacBio and +Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw +read alignments without an error correction stage. It also provides +tools to generate accurate consensus sequences, though a platform +dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish +for ONT) are still required for higher accuracy.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +commit = '5cc1356bffb87197b0fb9b835cfe1adc5a764dc6' +sources = [{ + 'filename': '%%(name)s-master-20190215-%s.tar.gz' % commit, + 'git_config': { + 'url': 'https://github.com/ruanjue', + 'repo_name': 'smartdenovo', + 'commit': commit, + } +}] +patches = [ + '%(name)s-%(version)s_fix_build_flags_and_install.patch', + '%(name)s-%(version)s_use_env_perl_for_startup.patch', +] +checksums = [ + # SMARTdenovo-master-20190215-5cc1356bffb87197b0fb9b835cfe1adc5a764dc6.tar.gz + 'd1dc8b0f1ba19cbdf2572f29c91d57d4b7b75508ad6ef4eca39ecc7db049c544', + # SMARTdenovo-20180219_fix_build_flags_and_install.patch + '6138fb6db730372ee50a5cc87cadf2d99f11b48165e45832eb985804910d2420', + # SMARTdenovo-20180219_use_env_perl_for_startup.patch + 'e9ee4d00f977b0c8694fffb15b9fbf7d3aa575b71f3adb979f9203c48c1ee22c', +] + +# Checksum will probably not match since the tar file is generated on the fly. + +dependencies = [('Perl', '5.28.0')] + +skipsteps = ['configure'] + +installopts = ' INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['dbm_index_fa.pl', 'dbm_read_fa.pl', + 'fq2fa.pl', 'large_seqs.pl', + 'longest_pacbio_subreads_f5q.pl', + 'longest_pacbio_subreads.pl', 'pairaln', + 'pbcluster_haplo.pl', 'pbcluster_upgma.pl', + 'rename_fa.pl', 'rename_fq.pl', + 'run_dmo.sh', 'run_zmo.sh', 'seq_n50.pl', + 'smartdenovo.pl', 'wtclp', 'wtcns', + 'wtcyc', 'wtext', 'wtgbo', 'wtlay', + 'wtmer', 'wtmsa', 'wtobt', 'wtpre', 'wtzmo' + ]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219_fix_build_flags_and_install.patch b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219_fix_build_flags_and_install.patch new file mode 100644 index 00000000000..b2ba1080046 --- /dev/null +++ b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219_fix_build_flags_and_install.patch @@ -0,0 +1,39 @@ +Patch the Makefile to use CFLAGS from EasyBuild. +Make it install everything in a useful directory. + +Åke Sandgren, 20190215 +diff -ru smartdenovo.orig/Makefile smartdenovo/Makefile +--- smartdenovo.orig/Makefile 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/Makefile 2019-02-15 16:04:50.409061286 +0100 +@@ -1,20 +1,15 @@ + VERSION=1.0.0 + MINOR_VER=20140314 +-CC=gcc +-ifdef DEBUG +-CFLAGS=-g3 -W -Wall -O0 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 +-else +-CFLAGS=-W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 +-endif +-INSTALLDIR=/usr/local/bin ++ ++CFLAGS += -W -Wall -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE ++ + GLIBS=-lm -lpthread +-#GENERIC_SRC=Makefile mem_share.h string.h file_reader.h file_reader.c bitvec.h hashset.h sort.h list.h dna.h thread.h timer.h ksw.h ksw.c kswx.h ++ + GENERIC_SRC=mem_share.h string.h file_reader.h file_reader.c bitvec.h hashset.h sort.h list.h dna.h thread.h timer.h ksw.h ksw.c kswx.h + + ifeq (0, ${MAKELEVEL}) + UNIQ_ID=$(shell date +"%s") + endif +-#all: pairaln wtcyc wtmer wtzmo wtobt wtclp wtext wtlay wtcns wtdif wtcorr wtjnt + all: pairaln wtpre wtcyc wtmer wtzmo wtobt wtclp wtext wtgbo wtlay wtcns wtmsa + + pairaln: $(GENERIC_SRC) pairaln.c +@@ -69,4 +64,5 @@ + rm -f *.o *.gcda *.gcno *.gcov gmon.out + + install: +- cp pairaln wtpre wtcyc wtmer wtzmo wtobt wtclp wtext wtgbo wtlay wtcns wtmsa $(INSTALLDIR) ++ mkdir -p $(INSTALLDIR)/bin ++ cp *.sh *.pl pairaln wtpre wtcyc wtmer wtzmo wtobt wtclp wtext wtgbo wtlay wtcns wtmsa $(INSTALLDIR)/bin diff --git a/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219_use_env_perl_for_startup.patch b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219_use_env_perl_for_startup.patch new file mode 100644 index 00000000000..0d10f30f74a --- /dev/null +++ b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219_use_env_perl_for_startup.patch @@ -0,0 +1,103 @@ +Make all perl script use perl from the environment. +So it uses the Perl from the dependency. + +Åke Sandgren, 20190215 +diff -ru smartdenovo.orig/dbm_index_fa.pl smartdenovo/dbm_index_fa.pl +--- smartdenovo.orig/dbm_index_fa.pl 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/dbm_index_fa.pl 2019-02-15 15:31:18.498319518 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + # + #Author: Ruan Jue + # +diff -ru smartdenovo.orig/dbm_read_fa.pl smartdenovo/dbm_read_fa.pl +--- smartdenovo.orig/dbm_read_fa.pl 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/dbm_read_fa.pl 2019-02-15 15:31:22.298105625 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + # + #Author: Ruan Jue + # +diff -ru smartdenovo.orig/fq2fa.pl smartdenovo/fq2fa.pl +--- smartdenovo.orig/fq2fa.pl 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/fq2fa.pl 2019-02-15 15:31:24.082005208 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + my $count=0; + while(<>){ + if($count%4==0){ +diff -ru smartdenovo.orig/large_seqs.pl smartdenovo/large_seqs.pl +--- smartdenovo.orig/large_seqs.pl 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/large_seqs.pl 2019-02-15 15:31:26.121890381 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + # + #Author: Ruan Jue + +diff -ru smartdenovo.orig/longest_pacbio_subreads_f5q.pl smartdenovo/longest_pacbio_subreads_f5q.pl +--- smartdenovo.orig/longest_pacbio_subreads_f5q.pl 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/longest_pacbio_subreads_f5q.pl 2019-02-15 15:31:27.913789513 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + # + # Author: Jue Ruan + # +diff -ru smartdenovo.orig/longest_pacbio_subreads.pl smartdenovo/longest_pacbio_subreads.pl +--- smartdenovo.orig/longest_pacbio_subreads.pl 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/longest_pacbio_subreads.pl 2019-02-15 15:31:29.577695850 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + # + # Author: Jue Ruan + # +diff -ru smartdenovo.orig/pbcluster_haplo.pl smartdenovo/pbcluster_haplo.pl +--- smartdenovo.orig/pbcluster_haplo.pl 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/pbcluster_haplo.pl 2019-02-15 15:31:31.457590029 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + # + # AUthor: Jue Ruan + # +diff -ru smartdenovo.orig/pbcluster_upgma.pl smartdenovo/pbcluster_upgma.pl +--- smartdenovo.orig/pbcluster_upgma.pl 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/pbcluster_upgma.pl 2019-02-15 15:31:34.241433323 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + # + # Author: Jue Ruan + # +diff -ru smartdenovo.orig/rename_fa.pl smartdenovo/rename_fa.pl +--- smartdenovo.orig/rename_fa.pl 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/rename_fa.pl 2019-02-15 15:31:36.097328852 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + # + # Author: Ruan Jue + # +diff -ru smartdenovo.orig/rename_fq.pl smartdenovo/rename_fq.pl +--- smartdenovo.orig/rename_fq.pl 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/rename_fq.pl 2019-02-15 15:31:37.985222580 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + # + # Author: Ruan Jue + # +diff -ru smartdenovo.orig/seq_n50.pl smartdenovo/seq_n50.pl +--- smartdenovo.orig/seq_n50.pl 2019-02-15 15:12:43.000000000 +0100 ++++ smartdenovo/seq_n50.pl 2019-02-15 15:31:40.425085237 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl -w + # + # Author: Ruan Jue + # From ee7d9da6d2796bd2adc3ff1971ec026d884700b3 Mon Sep 17 00:00:00 2001 From: murfreesboro Date: Fri, 15 Feb 2019 10:32:13 -0600 Subject: [PATCH 0385/5331] builddependencies should be the list symbol --- easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb index e772d6e59f6..ea7cd42870c 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.8.4-GCCcore-6.4.0.eb @@ -16,11 +16,11 @@ source_urls = ['http://lftp.yar.ru/ftp/'] sources = [SOURCE_TAR_GZ] checksums = ['19f3a4236558fbdb88eec01bc9d693c51b122d23487b6bedad4cc67ae6825fc2'] -builddependencies = { +builddependencies = [ ('binutils', '2.28'), ('libreadline', '7.0'), ('zlib', '1.2.11') -} +] # for this version of lftp the gnutls library is optional configopts = "--with-readline=$EBROOTLIBREADLINE --without-gnutls" From cf172787f3763872ee463d4bca33af9e5521a021 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 15 Feb 2019 10:44:09 -0600 Subject: [PATCH 0386/5331] Resolve conflict with develop --- .../easyconfigs/a/ABySS/ABySS-2.0.2-foss-2016b.eb | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-foss-2016b.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-foss-2016b.eb index 16e620b71af..57f9dde091c 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-foss-2016b.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.0.2-foss-2016b.eb @@ -1,13 +1,3 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Maxime Schmitt , Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -## - easyblock = 'ConfigureMake' name = 'ABySS' @@ -24,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df'] dependencies = [ - ('Boost', '1.63.0', '-Python-2.7.12'), + ('Boost', '1.61.0'), ('sparsehash', '2.0.3'), ('SQLite', '3.13.0'), ] From 0b1b348fcb53ee1cd1688e0aa0e4e0d059dc1bc8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 15 Feb 2019 23:36:33 +0200 Subject: [PATCH 0387/5331] Fix style issue. --- .../s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb index 342dc16e189..482e7cc68bf 100644 --- a/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb +++ b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb @@ -53,8 +53,7 @@ sanity_check_paths = { 'run_dmo.sh', 'run_zmo.sh', 'seq_n50.pl', 'smartdenovo.pl', 'wtclp', 'wtcns', 'wtcyc', 'wtext', 'wtgbo', 'wtlay', - 'wtmer', 'wtmsa', 'wtobt', 'wtpre', 'wtzmo' - ]], + 'wtmer', 'wtmsa', 'wtobt', 'wtpre', 'wtzmo']], 'dirs': [], } From 59c875eefd80361fb153b955d2e195c238f9154d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 16 Feb 2019 11:39:34 +0000 Subject: [PATCH 0388/5331] adding use_pip and download_dep_fail to the python bits --- .../hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb | 5 ++++- .../hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb | 5 ++++- .../p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb | 3 +++ .../easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb | 7 +++++++ 4 files changed, 18 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb index f19717fa4c1..5f8a0a674d8 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb @@ -16,10 +16,13 @@ dependencies = [ ('Python', '3.6.6'), ] - # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_filter = ("python -c 'import %(ext_name)s'", '') +exts_default_options = {'use_pip': True} + +exts_download_dep_fail = True +use_pip = True exts_list = [ ('attrs', '18.2.0', { diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb index 4020f1b51ad..fb9d4d463bf 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb @@ -16,10 +16,13 @@ dependencies = [ ('Python', '3.6.6'), ] - # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' exts_filter = ("python -c 'import %(ext_name)s'", '') +exts_default_options = {'use_pip': True} + +exts_download_dep_fail = True +use_pip = True exts_list = [ ('attrs', '18.2.0', { diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb index 33906e08e06..f134c1e17ad 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb @@ -18,6 +18,9 @@ dependencies = [ ('libyaml', '0.2.1'), ] +use_pip = True +download_dep_fail = True + options = {'modulename': 'yaml'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb index 8a8e6ea997d..4163f294a45 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb @@ -29,6 +29,9 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +# Try to make sure stack limit is set to unlimited, to avoid compilation errors for hashlib with Intel compilers +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/6484 +ulimit_unlimited = True exts_download_dep_fail = True # workaround for "undefined symbol: __stack_chk_guard" @@ -226,6 +229,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), ] moduleclass = 'lang' From 06a8c669ff39f133513b72b0b9332bf966379cc0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 16 Feb 2019 11:44:02 +0000 Subject: [PATCH 0389/5331] fixing the hypothesis sanity check --- .../h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb | 5 ++++- .../hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb index 5f8a0a674d8..4e05e8168ec 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb @@ -42,7 +42,10 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg-info' + 'lib/python%(pyshortver)s/site-packages/%(namelower)s' + ], } moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb index fb9d4d463bf..2e18ee58df2 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb @@ -42,7 +42,10 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg-info' + 'lib/python%(pyshortver)s/site-packages/%(namelower)s' + ], } moduleclass = 'tools' From ba84a55e9dbbafad27be348814c2d71b39898b47 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 16 Feb 2019 11:45:20 +0000 Subject: [PATCH 0390/5331] typo fix --- .../h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb | 2 +- .../hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb index 4e05e8168ec..91ea0c1d0db 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb @@ -43,7 +43,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg-info' + 'lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg-info', 'lib/python%(pyshortver)s/site-packages/%(namelower)s' ], } diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb index 2e18ee58df2..0179009f3af 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb @@ -43,7 +43,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg-info' + 'lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg-info', 'lib/python%(pyshortver)s/site-packages/%(namelower)s' ], } From 5e8958f723ec2e2c679d9d12ce389524c03b48f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 Feb 2019 17:10:56 +0100 Subject: [PATCH 0391/5331] adding easyconfigs: Clang-6.0.1-GCC-7.3.0-2.30.eb --- .../c/Clang/Clang-6.0.1-GCC-7.3.0-2.30.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-7.3.0-2.30.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..de357910d8a --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-7.3.0-2.30.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '6.0.1' + +homepage = 'http://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'cfe-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', +] +checksums = [ + 'b6d6c324f9c71494c0ccaf3dac1f16236d970002b42bb24a6c9e1634f7d0f4e2', # llvm-6.0.1.src.tar.xz + '7c243f1485bddfdfedada3cd402ff4792ea82362ff91fbdac2dae67c6026b667', # cfe-6.0.1.src.tar.xz + 'f4cd1e15e7d5cb708f9931d4844524e4904867240c306b06a4287b22ac1c99b9', # compiler-rt-6.0.1.src.tar.xz + 'e7765fdf6c8c102b9996dbb46e8b3abc41396032ae2315550610cf5a1ecf4ecc', # polly-6.0.1.src.tar.xz + '66afca2b308351b180136cf899a3b22865af1a775efaf74dc8a10c96d4721c5a', # openmp-6.0.1.src.tar.xz +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +builddependencies = [ + ('CMake', '3.12.1'), + ('Python', '2.7.15', '-bare'), + ('libxml2', '2.9.8'), +] + +assertions = True +usepolly = True +skip_all_tests = True + +moduleclass = 'compiler' From ca72934c30b967712b6374b9ddd78be385d88ff1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 17 Feb 2019 10:46:21 +0100 Subject: [PATCH 0392/5331] add suggested options --- .../imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb index fe59988cbf4..4c7a6ab1e30 100644 --- a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.4.3-foss-2018b-Python-3.6.6.eb @@ -19,6 +19,9 @@ dependencies = [ ('scikit-learn', '0.20.0', versionsuffix), ] +use_pip = True +download_dep_fail = True + options = {'modulename': 'imblearn'} sanity_check_paths = { From 59ba992069c876adeb8f065c9bd7b73524aeb108 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 18 Feb 2019 09:12:10 +0000 Subject: [PATCH 0393/5331] fixes for review comments --- .../p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb | 3 +++ .../p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb index 653c5d789ed..ea1c91595c5 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb @@ -206,6 +206,9 @@ dependencies = [ ('Ninja', '1.8.2'), ] +use_pip = True +download_dep_fail = True + # This environment is needed to prevent setup.py from invoking git to determine version. prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb index ffa97254219..670609ca9ca 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -206,6 +206,9 @@ dependencies = [ ('Ninja', '1.8.2'), ] +use_pip = True +download_dep_fail = True + # This environment is needed to prevent setup.py from invoking git to determine version. prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' From f908f244e240b6107ecf9846736c8fe04e6456dd Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 18 Feb 2019 09:14:03 +0000 Subject: [PATCH 0394/5331] Update hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb --- ...hesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb | 20 +------------------ 1 file changed, 1 insertion(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb index 0179009f3af..7bde035e223 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb @@ -1,5 +1,5 @@ # This easyconfig was created by the BEAR Software team at the University of Birmingham. -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'hypothesis' version = '4.5.0' @@ -16,12 +16,6 @@ dependencies = [ ('Python', '3.6.6'), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') -exts_default_options = {'use_pip': True} - -exts_download_dep_fail = True use_pip = True exts_list = [ @@ -36,16 +30,4 @@ exts_list = [ }), ] -modextrapaths = { - 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_paths = { - 'files': [], - 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg-info', - 'lib/python%(pyshortver)s/site-packages/%(namelower)s' - ], -} - moduleclass = 'tools' From 128f904f4da2341cc5546c5c26b264187a34d50e Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 18 Feb 2019 09:14:20 +0000 Subject: [PATCH 0395/5331] Update hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb --- ...ypothesis-4.5.0-foss-2018b-Python-3.6.6.eb | 20 +------------------ 1 file changed, 1 insertion(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb index 91ea0c1d0db..b601f23494d 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb @@ -1,5 +1,5 @@ # This easyconfig was created by the BEAR Software team at the University of Birmingham. -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'hypothesis' version = '4.5.0' @@ -16,12 +16,6 @@ dependencies = [ ('Python', '3.6.6'), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') -exts_default_options = {'use_pip': True} - -exts_download_dep_fail = True use_pip = True exts_list = [ @@ -36,16 +30,4 @@ exts_list = [ }), ] -modextrapaths = { - 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_paths = { - 'files': [], - 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/%(namelower)s-%(version)s-py%(pyshortver)s.egg-info', - 'lib/python%(pyshortver)s/site-packages/%(namelower)s' - ], -} - moduleclass = 'tools' From 3656b59738f38f966c28aab53aa5e75a8a86d7b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 18 Feb 2019 11:22:30 +0100 Subject: [PATCH 0396/5331] switch to GCCcore toolchain --- ...{PEAR-0.9.11-foss-2018b.eb => PEAR-0.9.11-GCCcore-7.3.0.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/p/PEAR/{PEAR-0.9.11-foss-2018b.eb => PEAR-0.9.11-GCCcore-7.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-foss-2018b.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCCcore-7.3.0.eb similarity index 92% rename from easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-foss-2018b.eb rename to easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCCcore-7.3.0.eb index 38188f1670d..2d8fca83c2c 100644 --- a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-foss-2018b.eb +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCCcore-7.3.0.eb @@ -9,7 +9,7 @@ homepage = 'https://cme.h-its.org/exelixis/web/software/%(namelower)s/' description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} # Needs manual download via web-form, # https://www.h-its.org/en/research/sco/software/#NextGenerationSequencingSequenceAnalysis @@ -19,6 +19,7 @@ checksums = ['94f4a1835cd75ec6fab83405c2545ddba6b6bb1644579222e9cc2ad57a59d654'] builddependencies = [ ('Autotools', '20180311'), + ('binutils', '2.30'), ] dependencies = [ From e3159f76bd5431fe6dd7c0f920e35bd2eea358f9 Mon Sep 17 00:00:00 2001 From: ebtest Date: Mon, 18 Feb 2019 11:08:01 +0000 Subject: [PATCH 0397/5331] adding easyconfigs: randfold-2.0.1-foss-2018b.eb, ViennaRNA-2.4.11-foss-2018b-Python-3.6.6.eb, miRDeep2-0.1.1-foss-2018b-Python-3.6.6.eb --- .../miRDeep2-0.1.1-foss-2018b-Python-3.6.6.eb | 36 ++++++++++++ .../r/randfold/randfold-2.0.1-foss-2018b.eb | 31 +++++++++++ ...iennaRNA-2.4.11-foss-2018b-Python-3.6.6.eb | 55 +++++++++++++++++++ 3 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/m/miRDeep2/miRDeep2-0.1.1-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/r/randfold/randfold-2.0.1-foss-2018b.eb create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.4.11-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/m/miRDeep2/miRDeep2-0.1.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-0.1.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..eaeea7bea22 --- /dev/null +++ b/easybuild/easyconfigs/m/miRDeep2/miRDeep2-0.1.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,36 @@ +easyblock = 'PackedBinary' + +name = 'miRDeep2' +version = '0.1.1' +versionsuffix = '-Python-3.6.6' + +homepage = 'https://github.com/rajewsky-lab/mirdeep2' +description = """ miRDeep2 is a completely overhauled tool which +discovers microRNA genes by analyzing sequenced RNAs """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/rajewsky-lab/mirdeep2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0083202626bb444c2b4a4434d273e044ed164661a5de0bb4d5034c792e687ff9'] + +dependencies = [ + ('Perl', '5.28.0'), # provides PDF::API2 + ('Bowtie', '1.2.2'), + ('ViennaRNA', '2.4.11', versionsuffix), + ('randfold', '2.0.1'), # also provides SQUID +] + +install_cmd = "cp -a mirdeep*/src %(installdir)s/bin && chmod a+x %(installdir)s/bin/*.pl && " +install_cmd += 'sed -i "s@#!/usr/bin/perl@#!$EBROOTPERL/bin/perl@" %(installdir)s/bin/*.pl && ' +install_cmd += "cp -a mirdeep*/Rfam_for_miRDeep.fa %(installdir)s && " + +# scripts include a hard check for a file called 'install_successful' in the install directory... +install_cmd += "touch %(installdir)s/install_successful" + +sanity_check_paths = { + 'files': ['bin/mapper.pl', 'bin/miRDeep2.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/randfold/randfold-2.0.1-foss-2018b.eb b/easybuild/easyconfigs/r/randfold/randfold-2.0.1-foss-2018b.eb new file mode 100644 index 00000000000..30c1e969e2d --- /dev/null +++ b/easybuild/easyconfigs/r/randfold/randfold-2.0.1-foss-2018b.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'randfold' +version = '2.0.1' + +homepage = 'http://bioinformatics.psb.ugent.be/software/details/Randfold' +description = "Minimum free energy of folding randomization test software" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b286145deb9ac6197062d98e209da095f00c45a5a615616bcf2b2a6609ed113f'] + +cleanupoldinstall = False + +# also install included SQUID dependency, since it can't be found online anymore... +prebuildopts = "tar xfvz squid.tar.gz && cd squid-*/ && mkdir -p %(installdir)s && " +prebuildopts += "./configure --prefix=%(installdir)s && make && make install && cd .. && " +prebuildopts += "export CPATH=%(installdir)s/include:$CPATH && export LIBRARY_PATH=%(installdir)s/lib:$LIBRARY_PATH && " + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [(['randfold'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/randfold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.4.11-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.4.11-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..a1535a27d42 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.4.11-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'ViennaRNA' +version = '2.4.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.tbi.univie.ac.at/RNA/' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] +sources = [SOURCE_TAR_GZ] +checksums = ['9913fc04a6f2ab380bd492301f9c5a07cfe1b6c9ca437261de03691c3d3d6837'] + +builddependencies = [ + ('Autotools', '20180311'), + ('flex', '2.6.4'), + ('pkg-config', '0.29.2'), + ('Bison', '3.0.5'), + ('SWIG', '3.0.12', versionsuffix), +] + +dependencies = [ + ('Python', '3.6.6'), + ('Perl', '5.28.0'), + ('GSL', '2.5'), + ('libgd', '2.2.5'), + ('X11', '20180604'), +] + +configopts = "--with-cluster --with-kinwalker --with-python3" +# Uncomment this if you compile on pre SSE4.1 CPU +# configopts += "--enable-sse " + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/', 'lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 6eac126032a8288bfedf4a155c35830552496235 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Mon, 18 Feb 2019 12:14:39 +0100 Subject: [PATCH 0398/5331] URL of source changed to archive.apache.org --- easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb b/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb index 069a173f79f..384cbea2cf3 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb @@ -15,7 +15,7 @@ central piece of information. toolchain = {'name': 'dummy', 'version': 'dummy'} sources = ['apache-maven-%(version)s-bin.tar.gz'] -source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] +source_urls = ['http://archive.apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] checksums = ['6a1b346af36a1f1a491c1c1a141667c5de69b42e6611d3687df26868bc0f4637'] sanity_check_paths = { From b6b948115315e8b3ad2eba010926f98ce7fd874f Mon Sep 17 00:00:00 2001 From: sassmaj Date: Mon, 18 Feb 2019 12:33:36 +0100 Subject: [PATCH 0399/5331] Java wrapper added --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb index c01cfb1dbdb..0e3f9e4fc4a 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb @@ -14,9 +14,8 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://imagej.nih.gov/ij/download/src/'] sources = ['ij%(version_major)s%(version_minor)s-src.zip'] -dependencies = [ - ('Java', '1.8.0_202'), -] +# specify dependency on Java/1.8 "wrapper", rather than a specific Java version +dependencies = [('Java', '1.8', '', True)] builddependencies = [('ant', '1.10.1', '-Java-%(javaver)s')] From 2160ce2af6416e86d5ca9d0c5ee6f0ff7129307f Mon Sep 17 00:00:00 2001 From: sassmaj Date: Mon, 18 Feb 2019 14:03:22 +0100 Subject: [PATCH 0400/5331] checksum added --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb index 0e3f9e4fc4a..e70e5ac1e44 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://imagej.nih.gov/ij/download/src/'] sources = ['ij%(version_major)s%(version_minor)s-src.zip'] +checksums = ['1fe77bedd792f095bc51d7b12083319b04124bb82f2dc5eb0552089880cf1a4f'] # specify dependency on Java/1.8 "wrapper", rather than a specific Java version dependencies = [('Java', '1.8', '', True)] From f6a368f4ecfc7ee5b49307aead65edbf33e2f356 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 18 Feb 2019 14:09:15 +0100 Subject: [PATCH 0401/5331] switch to PythonBundle and other remarks --- .../bx-python-0.8.2-foss-2018b-Python-3.6.6.eb | 15 +++++---------- .../pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb | 6 ++---- .../RSeQC/RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb | 2 +- 3 files changed, 8 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb index e1f614e8280..8218983a26c 100644 --- a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'bx-python' version = '0.8.2' @@ -15,11 +15,10 @@ dependencies = [ ('LZO', '2.10'), ] -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " +use_pip = True + exts_download_dep_fail = True exts_list = [ @@ -35,14 +34,10 @@ exts_list = [ }), ] -# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module -full_sanity_check = True - sanity_check_paths = { 'files': [], - 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/bx_python-%(version)s-py%(pyshortver)s.egg-info', + 'lib/python%(pyshortver)s/site-packages/python_lzo-1.12-py%(pyshortver)s.egg-info'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb index 51aaaa924c1..8f75788c881 100644 --- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb @@ -28,10 +28,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ['python lib/python%(pyshortver)s/site-packages/pyBigWigTest/test.py'] +sanity_check_commands = ['python lib/python%(pyshortver)s/site-packages/%(name)sTest/test.py'] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -options = {'modulename': 'pyBigWig'} +options = {'modulename': name} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb index bb38004db19..09ff38c641b 100644 --- a/easybuild/easyconfigs/r/RSeQC/RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-3.0.0-foss-2018b-Python-3.6.6.eb @@ -35,7 +35,7 @@ download_dep_fail = True sanity_check_paths = { 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', 'bin/split_paired_bam.py'], - 'dirs': ['lib'] + 'dirs': ['lib/python%(pyshortver)s/site-packages'] } options = {'modulename': 'qcmodule'} From 153762420359ef74a43c47354e6279b1657249db Mon Sep 17 00:00:00 2001 From: sassmaj Date: Mon, 18 Feb 2019 15:58:13 +0100 Subject: [PATCH 0402/5331] Updated Java version to 202 --- easybuild/easyconfigs/j/Java/Java-1.8.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.eb b/easybuild/easyconfigs/j/Java/Java-1.8.eb index 3ed862812e5..353e55e8b14 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.eb @@ -1,3 +1,7 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# updated to version 202 + easyblock = 'ModuleRC' name = 'Java' @@ -9,6 +13,6 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = {'name': 'dummy', 'version': 'dummy'} -dependencies = [('Java', '%(version)s.0_192')] +dependencies = [('Java', '%(version)s.0_202')] moduleclass = 'lang' From b19a9f7e9f15e1061d5ab16f2f09d87f3b0c609f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 18 Feb 2019 21:59:33 +0200 Subject: [PATCH 0403/5331] Move comment about non-matching checksum to the correct place. --- .../s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb index 482e7cc68bf..451a308de9f 100644 --- a/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb +++ b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb @@ -27,6 +27,7 @@ patches = [ '%(name)s-%(version)s_use_env_perl_for_startup.patch', ] checksums = [ + # Checksum will not match since the tar file is generated on the fly. # SMARTdenovo-master-20190215-5cc1356bffb87197b0fb9b835cfe1adc5a764dc6.tar.gz 'd1dc8b0f1ba19cbdf2572f29c91d57d4b7b75508ad6ef4eca39ecc7db049c544', # SMARTdenovo-20180219_fix_build_flags_and_install.patch @@ -35,8 +36,6 @@ checksums = [ 'e9ee4d00f977b0c8694fffb15b9fbf7d3aa575b71f3adb979f9203c48c1ee22c', ] -# Checksum will probably not match since the tar file is generated on the fly. - dependencies = [('Perl', '5.28.0')] skipsteps = ['configure'] From 82c3de8f7eff6e2fcd2ec57cd59a722379cdd778 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Mon, 18 Feb 2019 15:48:58 -0600 Subject: [PATCH 0404/5331] adding easyconfigs: HISAT2-2.1.0-foss-2017b.eb, HISAT2-2.1.0-intel-2017b.eb, ncbi-vdb-2.8.2-foss-2017b.eb, ncbi-vdb-2.8.2-intel-2017b.eb, NGS-1.3.0-GCCcore-6.4.0.eb --- .../h/HISAT2/HISAT2-2.1.0-foss-2017b.eb | 33 +++++++++++++++ .../h/HISAT2/HISAT2-2.1.0-intel-2017b.eb | 37 +++++++++++++++++ .../n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb | 40 +++++++++++++++++++ .../n/ncbi-vdb/ncbi-vdb-2.8.2-foss-2017b.eb | 39 ++++++++++++++++++ .../n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017b.eb | 39 ++++++++++++++++++ 5 files changed, 188 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-foss-2017b.eb create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-intel-2017b.eb create mode 100644 easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-foss-2017b.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017b.eb diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-foss-2017b.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-foss-2017b.eb new file mode 100644 index 00000000000..257fdf842dd --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-foss-2017b.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.1.0' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['89a276eed1fc07414b1601947bc9466bdeb50e8f148ad42074186fe39a1ee781'] + +dependencies = [ + ('NGS', '1.3.0'), + ('ncbi-vdb', '2.8.2'), +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in executables], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-intel-2017b.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-intel-2017b.eb new file mode 100644 index 00000000000..74b2b14855f --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.1.0-intel-2017b.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.1.0' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] +sources = ['%(namelower)s-%(version)s-source.zip'] +patches = ['HISAT2-%(version)s_intel-fixes.patch'] +checksums = [ + '89a276eed1fc07414b1601947bc9466bdeb50e8f148ad42074186fe39a1ee781', # hisat2-2.1.0-source.zip + '7986dbcdb56b4bf5494dd70b215e90e321ca887dbdafc48de7a13e6b5abd038b', # HISAT2-2.1.0_intel-fixes.patch +] + +dependencies = [ + ('NGS', '1.3.0'), + ('ncbi-vdb', '2.8.2'), +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in executables], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..85280ff5970 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '1.3.0' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['803c650a6de5bb38231d9ced7587f3ab788b415cac04b0ef4152546b18713ef2'] + +dependencies = [('Java', '1.8.0_192', '', True)] + +builddependencies = [ + ('binutils', '2.28'), +] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-java' + +installopts = "-C ngs-sdk && make install -C ngs-java" + +parallel = 1 + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-foss-2017b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-foss-2017b.eb new file mode 100644 index 00000000000..752bf32b32e --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-foss-2017b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.8.2' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['15c9a47a9ebaf01822c567817acd681c4a594b4ac92e8bcf08d4d580f62296a9'] + +dependencies = [ + ('libxml2', '2.9.4'), + ('file', '5.33'), + ('HDF5', '1.10.1'), + ('NGS', '1.3.0') +] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +parallel = 1 + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-vdb.%s' % SHLIB_EXT, 'lib64/libncbi-vdb.%s' % SHLIB_EXT), + ('lib/libncbi-wvdb.%s' % SHLIB_EXT, 'lib64/libncbi-wvdb.%s' % SHLIB_EXT), + ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a'), ('lib/libncbi-vdb.a', 'lib64/libncbi-vdb.a'), + ('lib/libncbi-wvdb.a', 'lib64/libncbi-wvdb.a')], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017b.eb new file mode 100644 index 00000000000..3e9eb122dc9 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.8.2' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://github.com/ncbi/ncbi-vdb/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['15c9a47a9ebaf01822c567817acd681c4a594b4ac92e8bcf08d4d580f62296a9'] + +dependencies = [ + ('libxml2', '2.9.4'), + ('file', '5.33'), + ('HDF5', '1.10.1'), + ('NGS', '1.3.0') +] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir " + +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +parallel = 1 + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-vdb.%s' % SHLIB_EXT, 'lib64/libncbi-vdb.%s' % SHLIB_EXT), + ('lib/libncbi-wvdb.%s' % SHLIB_EXT, 'lib64/libncbi-wvdb.%s' % SHLIB_EXT), + ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a'), ('lib/libncbi-vdb.a', 'lib64/libncbi-vdb.a'), + ('lib/libncbi-wvdb.a', 'lib64/libncbi-wvdb.a')], + 'dirs': [], +} + +moduleclass = 'bio' From 53ced8afce9ab4a88cc7aea64877d6ea0de0f331 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 19 Feb 2019 08:02:47 +0100 Subject: [PATCH 0405/5331] add cURL as dependency --- .../p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb index 8f75788c881..aa29122858f 100644 --- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.13-foss-2018b-Python-3.6.6.eb @@ -17,7 +17,10 @@ source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] checksums = ['1e0114bb106b7b05613d8be753759b578e7a16b3cd03f21bedcdace13b2bea08'] -dependencies = [('Python', '3.6.6')] +dependencies = [ + ('cURL', '7.60.0'), + ('Python', '3.6.6'), +] use_pip = True From 58213678c9bbdd5bd88dfabb9c4f3da9a94f2baa Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:25:17 +0200 Subject: [PATCH 0406/5331] adding easyconfigs: Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb --- ...Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..0d444b57aa8 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] + +dependencies = [('Python', '2.7.15')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' From 7634e595f6eef6bb0df9d54da075a00379ee1960 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:27:14 +0200 Subject: [PATCH 0407/5331] adding easyconfigs: nettle-3.4-fosscuda-2018b.eb --- .../n/nettle/nettle-3.4-fosscuda-2018b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.4-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.4-fosscuda-2018b.eb b/easybuild/easyconfigs/n/nettle/nettle-3.4-fosscuda-2018b.eb new file mode 100644 index 00000000000..02c6bd3be42 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.4-fosscuda-2018b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.4' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' + +description = """ + Nettle is a cryptographic library that is designed to fit easily in more or + less any context: In crypto toolkits for object-oriented languages (C++, + Python, Pike, ...), in applications like LSH or GNUPG, or even in + kernel space. +""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ae7a42df026550b85daca8389b6a60ba6313b0567f374392e54918588a411e94'] + +builddependencies = [ + ('M4', '1.4.18'), +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' From e310b444173aedb6586cfb5dbb4397f9738f98f6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:30:33 +0200 Subject: [PATCH 0408/5331] adding easyconfigs: Mesa-18.1.1-fosscuda-2018b.eb --- .../m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb new file mode 100644 index 00000000000..480d0e6244a --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb @@ -0,0 +1,74 @@ +# Automatically converted from Mesa-17.2.4-intel-2017b.eb +# Original message: +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '18.1.1' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. +toolchainopts = {'optarch': False} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] +sources = [SOURCELOWER_TAR_XZ] +patches = ['Mesa-17.3.6_fix-strip-llvm-flags.patch'] +checksums = [ + 'd3312a2ede5aac14a47476b208b8e3a401367838330197c4588ab8ad420d7781', # mesa-18.1.1.tar.xz + '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.3.6_fix-strip-llvm-flags.patch +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.5'), + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), + ('Mako', '1.0.7', '-Python-2.7.15'), + ('libxml2', '2.9.8'), + ('expat', '2.2.5'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('nettle', '3.4'), + ('libdrm', '2.4.92'), + ('LLVM', '6.0.0'), + ('X11', '20180604'), + ('libunwind', '1.2.1'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx " +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' " +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' From a81c07681e168241c1eac689a9a107947448edfb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:32:53 +0200 Subject: [PATCH 0409/5331] adding easyconfigs: libGLU-9.0.0-fosscuda-2018b.eb --- .../l/libGLU/libGLU-9.0.0-fosscuda-2018b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-fosscuda-2018b.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-fosscuda-2018b.eb new file mode 100644 index 00000000000..1c00fe1751f --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-fosscuda-2018b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] +checksums = ['1f7ad0d379a722fcbd303aa5650c6d7d5544fde83196b42a73d1193568a4df12'] + +dependencies = [ + ('Mesa', '18.1.1'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From fdd0fd1a7709c85ea9ffbdfbf95fbea11201d154 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:34:17 +0200 Subject: [PATCH 0410/5331] adding easyconfigs: FTGL-2.1.3-rc5-fosscuda-2018b.eb and patches: FTGL-2.1.3-rc5_fix_missing-GL_lib.patch, FTGL-2.1.3-rc5_ignore_docs.patch --- .../f/FTGL/FTGL-2.1.3-rc5-fosscuda-2018b.eb | 36 +++++++++++++ .../FTGL-2.1.3-rc5_fix_missing-GL_lib.patch | 53 +++++++++++++++++++ .../f/FTGL/FTGL-2.1.3-rc5_ignore_docs.patch | 15 ++++++ 3 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-fosscuda-2018b.eb create mode 100644 easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5_fix_missing-GL_lib.patch create mode 100644 easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5_ignore_docs.patch diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-fosscuda-2018b.eb b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-fosscuda-2018b.eb new file mode 100644 index 00000000000..1265cd4aedd --- /dev/null +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-fosscuda-2018b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'FTGL' +version = '2.1.3-rc5' + +homepage = 'http://ftgl.sourceforge.net/docs/html/' +description = """ FTGL is a free open source library to enable developers to use arbitrary +fonts in their OpenGL (www.opengl.org) applications. """ + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_fix_missing-GL_lib.patch', + '%(name)s-%(version)s_ignore_docs.patch', +] +checksums = [ + '5458d62122454869572d39f8aa85745fc05d5518001bcefa63bd6cbb8d26565b', # ftgl-2.1.3-rc5.tar.gz + '85ed3135ba6071de7b875dd8a0195a2b9d80e815ad53ba15be1a55e81cb21540', # FTGL-2.1.3-rc5_fix_missing-GL_lib.patch + '69d72821b4a092660cfdff2f63c84f729b3e7d5b3a9d1f51e041d6bbff0ae0e2', # FTGL-2.1.3-rc5_ignore_docs.patch +] + +dependencies = [ + ('freetype', '2.9.1'), + ('libGLU', '9.0.0'), + ('Mesa', '18.1.1'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/ftgl.pc', 'lib/libftgl.a', 'lib/libftgl.la', 'lib/libftgl.%s' % SHLIB_EXT], + 'dirs': ['include/FTGL'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5_fix_missing-GL_lib.patch b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5_fix_missing-GL_lib.patch new file mode 100644 index 00000000000..0ae4593f59d --- /dev/null +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5_fix_missing-GL_lib.patch @@ -0,0 +1,53 @@ +Fix missing GL_LIBS in demo and test. + +Åke Sandgren, 20181024 +diff -ru ftgl-2.1.3~rc5.orig/demo/Makefile.in ftgl-2.1.3~rc5/demo/Makefile.in +--- ftgl-2.1.3~rc5.orig/demo/Makefile.in 2008-06-12 16:33:01.000000000 +0200 ++++ ftgl-2.1.3~rc5/demo/Makefile.in 2018-10-24 08:48:50.364329615 +0200 +@@ -242,14 +242,14 @@ + $(NULL) + + simple_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) +-simple_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) ++simple_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) + simple_LDADD = ../src/libftgl.la + c_demo_SOURCES = \ + c-demo.c \ + $(NULL) + + c_demo_CFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) +-c_demo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) ++c_demo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) + c_demo_LDADD = ../src/libftgl.la + FTGLDemo_SOURCES = \ + FTGLDemo.cpp \ +@@ -260,7 +260,7 @@ + $(NULL) + + FTGLDemo_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) +-FTGLDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) ++FTGLDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) + FTGLDemo_LDADD = ../src/libftgl.la + FTGLMFontDemo_SOURCES = \ + FTGLMFontDemo.cpp \ +@@ -271,7 +271,7 @@ + $(NULL) + + FTGLMFontDemo_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) +-FTGLMFontDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) ++FTGLMFontDemo_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) + FTGLMFontDemo_LDADD = ../src/libftgl.la + NULL = + all: all-am +diff -ru ftgl-2.1.3~rc5.orig/test/Makefile.in ftgl-2.1.3~rc5/test/Makefile.in +--- ftgl-2.1.3~rc5.orig/test/Makefile.in 2008-06-12 16:33:01.000000000 +0200 ++++ ftgl-2.1.3~rc5/test/Makefile.in 2018-10-24 08:41:51.382472024 +0200 +@@ -294,7 +294,7 @@ + $(NULL) + + CXXTest_CXXFLAGS = $(FT2_CFLAGS) $(GL_CFLAGS) +-CXXTest_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) -lcppunit ++CXXTest_LDFLAGS = $(FT2_LIBS) $(GLUT_LIBS) $(GL_LIBS) -lcppunit + CXXTest_LDADD = ../src/libftgl.la + CTest_SOURCES = \ + CTest.c \ diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5_ignore_docs.patch b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5_ignore_docs.patch new file mode 100644 index 00000000000..89b2d0b8e45 --- /dev/null +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5_ignore_docs.patch @@ -0,0 +1,15 @@ +Ignore docs, we dont need to build it. + +Åke Sandgren, 20181024 +diff -ru ftgl-2.1.3~rc5.orig/Makefile.in ftgl-2.1.3~rc5/Makefile.in +--- ftgl-2.1.3~rc5.orig/Makefile.in 2008-06-12 16:33:01.000000000 +0200 ++++ ftgl-2.1.3~rc5/Makefile.in 2018-10-24 08:42:15.514118465 +0200 +@@ -219,7 +219,7 @@ + top_builddir = @top_builddir@ + top_srcdir = @top_srcdir@ + ACLOCAL_AMFLAGS = -I m4 +-SUBDIRS = src test demo docs ++SUBDIRS = src test demo + DIST_SUBDIRS = $(SUBDIRS) msvc + pkgconfigdir = $(libdir)/pkgconfig + pkgconfig_DATA = ftgl.pc From 788db9163a2471720e76b7d4c0b5bbc02348584f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:36:37 +0200 Subject: [PATCH 0411/5331] adding easyconfigs: bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb --- ...ddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..d48afbad3d7 --- /dev/null +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'bsddb3' +version = '6.2.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.org/project/bsddb3/' +description = """bsddb3 is a nearly complete Python binding of the +Oracle/Sleepycat C API for the Database Environment, Database, Cursor, +Log Cursor, Sequence and Transaction objects.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['42d621f4037425afcb16b67d5600c4556271a071a9a7f7f2c2b1ba65bc582d05'] + +osdependencies = [('libdb-dev')] + +dependencies = [('Python', '2.7.15')] + +use_pip = True +download_dep_fail = True + +preinstallopts = 'unset LIBS && ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' From e5ac353b3d0e0927a52255140818ef9003bd64c8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:37:18 +0200 Subject: [PATCH 0412/5331] adding easyconfigs: ZeroMQ-4.2.5-fosscuda-2018b.eb --- .../z/ZeroMQ/ZeroMQ-4.2.5-fosscuda-2018b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-fosscuda-2018b.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-fosscuda-2018b.eb new file mode 100644 index 00000000000..c6c57dbdb57 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-fosscuda-2018b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.2.5' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cc9090ba35713d59bb2f7d7965f877036c49c5558ea0c290b0dcc6f2a17e489f'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.32.1'), + ('libsodium', '1.0.16'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From ec9991136301962a2fe8c04fb108c7d5e27da97e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:38:34 +0200 Subject: [PATCH 0413/5331] adding easyconfigs: SIP-4.19.13-fosscuda-2018b-Python-2.7.15.eb --- ...IP-4.19.13-fosscuda-2018b-Python-2.7.15.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.19.13-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19.13-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19.13-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..10259008419 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19.13-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.19.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Python', '2.7.15')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' From a18f65af7ada0cf660afe9bf64c4f1d8c6e39b0c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:39:49 +0200 Subject: [PATCH 0414/5331] adding easyconfigs: Qt-4.8.7-fosscuda-2018b.eb --- .../q/Qt/Qt-4.8.7-fosscuda-2018b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt/Qt-4.8.7-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-fosscuda-2018b.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-fosscuda-2018b.eb new file mode 100644 index 00000000000..18048029ac1 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-fosscuda-2018b.eb @@ -0,0 +1,32 @@ +name = 'Qt' +version = '4.8.7' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'cstd': 'gnu++98'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] +patches = ['Qt-%(version)s_phonon-export.patch'] +checksums = [ + 'e2882295097e47fe089f8ac741a95fef47e0a73a3f3cdf21b56990638f626ea0', # qt-everywhere-opensource-src-4.8.7.tar.gz + '3853c87c33695bfa57e207ffb0d94cb2565aa462eccdf44d2b2804fd44ecbad6', # Qt-4.8.7_phonon-export.patch +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.54.3'), + ('libpng', '1.6.34'), + ('X11', '20180604'), + ('libGLU', '9.0.0'), +] + +moduleclass = 'devel' From c66d604275abf0a3e5b595d2f00996281cb83cf9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:41:14 +0200 Subject: [PATCH 0415/5331] adding easyconfigs: PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb --- ...yQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..4e71264b215 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.12.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] +sources = ['PyQt4_gpl_x11-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.15'), + ('SIP', '4.19.13', versionsuffix), + ('Qt', '4.8.7'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " +configopts += " --sipdir=%(installdir)s/share/sip/PyQt%(version_major)s" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s'], +} + +moduleclass = 'vis' From f50df7c0a3af1e132f27d513c784748e31792788 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:42:26 +0200 Subject: [PATCH 0416/5331] adding easyconfigs: IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb --- ...thon-5.8.0-fosscuda-2018b-Python-2.7.15.eb | 227 ++++++++++++++++++ 1 file changed, 227 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..d66086e0a89 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,227 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '5.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), + ('ZeroMQ', '4.2.5'), + ('matplotlib', '2.2.3', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +# let sanity check fail when auto-downloaded dependencies are detected when installing extensions +exts_download_dep_fail = True + +exts_list = [ + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], + }), + ('ipython_genutils', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], + }), + ('pexpect', '4.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], + }), + ('scandir', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], + }), + ('pathlib2', '2.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], + }), + ('pickleshare', '0.7.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('wcwidth', '0.1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + }), + ('prompt_toolkit', '1.0.15', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], + 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], + }), + ('ptyprocess', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('traitlets', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], + }), + ('parso', '0.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], + 'checksums': ['35704a43a3c113cce4de228ddb39aab374b8004f4f2407d070b6a2ca784ce8a2'], + }), + ('jedi', '0.13.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], + 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], + }), + ('testpath', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], + 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('configparser', '3.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], + 'use_pip': True, + 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], + }), + ('defusedxml', '0.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], + 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], + }), + ('nbconvert', '5.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'use_pip': True, + 'checksums': ['a8a2749f972592aa9250db975304af6b7337f32337e523a2c995cc9e12c07807'], + }), + ('nbformat', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + 'use_pip': True, + 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], + }), + ('MarkupSafe', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('Send2Trash', '1.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], + 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], + }), + ('webencodings', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], + 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], + }), + ('bleach', '3.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], + 'checksums': ['48d39675b80a75f6d1c3bdbffec791cf0bbbab665cf01e20da701c77de278718'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], + }), + ('pandocfilters', '1.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], + }), + ('pyzmq', '17.1.2', { + 'modulename': 'zmq', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], + 'checksums': ['a72b82ac1910f2cf61a49139f4974f994984475f771b0faa730839607eeedddf'], + }), + ('entrypoints', '0.2.3', { + 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], + 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], + }), + ('jupyter_core', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + 'use_pip': True, + 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], + }), + ('jupyter_client', '5.2.3', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + 'use_pip': True, + 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], + }), + ('mistune', '0.8.4', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('terminado', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], + }), + ('futures', '3.2.0', { + 'modulename': 'concurrent.futures', + 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], + 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('tornado', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], + }), + ('backcall', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], + 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], + }), + ('prometheus_client', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], + 'checksums': ['046cb4fffe75e55ff0e6dfd18e2ea16e54d86cc330f369bebcc683475c8b68a9'], + }), + ('ipykernel', '4.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + 'checksums': ['699103c8e64886e3ec7053f2a6aa83bb90426063526f63a818732ff385202bad'], + }), + ('notebook', '5.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + 'use_pip': True, + 'checksums': ['b85e4de3d54cf4f14fe1d0515a980ccb49ddd4cdd21250cc0d4fb6374d50b1a7'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "ipython notebook --help", + "iptest", +] + +moduleclass = 'tools' From 53a54324ddbfb7769a211bc5ffbe0781f72fa98e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:48:19 +0200 Subject: [PATCH 0417/5331] adding easyconfigs: GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb --- ...ion-1.54.1-fosscuda-2018b-Python-2.7.15.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..db184e9e865 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.54.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C + libraries (using GObject) and language bindings. The C library can be scanned + at compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b88ded5e5f064ab58a93aadecd6d58db2ec9d970648534c63807d4f9a7bb877e'] + +builddependencies = [ + ('Autotools', '20180311'), + ('flex', '2.6.4'), + ('Bison', '3.0.5'), + ('cairo', '1.14.12'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '2.7.15'), + ('util-linux', '2.32.1'), + ('GLib', '2.54.3'), + ('libffi', '3.2.1'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', + 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' From f9876f672bf88212a893f7e70171e6a36861aac7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:49:16 +0200 Subject: [PATCH 0418/5331] adding easyconfigs: ATK-2.28.1-fosscuda-2018b.eb --- .../a/ATK/ATK-2.28.1-fosscuda-2018b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.28.1-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.28.1-fosscuda-2018b.eb b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-fosscuda-2018b.eb new file mode 100644 index 00000000000..2925b9a2eb3 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.28.1-fosscuda-2018b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.28.1' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cd3a1ea6ecc268a2497f0cd018e970860de24a6d42086919d6bf6c8e8d53f4fc'] + +builddependencies = [ + ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), +] +dependencies = [ + ('GLib', '2.54.3'), +] + +configopts = "--enable-introspection=yes" + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From ff0ae76e1847dd9120ec65bf0de28df67e8b3f97 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:51:56 +0200 Subject: [PATCH 0419/5331] adding easyconfigs: dask-0.19.4-fosscuda-2018b-Python-3.6.6.eb --- ...dask-0.19.4-fosscuda-2018b-Python-3.6.6.eb | 87 +++++++++++++++++++ ...PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb | 28 ++++++ 2 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-0.19.4-fosscuda-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/d/dask/dask-0.19.4-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/dask/dask-0.19.4-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..851ce8a3fb6 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.19.4-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,87 @@ +easyblock = 'Bundle' + +name = 'dask' +version = '0.19.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('PyYAML', '3.13', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('toolz', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], + 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], + }), + ('HeapDict', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/h/HeapDict'], + 'checksums': ['40c9e3680616cfdf942f77429a3a9e0a76f31ce965d62f4ffbe63a83a5ef1b5a'], + }), + ('zict', '0.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], + 'checksums': ['63377f063086fc92e5c16e4d02162c571f6470b9e796cf3411ef9e815c96b799'], + }), + ('tornado', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], + }), + ('tblib', '1.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], + 'checksums': ['436e4200e63d92316551179dc540906652878df4ff39b43db30fcf6400444fe7'], + }), + ('sortedcontainers', '2.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], + 'checksums': ['b74f2756fb5e23512572cc76f0fe0832fd86310f77dfee54335a35fb33f6b950'], + }), + ('psutil', '5.4.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'checksums': ['5b6322b167a5ba0c5463b4d30dfd379cd4ce245a1162ebf8fc7ab5c5ffae4f3b'], + }), + ('msgpack-python', '0.5.6', { + 'modulename': 'msgpack', + 'source_urls': ['https://pypi.python.org/packages/source/s/msgpack-python'], + 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], + }), + ('msgpack', '0.5.6', { + 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'], + 'checksums': ['0ee8c8c85aa651be3aa0cd005b5931769eaa658c948ce79428766f1bd46ae2c3'], + }), + ('cloudpickle', '0.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], + 'checksums': ['f169a8523a40eb0a3452e1878aac31da6759409fbafa51dd50d89d4a6b42bcf1'], + }), + ('Click', '7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], + 'checksums': ['fd86d49d415de5f3a0e8efa47bb8bc454fb2cc9b7871b7d7007c10636880cdae'], + }), + ('distributed', '1.23.3', { + 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], + 'checksums': ['2d48a4de280fd7243ca76f9b12db5fe2486fc89dcdb510c77fa51f51733a04cc'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'remote', 'scheduler', 'ssh', 'submit', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..33906e08e06 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'] + +dependencies = [ + ('Python', '3.6.6'), + ('libyaml', '0.2.1'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From a6ad4b1930d3bb4895b63227cc7570507b9fdcb3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:52:59 +0200 Subject: [PATCH 0420/5331] adding easyconfigs: FFmpeg-4.1-fosscuda-2018b.eb --- .../f/FFmpeg/FFmpeg-4.1-fosscuda-2018b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1-fosscuda-2018b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1-fosscuda-2018b.eb new file mode 100644 index 00000000000..3abe7479f06 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1-fosscuda-2018b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '4.1' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['http://ffmpeg.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b684fb43244a5c4caae652af9022ed5d85ce15210835bce054a33fb26033a1a5'] + +builddependencies = [('pkg-config', '0.29.2')] +dependencies = [ + ('NASM', '2.13.03'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('x264', '20181203'), + ('LAME', '3.100'), + ('x265', '2.9'), + ('X11', '20180604'), + ('freetype', '2.9.1'), + ('fontconfig', '2.13.0'), + ('FriBidi', '1.0.5'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' From 4da3c42f622bffa080080339d7d8a99ff5cfb2b7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:54:47 +0200 Subject: [PATCH 0421/5331] adding easyconfigs: HarfBuzz-1.9.0-fosscuda-2018b.eb --- .../HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb new file mode 100644 index 00000000000..56753c681bc --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.9.0' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('GLib', '2.54.3'), + ('cairo', '1.14.12'), + ('freetype', '2.9.1'), +] + +builddependencies = [ + ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), + ('pkg-config', '0.29.2'), +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' From 1d8f0f3c2dff71c15437c05ae1012dc1ffd92092 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 19 Feb 2019 08:54:56 +0100 Subject: [PATCH 0422/5331] remove source_urls because it needs manual download --- easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCCcore-7.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCCcore-7.3.0.eb index 2d8fca83c2c..12a7fb8df56 100644 --- a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCCcore-7.3.0.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} # Needs manual download via web-form, # https://www.h-its.org/en/research/sco/software/#NextGenerationSequencingSequenceAnalysis -# source_urls = ['https://cme.h-its.org/exelixis/web/software/pear/files/'] sources = ['%(namelower)s-src-%(version)s.tar.gz'] checksums = ['94f4a1835cd75ec6fab83405c2545ddba6b6bb1644579222e9cc2ad57a59d654'] From 584e1d0c7eeaa30bdfd92d86863d6e02d615180c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:56:39 +0200 Subject: [PATCH 0423/5331] adding easyconfigs: Meson-0.48.1-fosscuda-2018b-Python-3.6.6.eb --- ...eson-0.48.1-fosscuda-2018b-Python-3.6.6.eb | 28 +++++++++++++++++++ .../n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb | 26 +++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.48.1-fosscuda-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.48.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/Meson/Meson-0.48.1-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..d1c2d18855a --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.48.1-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.48.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef893e2d64083463fe41f05d683edbe8c44bc187cd9cc66cbc2b1ce399567447'] + +dependencies = [ + ('Python', '3.6.6'), + ('Ninja', '1.8.2'), +] + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb new file mode 100644 index 00000000000..ae099f03205 --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb @@ -0,0 +1,26 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.8.2' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['86b8700c3d0880c2b44c2ff67ce42774aaf8c28cbf57725cb881569288c1c6f4'] + +builddependencies = [('Python', '2.7.15')] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +moduleclass = 'tools' From 6943a50f5f76fbbc678b5fb418aba55138fa74ba Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:58:11 +0200 Subject: [PATCH 0424/5331] adding easyconfigs: libepoxy-1.5.3-fosscuda-2018b.eb --- .../libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb new file mode 100644 index 00000000000..fa2882324e3 --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb @@ -0,0 +1,31 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.3' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['https://github.com/anholt/%(name)s/releases/download/%(version)s'] +sources = [SOURCE_TAR_XZ] + +builddependencies = [ + ('Meson', '0.48.1', '-Python-3.6.6'), + ('Ninja', '1.8.2'), +] + +dependencies = [ + ('X11', '20180604'), + ('Mesa', '18.1.1'), +] + +configopts = '-Degl=no --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']], + 'dirs': ['lib'] +} + +moduleclass = 'lib' From 3bbca975969e8b258873da7ca56cf4355050ad77 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 09:59:15 +0200 Subject: [PATCH 0425/5331] adding easyconfigs: Pango-1.42.4-fosscuda-2018b.eb --- .../p/Pango/Pango-1.42.4-fosscuda-2018b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb new file mode 100644 index 00000000000..f8e908d1d37 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.42.4' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +builddependencies = [ + ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20180604'), + ('GLib', '2.54.3'), + ('cairo', '1.14.12'), + ('HarfBuzz', '1.9.0'), + ('FriBidi', '1.0.5'), +] + +configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' From 429a8a88e572e2e32507c118b8b93e8785d50b71 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:01:15 +0200 Subject: [PATCH 0426/5331] adding easyconfigs: Gdk-Pixbuf-2.36.11-fosscuda-2018b.eb --- .../Gdk-Pixbuf-2.36.11-fosscuda-2018b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-fosscuda-2018b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-fosscuda-2018b.eb new file mode 100644 index 00000000000..a0080e885b3 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.11-fosscuda-2018b.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.36.11' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +patches = ['Gdk-Pixbuf-2.36.10-disable-gio-sniffing.patch'] +checksums = [ + 'ae62ab87250413156ed72ef756347b10208c00e76b222d82d9ed361ed9dde2f3', # gdk-pixbuf-2.36.11.tar.xz + '840231db69ccc2a1335c4f29c305cdd0ba570254e779c2a274611aaff968878e', # Gdk-Pixbuf-2.36.10-disable-gio-sniffing.patch +] + +builddependencies = [ + ('GObject-Introspection', '1.54.1', '-Python-2.7.15') +] +dependencies = [ + ('GLib', '2.54.3'), + ('libjpeg-turbo', '2.0.0'), + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' From a1c4da6b05eb0585108ff5ff283df1493c61d4d3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:03:23 +0200 Subject: [PATCH 0427/5331] adding easyconfigs: GTK+-3.22.30-fosscuda-2018b.eb --- .../g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb new file mode 100644 index 00000000000..e1607fff762 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '3.22.30' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +builddependencies = [ + ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), +] + +dependencies = [ + ('ATK', '2.28.1'), + ('Gdk-Pixbuf', '2.36.11'), + ('Pango', '1.42.4'), + ('libepoxy', '1.5.3'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' From 8ecb63f3829d8046ee0359f2358ffbda6424b87e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:06:21 +0200 Subject: [PATCH 0428/5331] adding easyconfigs: GStreamer-1.15.1-fosscuda-2018b.eb --- .../GStreamer-1.15.1-fosscuda-2018b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb new file mode 100644 index 00000000000..154e2541f1f --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '1.15.1' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['780ae2347f9780fea264a602a7c04a87a43998188e7bd9c59afb4d7c864f3117'] + +builddependencies = [ + ('Bison', '3.0.5'), + ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), +] + +dependencies = [ + ('GLib', '2.54.3'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' From 98ae748424b1518b5532e528aa33c44f58711ede Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:09:17 +0200 Subject: [PATCH 0429/5331] adding easyconfigs: libwebp-1.0.2-GCCcore-7.3.0.eb --- .../l/libwebp/libwebp-1.0.2-GCCcore-7.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..702bc03c87e --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-7.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.0.2' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3d47b48c40ed6476e8047b2ddb81d93835e0ca1b8d3e8c679afbb3004dd564b1'] + +builddependencies = [('binutils', '2.30')] + +dependencies = [ + ('libjpeg-turbo', '2.0.0'), + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), + ('giflib', '5.1.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'lib'] +} + +moduleclass = 'lib' From 1f7e6401e86444280c7af7af1e6fdf9df0420e44 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:10:31 +0200 Subject: [PATCH 0430/5331] adding easyconfigs: giflib-5.1.4-GCCcore-7.3.0.eb --- .../g/giflib/giflib-5.1.4-GCCcore-7.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.1.4-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.1.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.1.4-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..1c45ff77ed7 --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.1.4-GCCcore-7.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.1.4' + +homepage = 'http://libungif.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [('http://sourceforge.net/projects/giflib/files', 'download')] +sources = [SOURCE_TAR_BZ2] +checksums = ['df27ec3ff24671f80b29e6ab1c4971059c14ac3db95406884fc26574631ba8d5'] + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +builddependencies = [('binutils', '2.30')] + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' From 0aa3ec7902aff2989b6ccd58806cefae78bd40a4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:12:25 +0200 Subject: [PATCH 0431/5331] adding easyconfigs: PyTables-3.4.4-fosscuda-2018b-Python-3.6.6.eb --- .../l/LZO/LZO-2.10-fosscuda-2018b.eb | 37 ++++++++++++++++ ...mexpr-2.6.5-fosscuda-2018b-Python-3.6.6.eb | 28 +++++++++++++ ...ables-3.4.4-fosscuda-2018b-Python-3.6.6.eb | 42 +++++++++++++++++++ 3 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-fosscuda-2018b.eb create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-fosscuda-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-fosscuda-2018b.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-fosscuda-2018b.eb new file mode 100644 index 00000000000..574dd387ff9 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-fosscuda-2018b.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: Copyright 2014-2017 adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exequiel Sepulveda +# License:: MIT/GPL +# +# Notes:: Adopted from EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Fotis Georgatos +## + +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'http://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..0d7df8c31a8 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'numexpr' +version = '2.6.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://code.google.com/p/numexpr/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['https://github.com/pydata/numexpr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fe78a78e002806e87e012b6105f3b3d52d47fc7a72bafb56341fcec7ce02cfd7'] + +dependencies = [ + ('Python', '3.6.6'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..3bb30ce4138 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.4.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['pyTables-3.4.2-fix-libs.patch'] +checksums = [ + 'c9682c0f35d8175e12bbd38d925bdb606d47b7c8e358ba056a9dbf3b1f183114', # v3.4.4.tar.gz + 'f34a05573e7843e67dab011bede8436074362041747c028b409fac9f599231a3', # pyTables-3.4.2-fix-libs.patch +] + +dependencies = [ + ('Python', '3.6.6'), + ('numexpr', '2.6.5', versionsuffix), + ('HDF5', '1.10.2'), + ('LZO', '2.10'), + ('Blosc', '1.14.4'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +moduleclass = 'data' From 297a14c05746f8dbae86050b63dc4fa9d8b8ad54 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:15:15 +0200 Subject: [PATCH 0432/5331] adding easyconfigs: libgcrypt-1.8.4-GCCcore-7.3.0.eb --- .../libgcrypt-1.8.4-GCCcore-7.3.0.eb | 37 +++++++++++++++++++ .../libgpg-error-1.35-GCCcore-7.3.0.eb | 22 +++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.8.4-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.35-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.8.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.8.4-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..8ea3b5673c6 --- /dev/null +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.8.4-GCCcore-7.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libgcrypt' +version = '1.8.4' + +homepage = 'https://gnupg.org/related_software/libgcrypt/index.html' +description = """Libgcrypt is a general purpose cryptographic library +originally based on code from GnuPG. It provides functions for all +cryptograhic building blocks: symmetric cipher algorithms (AES, Arcfour, +Blowfish, Camellia, CAST5, ChaCha20 DES, GOST28147, Salsa20, SEED, +Serpent, Twofish) and modes +(ECB,CFB,CBC,OFB,CTR,CCM,GCM,OCB,POLY1305,AESWRAP), hash algorithms +(MD2, MD4, MD5, GOST R 34.11, RIPE-MD160, SHA-1, SHA2-224, SHA2-256, +SHA2-384, SHA2-512, SHA3-224, SHA3-256, SHA3-384, SHA3-512, SHAKE-128, +SHAKE-256, TIGER-192, Whirlpool), MACs (HMAC for all hash algorithms, +CMAC for all cipher algorithms, GMAC-AES, GMAC-CAMELLIA, GMAC-TWOFISH, +GMAC-SERPENT, GMAC-SEED, Poly1305, Poly1305-AES, Poly1305-CAMELLIA, +Poly1305-TWOFISH, Poly1305-SERPENT, Poly1305-SEED), public key +algorithms (RSA, Elgamal, DSA, ECDSA, EdDSA, ECDH), large integer +functions, random numbers and a lot of supporting functions.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['f638143a0672628fde0cad745e9b14deb85dffb175709cacc1f4fe24b93f2227'] + +builddependencies = [('binutils', '2.30')] + +dependencies = [('libgpg-error', '1.35')] + +sanity_check_paths = { + 'files': ['bin/libgcrypt-config', 'include/gcrypt.h', 'lib/libgcrypt.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.35-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.35-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..fb54d3ab978 --- /dev/null +++ b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.35-GCCcore-7.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libgpg-error' +version = '1.35' + +homepage = 'https://gnupg.org/related_software/libgpg-error/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['cbd5ee62a8a8c88d48c158fff4fc9ead4132aacd1b4a56eb791f9f997d07e067'] + +builddependencies = [('binutils', '2.30')] + +sanity_check_paths = { + 'files': ['bin/gpg-error-config', 'include/gpg-error.h', 'lib/libgpg-error.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From 78147ab663979011bcd7b1d18d9bd0c25944f9b0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:17:33 +0200 Subject: [PATCH 0433/5331] Add missing checksum. --- .../s/SIP/SIP-4.19.13-fosscuda-2018b-Python-2.7.15.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19.13-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19.13-fosscuda-2018b-Python-2.7.15.eb index 10259008419..75c2bb9dde1 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.19.13-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19.13-fosscuda-2018b-Python-2.7.15.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['e353a7056599bf5fbd5d3ff9842a6ab2ea3cf4e0304a0f925ec5862907c0d15e'] dependencies = [('Python', '2.7.15')] From 18d28d74f6da9055c68fc82b127c22e5ea9f7c77 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:18:39 +0200 Subject: [PATCH 0434/5331] Add missing checksum. --- .../p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb index 4e71264b215..c7a51dc2379 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] sources = ['PyQt4_gpl_x11-%(version)s.tar.gz'] +checksums = ['a00f5abef240a7b5852b7924fa5fdf5174569525dc076cd368a566619e56d472'] dependencies = [ ('Python', '2.7.15'), From efc8ecf3c51455362cb3526ab6db515e4372c0ab Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:20:55 +0200 Subject: [PATCH 0435/5331] Add missing checksum. --- .../easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb index 56753c681bc..0f36122fcfd 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.9.0-fosscuda-2018b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['11eca62bf0ac549b8d6be55f4e130946399939cdfe7a562fdaee711190248b00'] dependencies = [ ('GLib', '2.54.3'), From d13d443fb079293280d17b1f45d7d2886b416b85 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:21:54 +0200 Subject: [PATCH 0436/5331] Add missing checksum. --- .../easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb index fa2882324e3..7a73538541b 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = ['https://github.com/anholt/%(name)s/releases/download/%(version)s'] sources = [SOURCE_TAR_XZ] +checksums = ['002958c5528321edd53440235d3c44e71b5b1e09b9177e8daf677450b6c4433d'] builddependencies = [ ('Meson', '0.48.1', '-Python-3.6.6'), From a7d5cba575bf8b512fd55642387dd0c6c1984359 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:22:39 +0200 Subject: [PATCH 0437/5331] Add missing checksum. --- easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb index f8e908d1d37..76d7c9524df 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['1d2b74cd63e8bd41961f2f8d952355aa0f9be6002b52c8aa7699d9f5da597c9d'] builddependencies = [ ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), From 9e6d507e6421a83874f4418f7ef058c694ad6485 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:23:38 +0200 Subject: [PATCH 0438/5331] Add missing checksum. --- easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb index e1607fff762..9a24a7902c0 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['a1a4a5c12703d4e1ccda28333b87ff462741dc365131fbc94c218ae81d9a6567'] builddependencies = [ ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), From ef07d2b81a01c6cbb0461374b284e538d276d726 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:26:44 +0200 Subject: [PATCH 0439/5331] adding easyconfigs: libpsl-0.20.2-GCCcore-7.3.0.eb --- .../l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..55c68957d56 --- /dev/null +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpsl' +version = '0.20.2' + +homepage = 'https://rockdaboot.github.io/libpsl' +description = "C library for the Public Suffix List" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://github.com/rockdaboot/%(name)s/releases/download/%(name)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f8fd0aeb66252dfcc638f14d9be1e2362fdaf2ca86bde0444ff4d5cc961b560f'] + +sanity_check_paths = { + 'files': ['bin/psl', 'lib/libpsl.a'], + 'dirs': [] +} + +moduleclass = 'lib' From bf0199af7be03513aadf1f89719617e3861eab2d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:29:01 +0200 Subject: [PATCH 0440/5331] adding easyconfigs: libtasn1-4.13-GCCcore-7.3.0.eb --- .../l/libtasn1/libtasn1-4.13-GCCcore-7.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtasn1/libtasn1-4.13-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.13-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.13-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..4323c6707d8 --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.13-GCCcore-7.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.13' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU +Shishi and some other packages. It was written by Fabio Fiorina, and +has been shipped as part of GnuTLS for some time but is now a proper GNU +package.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['7e528e8c317ddd156230c4e31d082cd13e7ddeb7a54824be82632209550c8cca'] + +builddependencies = [('binutils', '2.30')] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 2d50b80cf7309a17d7f3976455816b4d66635c6f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 10:30:17 +0200 Subject: [PATCH 0441/5331] adding easyconfigs: matplotlib-3.0.0-fosscuda-2018b-Python-3.6.6.eb --- ...otlib-3.0.0-fosscuda-2018b-Python-3.6.6.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..5495504ea54 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.0-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,64 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '3.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.6.6'), + ('libpng', '1.6.34'), + ('freetype', '2.9.1'), + ('Tkinter', '%(pyver)s', versionsuffix), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['b4e2333c98a7c2c1ff6eb930cd2b57d4b818de5437c5048802096b32f66e65f9'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From fdc6a5d83b3f760de52da2f1a4cb57e3a8db95f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 19 Feb 2019 10:21:10 +0100 Subject: [PATCH 0442/5331] use pip --- .../h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb index 5bb33ab8a40..80e3db3157e 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2018b-Python-3.6.6.eb @@ -24,9 +24,13 @@ dependencies = [ ('matplotlib', '3.0.0', versionsuffix), ] +use_pip = True + +download_dep_fail = True + sanity_check_paths = { 'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'], } sanity_check_commands = ['%(namelower)s-count --help'] From e76767d32aae6ffe90a877eec0c16e4550a902c7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 12:25:56 +0200 Subject: [PATCH 0443/5331] adding easyconfigs: Pillow-5.3.0-fosscuda-2018b-Python-3.6.6.eb --- ...illow-5.3.0-fosscuda-2018b-Python-3.6.6.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..5eb352d99d1 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '5.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] + +dependencies = [ + ('Python', '3.6.6'), + ('libjpeg-turbo', '2.0.0'), + ('libpng', '1.6.34'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.9'), + ('freetype', '2.9.1') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' From ec609da63d1ec5149ba854e4248f1722e43f3205 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 12:28:02 +0200 Subject: [PATCH 0444/5331] adding easyconfigs: SDL2-2.0.9-fosscuda-2018b.eb --- .../s/SDL2/SDL2-2.0.9-fosscuda-2018b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.9-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.9-fosscuda-2018b.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.9-fosscuda-2018b.eb new file mode 100644 index 00000000000..e3a6bf442d8 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.9-fosscuda-2018b.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.9' + +homepage = 'http://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['http://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['255186dc676ecd0c1dbf10ec8a2cc5d6869b5079d8a38194c2aecdff54b324b1'] + +dependencies = [ + ('X11', '20180604'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From b0a96303227f756dfc8f1741b72aa734c521210a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 12:32:12 +0200 Subject: [PATCH 0445/5331] adding easyconfigs: Tkinter-3.6.6-fosscuda-2018b-Python-3.6.6.eb --- ...inter-3.6.6-fosscuda-2018b-Python-3.6.6.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.6-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.6-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.6-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..ee1ccc1b7dc --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.6-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,21 @@ +name = 'Tkinter' +version = '3.6.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['7d56dadf6c7d92a238702389e80cfe66fbfae73e584189ed6f89c75bbf3eda58'] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.8'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' From e7154536ff10339a35fe847c29186caac19c05cb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 12:34:47 +0200 Subject: [PATCH 0446/5331] adding easyconfigs: scikit-image-0.14.1-fosscuda-2018b-Python-3.6.6.eb --- ...mage-0.14.1-fosscuda-2018b-Python-3.6.6.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..7c62432e87f --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.14.1-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,55 @@ +easyblock = 'Bundle' + +name = 'scikit-image' +version = '0.14.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} +exts_filter = ("python -c 'import %(ext_name)s'", '') + +dependencies = [ + ('Python', '3.6.6'), + ('Qhull', '2015.2'), + ('matplotlib', '3.0.0', versionsuffix), + ('Pillow', '5.3.0', versionsuffix), + ('dask', '0.19.4', versionsuffix), +] + +exts_list = [ + ('networkx', '2.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx'], + 'checksums': ['64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1'], + }), + ('PyWavelets', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PyWavelets'], + 'checksums': ['3c5cece36d4e17d395be6e9ac6b80ce7b774a1f71c251756c6163e63b6d878dc'], + 'modulename': 'pywt', + }), + (name, version, { + 'modulename': 'skimage', + 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image'], + 'checksums': ['86a9b3b4f74f231e0a6bcfd3235dcf3f0118df25dac21201da5e064d681e2c50'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' From 1c28882ed54df66cf17488b97130ffc17c510900 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 12:35:48 +0200 Subject: [PATCH 0447/5331] adding easyconfigs: scikit-learn-0.20.0-fosscuda-2018b-Python-3.6.6.eb --- ...earn-0.20.0-fosscuda-2018b-Python-3.6.6.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-fosscuda-2018b-Python-3.6.6.eb new file mode 100755 index 00000000000..87691aa1220 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.20.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18'] + +dependencies = [ + ('Python', '3.6.6'), + ('matplotlib', '3.0.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' From 86de2f88760cc5cd2868f4e9f7bd288563e2b33c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 13:21:49 +0200 Subject: [PATCH 0448/5331] Downgrade util-linux version to match what 2018b toolchain uses. --- easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-fosscuda-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-fosscuda-2018b.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-fosscuda-2018b.eb index c6c57dbdb57..a5e45c9423b 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.5-fosscuda-2018b.eb @@ -24,7 +24,7 @@ configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' dependencies = [ ('OpenPGM', '5.2.122'), - ('util-linux', '2.32.1'), + ('util-linux', '2.32'), ('libsodium', '1.0.16'), ] From 4deadf2603fb77d098257d2c6491bcb4b823e157 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 13:26:55 +0200 Subject: [PATCH 0449/5331] Explicitly use --enable-dri/egl to match https://github.com/easybuilders/easybuild-easyconfigs/pull/6487 --- easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb index 480d0e6244a..f76b50a13c2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb @@ -54,8 +54,8 @@ dependencies = [ ] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx " -configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' " +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --enable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --enable-egl" configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " buildopts = 'V=1' From 2fe37bbd451cd04e093899bdf4602ae0a66d5bef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Feb 2019 12:46:31 +0100 Subject: [PATCH 0450/5331] adding easyconfigs: pocl-1.2-GCC-7.3.0-2.30.eb --- .../p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..3071debe955 --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'pocl' +version = '1.2' + +homepage = 'http://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0c43e68f336892f3a64cba19beb99d9212f529bedb77f7879c0331450b982d46'] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + # must be Clang 6.x (7.x does not work, see https://github.com/pocl/pocl/issues/694) + ('Clang', '6.0.1'), + ('hwloc', '1.11.10'), + ('libtool', '2.4.6'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1" + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 0105e47fdee7e211997c68e1c33a09de7b2d0ce3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Feb 2019 12:57:23 +0100 Subject: [PATCH 0451/5331] add libxml2 dep for pocl --- easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb index 3071debe955..2d70027ca7e 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.2-GCC-7.3.0-2.30.eb @@ -19,6 +19,7 @@ dependencies = [ ('Clang', '6.0.1'), ('hwloc', '1.11.10'), ('libtool', '2.4.6'), + ('libxml2', '2.9.8'), ] separate_build_dir = True From 659dff2250eb56681eb77d70a10d3e7e76c55c13 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 16:47:34 +0200 Subject: [PATCH 0452/5331] Add comment why LIBS need to be unset. --- .../b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb index d48afbad3d7..b987f2a0213 100644 --- a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb @@ -22,6 +22,7 @@ dependencies = [('Python', '2.7.15')] use_pip = True download_dep_fail = True +# Need to unset LIBS or pip install crashes. preinstallopts = 'unset LIBS && ' sanity_check_paths = { From d25cabda1013fd54182167160261526fd8dec4f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 19 Feb 2019 15:48:29 +0100 Subject: [PATCH 0453/5331] only check parent directory --- .../b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb index 8218983a26c..b484b92185d 100644 --- a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.2-foss-2018b-Python-3.6.6.eb @@ -36,8 +36,7 @@ exts_list = [ sanity_check_paths = { 'files': [], - 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/bx_python-%(version)s-py%(pyshortver)s.egg-info', - 'lib/python%(pyshortver)s/site-packages/python_lzo-1.12-py%(pyshortver)s.egg-info'], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], } moduleclass = 'bio' From e4a0b6221afb899af88f51de34e5427d18690c68 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 19 Feb 2019 10:04:26 -0600 Subject: [PATCH 0454/5331] correct style problem captured by Travis test --- easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-foss-2017b.eb | 2 +- easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-foss-2017b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-foss-2017b.eb index 752bf32b32e..c693a4310de 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-foss-2017b.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-foss-2017b.eb @@ -15,7 +15,7 @@ checksums = ['15c9a47a9ebaf01822c567817acd681c4a594b4ac92e8bcf08d4d580f62296a9'] dependencies = [ ('libxml2', '2.9.4'), - ('file', '5.33'), + ('file', '5.33'), ('HDF5', '1.10.1'), ('NGS', '1.3.0') ] diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017b.eb index 3e9eb122dc9..b466a2c8f72 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017b.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.8.2-intel-2017b.eb @@ -15,7 +15,7 @@ checksums = ['15c9a47a9ebaf01822c567817acd681c4a594b4ac92e8bcf08d4d580f62296a9'] dependencies = [ ('libxml2', '2.9.4'), - ('file', '5.33'), + ('file', '5.33'), ('HDF5', '1.10.1'), ('NGS', '1.3.0') ] From f944b08b74ad91237e5a972d73a70bbc2ca50dee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Feb 2019 17:14:41 +0100 Subject: [PATCH 0455/5331] {bio}[foss/2018b] MaSuRCA v3.3.0 w/ Perl 5.28.0 --- .../MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..c122a16fb5a --- /dev/null +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2017 University of Geneva +# Authors:: Yann Sagon +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'MaSuRCA' +version = '3.3.0' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.genome.umd.edu/masurca.html' + +description = '''MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph + and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing + only short reads from Illumina sequencing or a mixture of short reads and long reads + (Sanger, 454, Pacbio and Nanopore).''' + +toolchain = {'name': 'foss', 'version': '2018b'} + +# note: the tagged 3.3.0 release is (slightly) older than the 3.3.0 tarball included *in* the repo... +source_urls = ['https://github.com/alekseyzimin/masurca/raw/9b3771/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['f4625de837c54311d2ff4a53cd7e60d28bae49c1e5e9f2c1cbd75b688454d078'] + +dependencies = [ + ('libreadline', '7.0'), + ('Tcl', '8.6.8'), + ('Boost', '1.67.0'), + ('zlib', '1.2.11'), + ('Perl', '5.28.0'), +] + +buildopts = "install-special" +start_dir = "global-1" + +sanity_check_paths = { + 'files': ['bin/masurca'], + 'dirs': ['include', 'lib'], +} + +sanity_check_commands = ["masurca --help"] + +moduleclass = 'bio' From e84e76e84bac75a7e37791b32f341c490fdecbed Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 19 Feb 2019 10:29:19 -0600 Subject: [PATCH 0456/5331] adding easyconfigs: PHAST-1.5-GCC-6.4.0-2.28.eb, PHAST-1.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb --- .../p/PHAST/PHAST-1.5-GCC-6.4.0-2.28.eb | 34 +++++++++++++++++++ ...-1.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/p/PHAST/PHAST-1.5-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/p/PHAST/PHAST-1.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/p/PHAST/PHAST-1.5-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PHAST/PHAST-1.5-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..14da348d5ad --- /dev/null +++ b/easybuild/easyconfigs/p/PHAST/PHAST-1.5-GCC-6.4.0-2.28.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'PHAST' +version = '1.5' + +homepage = 'http://compgen.cshl.edu/phast/' +description = "PHAST is a freely available software package for comparative and evolutionary genomics." + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = ['https://github.com/CshlSiepelLab/phast/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b8db6c83850ef5fdf10bf25cd7b22b1ef8eacec8ef746adb179b958d576a5f86'] + +dependencies = [ + ('CLAPACK', '3.2.1'), + ('PCRE', '8.41'), +] + +skipsteps = ['configure'] + +start_dir = 'src' + +prebuildopts = 'CPATH=$EBROOTCLAPACK/F2CLIBS/libf2c:$EBROOTCLAPACK/INCLUDE:$CPATH ' +buildopts = 'CC="$CC" CLAPACKPATH=$EBROOTCLAPACK' + +files_to_copy = ['bin', 'data', (['doc/man/*'], 'share/man/man1')] + +sanity_check_paths = { + 'files': ['bin/phast'], + 'dirs': ['data', 'share/man/man1'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PHAST/PHAST-1.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PHAST/PHAST-1.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..1a74d1048fb --- /dev/null +++ b/easybuild/easyconfigs/p/PHAST/PHAST-1.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'PHAST' +version = '1.5' + +homepage = 'http://compgen.cshl.edu/phast/' +description = "PHAST is a freely available software package for comparative and evolutionary genomics." + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +source_urls = ['https://github.com/CshlSiepelLab/phast/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b8db6c83850ef5fdf10bf25cd7b22b1ef8eacec8ef746adb179b958d576a5f86'] + +dependencies = [ + ('CLAPACK', '3.2.1'), + ('PCRE', '8.41'), +] + +skipsteps = ['configure'] + +start_dir = 'src' + +prebuildopts = 'CPATH=$EBROOTCLAPACK/F2CLIBS/libf2c:$EBROOTCLAPACK/INCLUDE:$CPATH ' +buildopts = 'CC="$CC" CLAPACKPATH=$EBROOTCLAPACK' + +files_to_copy = ['bin', 'data', (['doc/man/*'], 'share/man/man1')] + +sanity_check_paths = { + 'files': ['bin/phast'], + 'dirs': ['data', 'share/man/man1'], +} + +moduleclass = 'bio' From 2cc82e961b9fe2d0f75544dfba466ff7a9b24e4c Mon Sep 17 00:00:00 2001 From: sassmaj Date: Tue, 19 Feb 2019 17:38:52 +0100 Subject: [PATCH 0457/5331] adding easyconfigs: glew-2.1.0-foss-2018b.eb --- .../g/glew/glew-2.1.0-foss-2018b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/glew/glew-2.1.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/g/glew/glew-2.1.0-foss-2018b.eb b/easybuild/easyconfigs/g/glew/glew-2.1.0-foss-2018b.eb new file mode 100644 index 00000000000..31218926f03 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.1.0-foss-2018b.eb @@ -0,0 +1,38 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'glew' +version = '2.1.0' + +homepage = 'http://glew.sourceforge.net/' +description = """The OpenGL Extension Wrangler Library + +The OpenGL Extension Wrangler Library (GLEW) is a cross-platform +open-source C/C++ extension loading library. GLEW provides +efficient run-time mechanisms for determining which OpenGL +extensions are supported on the target platform. OpenGL +core and extension functionality is exposed in a single header +file. GLEW has been tested on a variety of operating systems, +including Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['04de91e7e6763039bc11940095cd9c7f880baba82196a7765f727ac05a993c95'] + +dependencies =[('Mesa','18.1.1')] + +files_to_copy = ['bin', 'lib', 'include',] + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/glew.h', 'include/GL/glxew.h', 'include/GL/wglew.h'], + 'dirs': ['',] +} + +moduleclass = 'devel' + From 35801a20699c9c5ef4b249f44d36e00eaff040fb Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 19 Feb 2019 10:54:44 -0600 Subject: [PATCH 0458/5331] adding easyconfigs: Geant4-10.03.p03-foss-2017b.eb, CLHEP-2.3.4.3-foss-2017b.eb --- .../c/CLHEP/CLHEP-2.3.4.3-foss-2017b.eb | 24 ++++++++++++++++++ .../g/Geant4/Geant4-10.03.p03-foss-2017b.eb | 25 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-foss-2017b.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-10.03.p03-foss-2017b.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-foss-2017b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-foss-2017b.eb new file mode 100644 index 00000000000..6f8910ad70e --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-foss-2017b.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.3.4.3' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] +sources = [SOURCELOWER_TGZ] +checksums = ['1019479265f956bd660c11cb439e1443d4fd1655e8d51accf8b1e703e4262dff'] + +builddependencies = [('CMake', '3.9.5')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.03.p03-foss-2017b.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.03.p03-foss-2017b.eb new file mode 100644 index 00000000000..9bdefc1c916 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.03.p03-foss-2017b.eb @@ -0,0 +1,25 @@ +name = 'Geant4' +version = '10.03.p03' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] +checksums = ['a164f49c038859ab675eec474d08c9d02be8c4be9c0c2d3aa8e69adf89e1e138'] + +builddependencies = [('CMake', '3.9.5')] +dependencies = [ + ('expat', '2.2.4'), + # recommended CLHEP version, see http://geant4.web.cern.ch/geant4/support/ReleaseNotes4.10.3.html#2. + ('CLHEP', '2.3.4.3'), +] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += " -DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' From d9ed090edb2d37a53cc05f135cfe2ffaf9940e26 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 20:36:23 +0200 Subject: [PATCH 0459/5331] Add missing download_dep_fail and use_pip. --- .../m/Meson/Meson-0.48.1-fosscuda-2018b-Python-3.6.6.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.48.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/Meson/Meson-0.48.1-fosscuda-2018b-Python-3.6.6.eb index d1c2d18855a..ea543eefa57 100644 --- a/easybuild/easyconfigs/m/Meson/Meson-0.48.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/Meson/Meson-0.48.1-fosscuda-2018b-Python-3.6.6.eb @@ -18,6 +18,9 @@ dependencies = [ ('Ninja', '1.8.2'), ] +download_dep_fail = True +use_pip = True + options = {'modulename': 'mesonbuild'} sanity_check_paths = { From b6e627195d1656126141651e95b540a5a599fb07 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Feb 2019 21:40:41 +0200 Subject: [PATCH 0460/5331] adding easyconfigs: FLTK-1.3.4-fosscuda-2018b.eb --- .../f/FLTK/FLTK-1.3.4-fosscuda-2018b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-fosscuda-2018b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-fosscuda-2018b.eb new file mode 100644 index 00000000000..154de5e7362 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-fosscuda-2018b.eb @@ -0,0 +1,41 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.4' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-%(version)s_fix-LDFLAGS.patch'] +checksums = [ + 'c8ab01c4e860d53e11d40dc28f98d2fe9c85aaf6dbb5af50fd6e66afec3dc58f', # fltk-1.3.4-source.tar.gz + 'b9d39f6dce92fdb34a149f686a5d56e72912f94fd09c4958f3bb12770603da7d', # FLTK-1.3.4_fix-LDFLAGS.patch +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '2.0.0'), + ('xprop', '1.2.3'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' From af38f40b1aa99e1d03f084ff33364308bc3646e4 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 19 Feb 2019 16:00:43 -0600 Subject: [PATCH 0461/5331] adding easyconfigs: Advisor-2019_update2.eb --- .../a/Advisor/Advisor-2019_update2.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb new file mode 100644 index 00000000000..c32ef0a445f --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb @@ -0,0 +1,21 @@ +name = 'Advisor' +version = '2019_update2' + +homepage = 'https://software.intel.com/intel-advisor-xe' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['advisor_%(version)s.tar.gz'] +checksums = ['b63e11b0601013ad21789869ad76be5a836da566ee47c125dcda19ff8277de77'] + +dontcreateinstalldir = 'True' + +# license file +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'perf' From 03b524bfea2e9480afd55aad97a180b5c5b1be27 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 19 Feb 2019 16:13:22 -0600 Subject: [PATCH 0462/5331] adding easyconfigs: Inspector-2019_update2.eb --- .../i/Inspector/Inspector-2019_update2.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb new file mode 100644 index 00000000000..f67933a3074 --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb @@ -0,0 +1,17 @@ +name = 'Inspector' +version = '2019_update2' + +homepage = 'http://software.intel.com/en-us/intel-inspector-xe' +description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial + and parallel applications""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['inspector_%(version)s.tar.gz'] +checksums = ['cf031f38ef685d780878e334c76deb3e295509f989e393ca17d1c496135e26d7'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' From 15d83cef89242dec08578ec64c9843ca9a339232 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 20 Feb 2019 09:04:11 +1030 Subject: [PATCH 0463/5331] New EasyConfig for fastp --- .../f/fastp/fastp-0.19.7-foss-2018b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb b/easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb new file mode 100644 index 00000000000..48883f9ba0c --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.19.7' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/OpenGene/fastp/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['de2737b2378a8dfc6aa141cb3bfed8c1fbcfbd6056e48515f856cfafcc5c3266'] + +skipsteps = ['configure'] + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'dirs': [], + 'files': ['bin/fastp'], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' From cbc7b621067f4ca675b4b10400b32141e51812fb Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 19 Feb 2019 18:01:30 -0600 Subject: [PATCH 0464/5331] adding easyconfigs: STAR-2.5.4b-foss-2017b.eb, STAR-2.5.4b-intel-2017b.eb --- .../s/STAR/STAR-2.5.4b-foss-2017b.eb | 45 +++++++++++++++++++ .../s/STAR/STAR-2.5.4b-intel-2017b.eb | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.5.4b-foss-2017b.eb create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.5.4b-intel-2017b.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.4b-foss-2017b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.4b-foss-2017b.eb new file mode 100644 index 00000000000..c42bc69d3dc --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.4b-foss-2017b.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.5.4b' + +homepage = 'https://github.com/alexdobin/%(name)s' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'openmp': True} + +github_account = 'alexdobin' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['bfa6ccd3b7b3878155a077a9c15eec5490dffad8e077ac93abe6f9bfa75bb2b4'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' %(name)s && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/%(name)s', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/STARlong'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.4b-intel-2017b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.4b-intel-2017b.eb new file mode 100644 index 00000000000..170038d8b6c --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.4b-intel-2017b.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.5.4b' + +homepage = 'https://github.com/alexdobin/%(name)s' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'openmp': True} + +github_account = 'alexdobin' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['bfa6ccd3b7b3878155a077a9c15eec5490dffad8e077ac93abe6f9bfa75bb2b4'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' %(name)s && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/%(name)s', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/STARlong'], + 'dirs': [], +} + +moduleclass = 'bio' From fb875f4d7d1c72d852c9a04fdb9caf1d11353a3e Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 19 Feb 2019 18:14:04 -0600 Subject: [PATCH 0465/5331] adding easyconfigs: SOAPdenovo2-r241-GCC-6.4.0-2.28.eb, SOAPdenovo2-r241-iccifort-2017.4.196-GCC-6.4.0-2.28.eb --- .../SOAPdenovo2-r241-GCC-6.4.0-2.28.eb | 41 +++++++++++++++++++ ...r241-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 39 ++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-iccifort-2017.4.196-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..3c550d88a89 --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-GCC-6.4.0-2.28.eb @@ -0,0 +1,41 @@ +# With <3 for EasyBuild +# +# EasyConfig for SOAPdenovo2: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = "MakeCp" + +name = 'SOAPdenovo2' +version = 'r241' + +homepage = 'http://soap.genomics.org.cn/index.html' +description = """SOAPdenovo is a novel short-read assembly method that can build a + de novo draft assembly for human-sized genomes. The program is specially designed to + assemble Illumina short reads. It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. + SOAPdenovo2 is the successor of SOAPdenovo.""" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/aquaskyline/SOAPdenovo2/archive'] +sources = ['%(version)s.tar.gz'] +checksums = [ + 'e623b11f78bf885c22ccf265f70b3952828c6cfb05cfb3d17c49c984bcb5eeda', # r241.tar.gz +] + +# parallel build is broken +maxparallel = 1 + +files_to_copy = [(['SOAPdenovo-127mer', 'SOAPdenovo-63mer', 'SOAPdenovo-fusion'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer', 'bin/SOAPdenovo-fusion'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..cf4af550081 --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r241-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,39 @@ +# With <3 for EasyBuild +# +# EasyConfig for SOAPdenovo2: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = "MakeCp" + +name = 'SOAPdenovo2' +version = 'r241' + +homepage = 'http://soap.genomics.org.cn/index.html' +description = """SOAPdenovo is a novel short-read assembly method that can build a + de novo draft assembly for human-sized genomes. The program is specially designed to + assemble Illumina short reads. It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. + SOAPdenovo2 is the successor of SOAPdenovo.""" + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +github_account = 'aquaskyline' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e623b11f78bf885c22ccf265f70b3952828c6cfb05cfb3d17c49c984bcb5eeda'] + +# parallel build is broken +maxparallel = 1 + +files_to_copy = [(['SOAPdenovo-127mer', 'SOAPdenovo-63mer', 'SOAPdenovo-fusion'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer', 'bin/SOAPdenovo-fusion'], + 'dirs': [], +} + +moduleclass = 'bio' From 7eb822210a3379743ef7b7d7332f794e417d5338 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Feb 2019 13:34:07 +0800 Subject: [PATCH 0466/5331] add/reorder missing/misplaced extensions in Python 2.7.15 and 3.6.6 easyconfigs --- .../p/Python/Python-2.7.15-foss-2018b.eb | 20 +++++++++++-------- .../p/Python/Python-2.7.15-fosscuda-2018b.eb | 20 +++++++++++-------- .../p/Python/Python-2.7.15-intel-2018b.eb | 20 +++++++++++-------- .../p/Python/Python-2.7.15-iomkl-2018b.eb | 20 +++++++++++-------- .../p/Python/Python-3.6.6-foss-2018b.eb | 4 ++++ .../p/Python/Python-3.6.6-fosscuda-2018b.eb | 4 ++++ .../p/Python/Python-3.6.6-intel-2018b.eb | 4 ++++ .../p/Python/Python-3.6.6-iomkl-2018b.eb | 4 ++++ 8 files changed, 64 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-foss-2018b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-foss-2018b.eb index 850e3901ee6..c94fbe693ae 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-foss-2018b.eb @@ -79,6 +79,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), + ('setuptools_scm', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], + }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], @@ -123,14 +127,6 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), - ('cryptography', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], - }), - ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], - 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], - }), ('pycparser', '2.18', { 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], @@ -139,6 +135,14 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), + ('cryptography', '2.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], + }), + ('pyasn1', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb index e02ad0868af..bd7285d48d0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-fosscuda-2018b.eb @@ -79,6 +79,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), + ('setuptools_scm', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], + }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], @@ -123,14 +127,6 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), - ('cryptography', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], - }), - ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], - 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], - }), ('pycparser', '2.18', { 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], @@ -139,6 +135,14 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), + ('cryptography', '2.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], + }), + ('pyasn1', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb index 731dcb04b29..407c1189a17 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-intel-2018b.eb @@ -83,6 +83,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), + ('setuptools_scm', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], + }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], @@ -127,14 +131,6 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), - ('cryptography', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], - }), - ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], - 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], - }), ('pycparser', '2.18', { 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], @@ -143,6 +139,14 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), + ('cryptography', '2.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], + }), + ('pyasn1', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb index 58ce721e76c..49edecd5c92 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-iomkl-2018b.eb @@ -83,6 +83,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), + ('setuptools_scm', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], + }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], @@ -127,14 +131,6 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], }), - ('cryptography', '2.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], - }), - ('pyasn1', '0.4.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], - 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], - }), ('pycparser', '2.18', { 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], @@ -143,6 +139,14 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), + ('cryptography', '2.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['9fc295bf69130a342e7a19a39d7bbeb15c0bcaabc7382ec33ef3b2b7d18d2f63'], + }), + ('pyasn1', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), ('PyNaCl', '1.2.1', { 'modulename': 'nacl', 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb index 3aa2b82f362..41b1f536bfa 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-foss-2018b.eb @@ -94,6 +94,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), + ('setuptools_scm', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], + }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb index 33c7eebb598..afdc17f51a5 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb @@ -93,6 +93,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), + ('setuptools_scm', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], + }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb index e0d49bcc75e..7a60c8e36e6 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-intel-2018b.eb @@ -98,6 +98,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), + ('setuptools_scm', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], + }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb index dd66cbcb17b..1a6d8c0f4ea 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.6-iomkl-2018b.eb @@ -98,6 +98,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], }), + ('setuptools_scm', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], + 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], + }), ('python-dateutil', '2.7.3', { 'modulename': 'dateutil', 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], From 546a9ff0033a387b23f70fc62b80b56e7b2bf19b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Feb 2019 08:44:06 +0200 Subject: [PATCH 0467/5331] Add more things to sanity_check. --- .../l/libwebp/libwebp-1.0.2-GCCcore-7.3.0.eb | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-7.3.0.eb index 702bc03c87e..d8c3fe5c83b 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-7.3.0.eb @@ -1,3 +1,8 @@ +# John Dey +# +# Fred Hutch Cancer Research Ceneter +# Åke Sandgren, HPC2N, Umea University + easyblock = 'ConfigureMake' name = 'libwebp' @@ -25,8 +30,14 @@ dependencies = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ['include', 'lib'] + 'files': ['bin/cwebp', 'bin/dwebp', + 'include/webp/decode.h', 'include/webp/encode.h', + 'lib/libwebp.%s' % SHLIB_EXT, + 'lib/pkgconfig/libwebp.pc', + 'share/man/man1/cwebp.1', + 'share/man/man1/dwebp.1', + ], + 'dirs': ['bin', 'include', 'lib', 'share'] } moduleclass = 'lib' From 6204b69e995a4a32eadc8a49ceed194d2159005a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Feb 2019 10:31:18 +0200 Subject: [PATCH 0468/5331] Go back to using --disable-dri/egl for standard Mesa. --- easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb index f76b50a13c2..4adccd2fe8f 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb @@ -54,8 +54,8 @@ dependencies = [ ] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --enable-dri" -configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --enable-egl" +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " buildopts = 'V=1' From ad7ea53405ac3d1c2fbb7c7442b92d2be5fe1ee4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Feb 2019 10:32:11 +0200 Subject: [PATCH 0469/5331] Replace deprecated config option --enable-gallium-llvm with --enable-llvm for Mesa 18. --- easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb index 4adccd2fe8f..428bb968c41 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb @@ -54,7 +54,7 @@ dependencies = [ ] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-llvm --enable-glx --disable-dri" configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " From e05740032bd5585e3c71559618ed75255a20c228 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Wed, 20 Feb 2019 10:07:38 +0100 Subject: [PATCH 0470/5331] Changed some style issues --- easybuild/easyconfigs/g/glew/glew-2.1.0-foss-2018b.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/glew/glew-2.1.0-foss-2018b.eb b/easybuild/easyconfigs/g/glew/glew-2.1.0-foss-2018b.eb index 31218926f03..31ab2afe528 100644 --- a/easybuild/easyconfigs/g/glew/glew-2.1.0-foss-2018b.eb +++ b/easybuild/easyconfigs/g/glew/glew-2.1.0-foss-2018b.eb @@ -23,16 +23,15 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-%(version)s.tgz'] checksums = ['04de91e7e6763039bc11940095cd9c7f880baba82196a7765f727ac05a993c95'] -dependencies =[('Mesa','18.1.1')] +dependencies = [('Mesa', '18.1.1')] -files_to_copy = ['bin', 'lib', 'include',] +files_to_copy = ['bin', 'lib', 'include', ] sanity_check_paths = { - 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + - ['bin/glewinfo', 'bin/visualinfo'] + + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + ['include/GL/glew.h', 'include/GL/glxew.h', 'include/GL/wglew.h'], - 'dirs': ['',] + 'dirs': ['', ] } moduleclass = 'devel' - From e5467e19e6c3179386575978d37f6fd6a2dbf8aa Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Feb 2019 11:44:10 +0200 Subject: [PATCH 0471/5331] Update osdependencies to include RH based name. --- .../b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb index b987f2a0213..6e90acf6729 100644 --- a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.6-fosscuda-2018b-Python-2.7.15.eb @@ -15,7 +15,7 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['42d621f4037425afcb16b67d5600c4556271a071a9a7f7f2c2b1ba65bc582d05'] -osdependencies = [('libdb-dev')] +osdependencies = [('libdb-dev', 'libdb-devel')] dependencies = [('Python', '2.7.15')] From 9d9b06f24c0a438fdf8577e799912f880987f9d5 Mon Sep 17 00:00:00 2001 From: sassmaj Date: Wed, 20 Feb 2019 10:48:59 +0100 Subject: [PATCH 0472/5331] some cosmetics and change to toolchain --- ...admix-32-foss-2018b.eb => NGSadmix-32-GCC-7.3.0-2.30.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/n/NGSadmix/{NGSadmix-32-foss-2018b.eb => NGSadmix-32-GCC-7.3.0-2.30.eb} (83%) diff --git a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb similarity index 83% rename from easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb rename to easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb index 9539af13a2d..dd1cf272297 100644 --- a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-foss-2018b.eb +++ b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb @@ -5,10 +5,10 @@ version = '32' homepage = 'http://www.popgen.dk/software/index.php/NgsAdmix' description = """This page contains information about the program called -NGSadmix, which is a very nice tool for finding admixture proportions -from NGS data. It is based on genotype likelihoods.""" +NGSadmix, which is a tool for finding admixture proportions +from NGS data, based on genotype likelihoods.""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} # This is a bit of a hack as there is no easyblock to simply download a cpp file and compile it. # So we download the file from the source and copy it to the build directory. From 2ff83561227f035056b32875b8090211135e4387 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 20 Feb 2019 10:58:06 +0100 Subject: [PATCH 0473/5331] use TIFF 4.0.9 --- .../w/wxPython/wxPython-3.0.2.0-intel-2017b-Python-2.7.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2017b-Python-2.7.14.eb index bb1d59e72c6..4ba1367f763 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2017b-Python-2.7.14.eb @@ -29,7 +29,7 @@ dependencies = [ ('libpng', '1.6.32'), ('zlib', '1.2.11'), ('libjpeg-turbo', '1.5.2'), - ('LibTIFF', '4.0.8'), + ('LibTIFF', '4.0.9'), ('expat', '2.2.4'), ('GTK+', '2.24.32'), ('GConf', '3.2.6'), From 98c8c7ea4ed7c307d133bd7200761b514f63703a Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 20 Feb 2019 08:00:00 -0600 Subject: [PATCH 0474/5331] apply patch to fix the compilation error --- .../lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb | 7 +- ....2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 7 +- ....5.2.5_Fix_expected_identifier_error.patch | 6339 +++++++++++++++++ 3 files changed, 6351 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5_Fix_expected_identifier_error.patch diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb index bd7854d8b4d..fa899fc0053 100644 --- a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb @@ -10,7 +10,12 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = [SOURCEFORGE_SOURCE] sources = ['lp_solve_%(version)s_source.tar.gz'] -checksums = ['201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a'] +patches = ['lpsolve-5.5.2.5_Fix_expected_identifier_error.patch'] +checksums = [ + '201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a', # lp_solve_5.5.2.5_source.tar.gz + # lpsolve-5.5.2.5_Fix_expected_identifier_error.patch + 'be46d06035797b455ff616c74f83c4e36c9cad6c41b0c8680b29cb6b3208f49c', +] lpsolve_ver = '%(version_major)s%(version_minor)s' start_dir = 'lpsolve%s' % lpsolve_ver diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index a63a3263953..2895e0056b0 100644 --- a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -10,7 +10,12 @@ toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} source_urls = [SOURCEFORGE_SOURCE] sources = ['lp_solve_%(version)s_source.tar.gz'] -checksums = ['201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a'] +patches = ['lpsolve-5.5.2.5_Fix_expected_identifier_error.patch'] +checksums = [ + '201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a', # lp_solve_5.5.2.5_source.tar.gz + # lpsolve-5.5.2.5_Fix_expected_identifier_error.patch + 'be46d06035797b455ff616c74f83c4e36c9cad6c41b0c8680b29cb6b3208f49c', +] lpsolve_ver = '%(version_major)s%(version_minor)s' start_dir = 'lpsolve%s' % lpsolve_ver diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5_Fix_expected_identifier_error.patch b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5_Fix_expected_identifier_error.patch new file mode 100644 index 00000000000..246b9b28b2d --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5_Fix_expected_identifier_error.patch @@ -0,0 +1,6339 @@ +Rename FALSE macro to prevent the following error: + +../shared/commonlib.h:88:24: error: expected identifier or ‘(’ before numeric constant + #define FALSE 0 + +See https://github.com/chandu-atina/lp_solve_python_3x/issues/1 +author: Davide Vanzo (Vanderbilt University) +diff -ru lp_solve_5.5.orig/lp_crash.c lp_solve_5.5/lp_crash.c +--- lp_solve_5.5.orig/lp_crash.c 2019-02-19 10:42:21.368737063 -0600 ++++ lp_solve_5.5/lp_crash.c 2019-02-19 11:55:26.088858391 -0600 +@@ -39,7 +39,7 @@ + + /* Initialize basis indicators */ + if(lp->basis_valid) +- lp->var_basic[0] = FALSE; ++ lp->var_basic[0] = FFALSE; + else + default_basis(lp); + +@@ -64,8 +64,8 @@ + /* Tally row and column non-zero counts */ + ok = allocINT(lp, &rowNZ, lp->rows+1, TRUE) && + allocINT(lp, &colNZ, lp->columns+1, TRUE) && +- allocREAL(lp, &rowMAX, lp->rows+1, FALSE) && +- allocREAL(lp, &colMAX, lp->columns+1, FALSE); ++ allocREAL(lp, &rowMAX, lp->rows+1, FFALSE) && ++ allocREAL(lp, &colMAX, lp->columns+1, FFALSE); + if(!ok) + goto Finish; + +@@ -241,9 +241,9 @@ + report(lp, NORMAL, "crash_basis: 'Least degenerate' basis crashing selected\n"); + + /* Create temporary arrays */ +- ok = allocINT(lp, &merit, lp->columns + 1, FALSE) && +- allocREAL(lp, &eta, lp->rows + 1, FALSE) && +- allocREAL(lp, &rhs, lp->rows + 1, FALSE); ++ ok = allocINT(lp, &merit, lp->columns + 1, FFALSE) && ++ allocREAL(lp, &eta, lp->rows + 1, FFALSE) && ++ allocREAL(lp, &rhs, lp->rows + 1, FFALSE); + createLink(lp->columns, &colLL, NULL); + createLink(lp->rows, &rowLL, NULL); + ok &= (colLL != NULL) && (rowLL != NULL); +@@ -337,7 +337,7 @@ + #if 0 + MYBOOL __WINAPI guess_basis(lprec *lp, REAL *guessvector, int *basisvector) + { +- MYBOOL status = FALSE; ++ MYBOOL status = FFALSE; + REAL *values = NULL, *violation = NULL, + *value, error, upB, loB, sortorder = 1.0; + int i, n, *rownr, *colnr; +@@ -411,7 +411,7 @@ + + /* Sort decending by violation; this means that variables with + the largest violations will be designated as basic */ +- sortByREAL(basisvector, violation, lp->sum, 1, FALSE); ++ sortByREAL(basisvector, violation, lp->sum, 1, FFALSE); + + /* Adjust the non-basic indeces for the (proximal) bound state */ + error = lp->epsprimal; +@@ -439,7 +439,7 @@ + #if 0 + MYBOOL __WINAPI guess_basis(lprec *lp, REAL *guessvector, int *basisvector) + { +- MYBOOL *isnz, status = FALSE; ++ MYBOOL *isnz, status = FFALSE; + REAL *values = NULL, *violation = NULL, + eps = lp->epsprimal, + *value, error, upB, loB, sortorder = 1.0; +@@ -515,7 +515,7 @@ + + /* Sort decending by violation; this means that variables with + the largest violations will be designated as basic */ +- sortByREAL(basisvector, violation, lp->sum, 1, FALSE); ++ sortByREAL(basisvector, violation, lp->sum, 1, FFALSE); + error = violation[1]; + + /* Adjust the non-basic indeces for the (proximal) bound state */ +@@ -583,7 +583,7 @@ + #if 0 + MYBOOL __WINAPI guess_basis(lprec *lp, REAL *guessvector, int *basisvector) + { +- MYBOOL *isnz, status = FALSE; ++ MYBOOL *isnz, status = FFALSE; + REAL *values = NULL, *violation = NULL, + eps = lp->epsprimal, + *value, error, upB, loB, sortorder = 1.0; +@@ -659,7 +659,7 @@ + + /* Sort decending by violation; this means that variables with + the largest violations will be designated as basic */ +- sortByREAL(basisvector, violation, lp->sum, 1, FALSE); ++ sortByREAL(basisvector, violation, lp->sum, 1, FFALSE); + error = violation[1]; + + /* Adjust the non-basic indeces for the (proximal) bound state */ +@@ -730,7 +730,7 @@ + + MYBOOL __WINAPI guess_basis(lprec *lp, REAL *guessvector, int *basisvector) + { +- MYBOOL *isnz = NULL, status = FALSE; ++ MYBOOL *isnz = NULL, status = FFALSE; + REAL *values = NULL, *violation = NULL, + eps = lp->epsprimal, + *value, error, upB, loB, sortorder = -1.0; +@@ -793,7 +793,7 @@ + /* Sort decending , meaning that variables with the largest + "violations" will be designated basic. Effectively, we are performing a + greedy type algorithm, but start at the "least interesting" end. */ +- sortByREAL(basisvector, violation, nsum, 1, FALSE); ++ sortByREAL(basisvector, violation, nsum, 1, FFALSE); + error = violation[1]; /* Used for setting the return value */ + + /* Let us check for obvious row singularities and try to fix these. +diff -ru lp_solve_5.5.orig/lp_lib.c lp_solve_5.5/lp_lib.c +--- lp_solve_5.5.orig/lp_lib.c 2019-02-19 10:42:21.372737063 -0600 ++++ lp_solve_5.5/lp_lib.c 2019-02-19 12:07:38.248878651 -0600 +@@ -157,7 +157,7 @@ + lp->outstream = stdout; + else + lp->outstream = stream; +- lp->streamowned = FALSE; ++ lp->streamowned = FFALSE; + } + + MYBOOL __WINAPI set_outputfile(lprec *lp, char *filename) +@@ -327,7 +327,7 @@ + #ifndef PARSER_LP + MYBOOL __WINAPI LP_readhandle(lprec **lp, FILE *filename, int verbose, char *lp_name) + { +- return(FALSE); ++ return(FFALSE); + } + lprec * __WINAPI read_lp(FILE *filename, int verbose, char *lp_name) + { +@@ -354,7 +354,7 @@ + if(typeMPS) { + set_action(&lp->spx_action, ACTION_REBASE | ACTION_REINVERT | ACTION_RECOMPUTE); + lp->basis_valid = TRUE; /* Do not re-initialize basis on entering Solve */ +- lp->var_basic[0] = FALSE; /* Set to signal that this is a non-default basis */ ++ lp->var_basic[0] = FFALSE; /* Set to signal that this is a non-default basis */ + } + return( (MYBOOL) typeMPS ); + } +@@ -369,7 +369,7 @@ + /* lp->lag_accept = DEF_LAGACCEPT; */ + set_epslevel(lp, EPS_DEFAULT); + +- lp->tighten_on_set = FALSE; ++ lp->tighten_on_set = FFALSE; + lp->negrange = DEF_NEGRANGE; + + #if 0 +@@ -432,10 +432,10 @@ + + set_outputstream(lp, NULL); /* Set to default output stream */ + lp->verbose = NORMAL; +- lp->print_sol = FALSE; /* Can be FALSE, TRUE, AUTOMATIC (only non-zeros printed) */ +- lp->spx_trace = FALSE; +- lp->lag_trace = FALSE; +- lp->bb_trace = FALSE; ++ lp->print_sol = FFALSE; /* Can be FALSE, TRUE, AUTOMATIC (only non-zeros printed) */ ++ lp->spx_trace = FFALSE; ++ lp->lag_trace = FFALSE; ++ lp->bb_trace = FFALSE; + } + + void __WINAPI unscale(lprec *lp) +@@ -451,7 +451,7 @@ + if(has_BFP(lp)) { + lp->solvecount++; + if(is_add_rowmode(lp)) +- set_add_rowmode(lp, FALSE); ++ set_add_rowmode(lp, FFALSE); + return(lin_solve(lp)); + } + else +@@ -677,14 +677,14 @@ + { + if(colnr > lp->columns || colnr < 1) { + report(lp, IMPORTANT, "set_var_branch: Column %d out of range\n", colnr); +- return( FALSE ); ++ return( FFALSE ); + } + + if(lp->bb_varbranch == NULL) { + int i; + if(branch_mode == BRANCH_DEFAULT) + return( TRUE ); +- allocMYBOOL(lp, &lp->bb_varbranch, lp->columns_alloc, FALSE); ++ allocMYBOOL(lp, &lp->bb_varbranch, lp->columns_alloc, FFALSE); + for(i = 0; i < lp->columns; i++) + lp->bb_varbranch[i] = BRANCH_DEFAULT; + } +@@ -734,13 +734,13 @@ + if(fabs(value) >= lp->infinite) + return( TRUE ); + else +- return( FALSE ); ++ return( FFALSE ); + #endif + } + + void __WINAPI set_infinite(lprec *lp, REAL infinite) + { +- set_infiniteex(lp, infinite, FALSE); ++ set_infiniteex(lp, infinite, FFALSE); + } + + REAL __WINAPI get_infinite(lprec *lp) +@@ -825,7 +825,7 @@ + case EPS_BAGGY: SPX_RELAX = 1000; + MIP_RELAX = 100; + break; +- default: return( FALSE ); ++ default: return( FFALSE ); + } + lp->epsvalue = SPX_RELAX*DEF_EPSVALUE; + lp->epsprimal = SPX_RELAX*DEF_EPSPRIMAL; +@@ -1015,11 +1015,11 @@ + { + if((rownr < 0) || (rownr > lp->rows)) { + report(lp, IMPORTANT, "set_mat: Row %d out of range\n", rownr); +- return( FALSE ); ++ return( FFALSE ); + } + if((colnr < 1) || (colnr > lp->columns)) { + report(lp, IMPORTANT, "set_mat: Column %d out of range\n", colnr); +- return( FALSE ); ++ return( FFALSE ); + } + + #ifdef DoMatrixRounding +@@ -1032,7 +1032,7 @@ + return( TRUE ); + } + else +- return( mat_setvalue(lp->matA, rownr, colnr, value, FALSE) ); ++ return( mat_setvalue(lp->matA, rownr, colnr, value, FFALSE) ); + } + + REAL __WINAPI get_working_objective(lprec *lp) +@@ -1087,7 +1087,7 @@ + ; + else if(!lp->basis_valid) { + report(lp, CRITICAL, "get_variables: Not a valid basis\n"); +- return(FALSE); ++ return(FFALSE); + } + + MEMCOPY(var, lp->best_solution + (1 + lp->rows), lp->columns); +@@ -1100,7 +1100,7 @@ + ; + else if(!lp->basis_valid) { + report(lp, CRITICAL, "get_ptr_variables: Not a valid basis\n"); +- return(FALSE); ++ return(FFALSE); + } + + if(var != NULL) +@@ -1114,7 +1114,7 @@ + ; + else if(!lp->basis_valid) { + report(lp, CRITICAL, "get_constraints: Not a valid basis\n"); +- return(FALSE); ++ return(FFALSE); + } + + MEMCOPY(constr, lp->best_solution + 1, lp->rows); +@@ -1127,7 +1127,7 @@ + ; + else if(!lp->basis_valid) { + report(lp, CRITICAL, "get_ptr_constraints: Not a valid basis\n"); +- return(FALSE); ++ return(FFALSE); + } + + if(constr != NULL) +@@ -1141,14 +1141,14 @@ + + if(!lp->basis_valid) { + report(lp, CRITICAL, "get_sensitivity_rhs: Not a valid basis\n"); +- return(FALSE); ++ return(FFALSE); + } + + if(!get_ptr_sensitivity_rhs(lp, + (duals != NULL) ? &duals0 : NULL, + (dualsfrom != NULL) ? &dualsfrom0 : NULL, + (dualstill != NULL) ? &dualstill0 : NULL)) +- return(FALSE); ++ return(FFALSE); + + if(duals != NULL) + MEMCOPY(duals, duals0, lp->sum); +@@ -1163,17 +1163,17 @@ + { + if(!lp->basis_valid) { + report(lp, CRITICAL, "get_ptr_sensitivity_rhs: Not a valid basis\n"); +- return(FALSE); ++ return(FFALSE); + } + + if(duals != NULL) { + if(lp->duals == NULL) { + if((MIP_count(lp) > 0) && (lp->bb_totalnodes > 0)) { + report(lp, CRITICAL, "get_ptr_sensitivity_rhs: Sensitivity unknown\n"); +- return(FALSE); ++ return(FFALSE); + } + if(!construct_duals(lp)) +- return(FALSE); ++ return(FFALSE); + } + *duals = lp->duals + 1; + } +@@ -1182,11 +1182,11 @@ + if((lp->dualsfrom == NULL) || (lp->dualstill == NULL)) { + if((MIP_count(lp) > 0) && (lp->bb_totalnodes > 0)) { + report(lp, CRITICAL, "get_ptr_sensitivity_rhs: Sensitivity unknown\n"); +- return(FALSE); ++ return(FFALSE); + } + construct_sensitivity_duals(lp); + if((lp->dualsfrom == NULL) || (lp->dualstill == NULL)) +- return(FALSE); ++ return(FFALSE); + } + if(dualsfrom != NULL) + *dualsfrom = lp->dualsfrom + 1; +@@ -1202,14 +1202,14 @@ + + if(!lp->basis_valid) { + report(lp, CRITICAL, "get_sensitivity_objex: Not a valid basis\n"); +- return(FALSE); ++ return(FFALSE); + } + + if(!get_ptr_sensitivity_objex(lp, (objfrom != NULL) ? &objfrom0 : NULL, + (objtill != NULL) ? &objtill0 : NULL, + (objfromvalue != NULL) ? &objfromvalue0 : NULL, + (objtillvalue != NULL) ? &objtillvalue0 : NULL)) +- return(FALSE); ++ return(FFALSE); + + if((objfrom != NULL) && (objfrom0 != NULL)) + MEMCOPY(objfrom, objfrom0, lp->columns); +@@ -1231,18 +1231,18 @@ + { + if(!lp->basis_valid) { + report(lp, CRITICAL, "get_ptr_sensitivity_objex: Not a valid basis\n"); +- return(FALSE); ++ return(FFALSE); + } + + if((objfrom != NULL) || (objtill != NULL)) { + if((lp->objfrom == NULL) || (lp->objtill == NULL)) { + if((MIP_count(lp) > 0) && (lp->bb_totalnodes > 0)) { + report(lp, CRITICAL, "get_ptr_sensitivity_objex: Sensitivity unknown\n"); +- return(FALSE); ++ return(FFALSE); + } + construct_sensitivity_obj(lp); + if((lp->objfrom == NULL) || (lp->objtill == NULL)) +- return(FALSE); ++ return(FFALSE); + } + if(objfrom != NULL) + *objfrom = lp->objfrom + 1; +@@ -1254,11 +1254,11 @@ + if((lp->objfromvalue == NULL) /* || (lp->objtillvalue == NULL) */) { + if((MIP_count(lp) > 0) && (lp->bb_totalnodes > 0)) { + report(lp, CRITICAL, "get_ptr_sensitivity_objex: Sensitivity unknown\n"); +- return(FALSE); ++ return(FFALSE); + } + construct_sensitivity_duals(lp); + if((lp->objfromvalue == NULL) /* || (lp->objtillvalue == NULL) */) +- return(FALSE); ++ return(FFALSE); + } + } + +@@ -1382,7 +1382,7 @@ + return(NULL); + + set_lp_name(lp, NULL); +- lp->names_used = FALSE; ++ lp->names_used = FFALSE; + lp->use_row_names = TRUE; + lp->use_col_names = TRUE; + lp->rowcol_name = NULL; +@@ -1391,7 +1391,7 @@ + #if 1 + lp->obj_in_basis = DEF_OBJINBASIS; + #else +- lp->obj_in_basis = FALSE; ++ lp->obj_in_basis = FFALSE; + #endif + lp->verbose = NORMAL; + set_callbacks(lp); +@@ -1409,15 +1409,15 @@ + reset_params(lp); + + /* Do other initializations --------------------------------------------------------------- */ +- lp->source_is_file = FALSE; ++ lp->source_is_file = FFALSE; + lp->model_is_pure = TRUE; +- lp->model_is_valid = FALSE; ++ lp->model_is_valid = FFALSE; + lp->spx_status = NOTRUN; + lp->lag_status = NOTRUN; + + lp->workarrays = mempool_create(lp); +- lp->wasPreprocessed = FALSE; +- lp->wasPresolved = FALSE; ++ lp->wasPreprocessed = FFALSE; ++ lp->wasPresolved = FFALSE; + presolve_createUndo(lp); + + lp->bb_varactive = NULL; +@@ -1466,10 +1466,10 @@ + lp->bb_bounds = NULL; + lp->bb_basis = NULL; + +- lp->basis_valid = FALSE; ++ lp->basis_valid = FFALSE; + lp->simplex_mode = SIMPLEX_DYNAMIC; +- lp->scaling_used = FALSE; +- lp->columns_scaled = FALSE; ++ lp->scaling_used = FFALSE; ++ lp->columns_scaled = FFALSE; + lp->P1extraDim = 0; + lp->P1extraVal = 0.0; + lp->bb_strongbranches = 0; +@@ -1590,7 +1590,7 @@ + } + if(lp->bb_basis != NULL) { + /* report(lp, SEVERE, "delete_lp: The stack of saved bases was not empty on delete\n"); */ +- unload_basis(lp, FALSE); ++ unload_basis(lp, FFALSE); + } + + FREE(lp->rejectpivot); +@@ -1654,7 +1654,7 @@ + SOSrec *SOS; + + if((index < 1) || (index > SOS_count(lp))) +- return( FALSE ); ++ return( FFALSE ); + SOS = lp->SOS->sos_list[index-1]; + if(name != NULL) + strcpy(name, SOS->name); +@@ -1683,7 +1683,7 @@ + int i, n, *idx = NULL; + REAL hold, *val = NULL, infinite; + lprec *newlp = NULL; +- char buf[256], ok = FALSE; ++ char buf[256], ok = FFALSE; + int sostype, priority, count, *sosvars, rows, columns; + REAL *weights = NULL; + +@@ -1695,8 +1695,8 @@ + rows = get_Nrows(lp); + columns = get_Ncolumns(lp); + +- if(!allocINT(lp, &idx, rows+1, FALSE) || +- !allocREAL(lp, &val, rows+1, FALSE)) ++ if(!allocINT(lp, &idx, rows+1, FFALSE) || ++ !allocREAL(lp, &val, rows+1, FFALSE)) + goto Finish; + + /* Create the new object */ +@@ -1706,7 +1706,7 @@ + if(!resize_lp(newlp, rows, columns)) + goto Finish; + set_sense(newlp, is_maxim(lp)); +- set_use_names(newlp, FALSE, is_use_names(lp, FALSE)); ++ set_use_names(newlp, FFALSE, is_use_names(lp, FFALSE)); + set_use_names(newlp, TRUE, is_use_names(lp, TRUE)); + if(!set_lp_name(newlp, get_lp_name(lp))) + goto Finish; +@@ -1738,7 +1738,7 @@ + set_bb_depthlimit(newlp, get_bb_depthlimit(lp)); + set_bb_floorfirst(newlp, get_bb_floorfirst(lp)); + set_mip_gap(newlp, TRUE, get_mip_gap(lp, TRUE)); +- set_mip_gap(newlp, FALSE, get_mip_gap(lp, FALSE)); ++ set_mip_gap(newlp, FFALSE, get_mip_gap(lp, FFALSE)); + set_break_at_first(newlp, is_break_at_first(lp)); + set_break_at_value(newlp, get_break_at_value(lp)); + +@@ -1789,8 +1789,8 @@ + /* copy SOS data */ + for(i = 1; get_SOS(lp, i, buf, &sostype, &priority, &count, NULL, NULL); i++) + if (count) { +- if(!allocINT(lp, &sosvars, count, FALSE) || +- !allocREAL(lp, &weights, count, FALSE)) ++ if(!allocINT(lp, &sosvars, count, FFALSE) || ++ !allocREAL(lp, &weights, count, FFALSE)) + n = 0; + else { + get_SOS(lp, i, buf, &sostype, &priority, &count, sosvars, weights); +@@ -1811,7 +1811,7 @@ + MEMCOPY(newlp->is_lower, lp->is_lower, lp->sum+1); + MEMCOPY(newlp->solution, lp->solution, lp->sum+1); + if(lp->duals != NULL) { +- allocREAL(newlp, &newlp->duals, newlp->sum_alloc+1, FALSE); ++ allocREAL(newlp, &newlp->duals, newlp->sum_alloc+1, FFALSE); + MEMCOPY(newlp->duals, lp->duals, lp->sum+1); + } + newlp->solutioncount = lp->solutioncount; +@@ -1838,7 +1838,7 @@ + + /* Are we allowed to perform the operation? */ + if((MIP_count(lp) > 0) || (lp->solvecount > 0)) +- return( FALSE ); ++ return( FFALSE ); + + /* Modify sense */ + set_sense(lp, (MYBOOL) !is_maxim(lp)); +@@ -1881,7 +1881,7 @@ + /* Optimize memory usage */ + STATIC MYBOOL memopt_lp(lprec *lp, int rowextra, int colextra, int nzextra) + { +- MYBOOL status = FALSE; ++ MYBOOL status = FFALSE; + + if(lp == NULL) + return( status ); +@@ -1894,7 +1894,7 @@ + int colalloc = lp->columns_alloc - MIN(lp->columns_alloc, lp->columns + colextra), + rowalloc = lp->rows_alloc - MIN(lp->rows_alloc, lp->rows + rowextra); + +- status = inc_lag_space(lp, rowalloc, FALSE) && ++ status = inc_lag_space(lp, rowalloc, FFALSE) && + inc_row_space(lp, rowalloc) && + inc_col_space(lp, colalloc); + } +@@ -1914,7 +1914,7 @@ + STATIC void varmap_clear(lprec *lp) + { + presolve_setOrig(lp, 0, 0); +- lp->varmap_locked = FALSE; ++ lp->varmap_locked = FFALSE; + } + STATIC MYBOOL varmap_canunlock(lprec *lp) + { +@@ -1927,17 +1927,17 @@ + if(/*lp->names_used || + (psundo->orig_columns != lp->columns) || (psundo->orig_rows != lp->rows)) */ + (psundo->orig_columns > lp->columns) || (psundo->orig_rows > lp->rows)) +- return( FALSE ); ++ return( FFALSE ); + + /* Check for deletions */ + for(i = psundo->orig_rows + psundo->orig_columns; i > 0; i--) + if(psundo->orig_to_var[i] == 0) +- return( FALSE ); ++ return( FFALSE ); + + /* Check for insertions */ + for(i = lp->sum; i > 0; i--) + if(psundo->var_to_orig[i] == 0) +- return( FALSE ); ++ return( FFALSE ); + } + return( TRUE ); + } +@@ -2031,7 +2031,7 @@ + 2) shift the deleted variable to original mappings left + 3) decrement all subsequent original-to-current pointers + */ +- if(varmap_canunlock(lp)) lp->varmap_locked = FALSE; ++ if(varmap_canunlock(lp)) lp->varmap_locked = FFALSE; + for(i = base; i < base-delta; i++) { + ii = psundo->var_to_orig[i]; + if(ii > 0) +@@ -2267,7 +2267,7 @@ + + lp->sum += delta; + +- lp->matA->row_end_valid = FALSE; ++ lp->matA->row_end_valid = FFALSE; + + return(TRUE); + } +@@ -2319,7 +2319,7 @@ + k = 0; + for(i = 1; i <= lp->rows; i++) { + ii = lp->var_basic[i]; +- lp->is_basic[ii] = FALSE; ++ lp->is_basic[ii] = FFALSE; + if(ii >= base) { + /* Skip to next basis variable if this one is to be deleted */ + if(ii < base-delta) { +@@ -2362,7 +2362,7 @@ + basis and must create one (in most usage modes this should not happen, + unless there is a bug) */ + if(k+delta < 0) +- Ok = FALSE; ++ Ok = FFALSE; + if(isrow || (k != lp->rows)) + set_action(&lp->spx_action, ACTION_REINVERT); + +@@ -2664,10 +2664,10 @@ + + } + +- shift_basis(lp, lp->rows+base, delta, usedmap, FALSE); ++ shift_basis(lp, lp->rows+base, delta, usedmap, FFALSE); + if(SOS_count(lp) > 0) +- SOS_shift_col(lp->SOS, 0, base, delta, usedmap, FALSE); +- shift_rowcoldata(lp, lp->rows+base, delta, usedmap, FALSE); ++ SOS_shift_col(lp->SOS, 0, base, delta, usedmap, FFALSE); ++ shift_rowcoldata(lp, lp->rows+base, delta, usedmap, FFALSE); + inc_columns(lp, delta); + + return( TRUE ); +@@ -2729,7 +2729,7 @@ + !allocMYBOOL(lp, &lp->is_basic, rowcolsum, AUTOMATIC) || + !allocMYBOOL(lp, &lp->is_lower, rowcolsum, AUTOMATIC) || + ((lp->scalars != NULL) && !allocREAL(lp, &lp->scalars, rowcolsum, AUTOMATIC))) +- return( FALSE ); ++ return( FFALSE ); + + /* Fill in default values, where appropriate */ + for(i = oldrowcolalloc+1; i < rowcolsum; i++) { +@@ -2737,7 +2737,7 @@ + lp->orig_upbo[i] = lp->upbo[i]; + lp->lowbo[i] = 0; + lp->orig_lowbo[i] = lp->lowbo[i]; +- lp->is_basic[i] = FALSE; ++ lp->is_basic[i] = FFALSE; + lp->is_lower[i] = TRUE; + } + +@@ -2765,7 +2765,7 @@ + if(!allocREAL(lp, &lp->lag_rhs, newsize+1, AUTOMATIC) || + !allocREAL(lp, &lp->lambda, newsize+1, AUTOMATIC) || + !allocINT(lp, &lp->lag_con_type, newsize+1, AUTOMATIC)) +- return( FALSE ); ++ return( FFALSE ); + + /* Reallocate the matrix (note that the row scalars are stored at index 0) */ + if(!ignoreMAT) { +@@ -2824,7 +2824,7 @@ + !allocLREAL(lp, &lp->rhs, rowsum, AUTOMATIC) || + !allocINT(lp, &lp->row_type, rowsum, AUTOMATIC) || + !allocINT(lp, &lp->var_basic, rowsum, AUTOMATIC)) +- return( FALSE ); ++ return( FFALSE ); + + if(oldrowsalloc == 0) { + lp->var_basic[0] = AUTOMATIC; /*TRUE;*/ /* Indicates default basis */ +@@ -2848,7 +2848,7 @@ + ht = copy_hash_table(lp->rowname_hashtab, lp->row_name, lp->rows_alloc + 1); + if(ht == NULL) { + lp->spx_status = NOMEMORY; +- return( FALSE ); ++ return( FFALSE ); + } + free_hash_table(lp->rowname_hashtab); + lp->rowname_hashtab = ht; +@@ -2858,7 +2858,7 @@ + lp->row_name = (hashelem **) realloc(lp->row_name, (rowsum) * sizeof(*lp->row_name)); + if(lp->row_name == NULL) { + lp->spx_status = NOMEMORY; +- return( FALSE ); ++ return( FFALSE ); + } + for(i = oldrowsalloc + 1; i < rowsum; i++) + lp->row_name[i] = NULL; +@@ -2925,11 +2925,11 @@ + ((lp->var_priority != NULL) && !allocINT(lp, &lp->var_priority, colsum-1, AUTOMATIC)) || + ((lp->var_is_free != NULL) && !allocINT(lp, &lp->var_is_free, colsum, AUTOMATIC)) || + ((lp->bb_varbranch != NULL) && !allocMYBOOL(lp, &lp->bb_varbranch, colsum-1, AUTOMATIC))) +- return( FALSE ); ++ return( FFALSE ); + + /* Make sure that Lagrangean constraints have the same number of columns */ + if(get_Lrows(lp) > 0) +- inc_lag_space(lp, 0, FALSE); ++ inc_lag_space(lp, 0, FFALSE); + + /* Update column pointers */ + for(i = MIN(oldcolsalloc, lp->columns) + 1; i < colsum; i++) { +@@ -2952,7 +2952,7 @@ + lp->bb_varbranch[i] = BRANCH_DEFAULT; + } + +- inc_rowcol_space(lp, deltacols, FALSE); ++ inc_rowcol_space(lp, deltacols, FFALSE); + + } + return(TRUE); +@@ -2976,7 +2976,7 @@ + REAL value; + + if(row == NULL) +- return( FALSE ); ++ return( FFALSE ); + + else if(colno == NULL) { + if(count <= 0) +@@ -3016,14 +3016,14 @@ + REAL *arow; + char *p, *newp; + +- allocREAL(lp, &arow, lp->columns + 1, FALSE); ++ allocREAL(lp, &arow, lp->columns + 1, FFALSE); + p = row_string; + for(i = 1; i <= lp->columns; i++) { + arow[i] = (REAL) strtod(p, &newp); + if(p == newp) { + report(lp, IMPORTANT, "str_set_obj_fn: Bad string %s\n", p); + lp->spx_status = DATAIGNORED; +- ret = FALSE; ++ ret = FFALSE; + break; + } + else +@@ -3038,7 +3038,7 @@ + STATIC MYBOOL append_columns(lprec *lp, int deltacolumns) + { + if(!inc_col_space(lp, deltacolumns)) +- return( FALSE ); ++ return( FFALSE ); + varmap_add(lp, lp->sum+1, deltacolumns); + shift_coldata(lp, lp->columns+1, deltacolumns, NULL); + return( TRUE ); +@@ -3047,7 +3047,7 @@ + STATIC MYBOOL append_rows(lprec *lp, int deltarows) + { + if(!inc_row_space(lp, deltarows)) +- return( FALSE ); ++ return( FFALSE ); + varmap_add(lp, lp->rows+1, deltarows); + shift_rowdata(lp, lp->rows+1, deltarows, NULL); + +@@ -3059,7 +3059,7 @@ + if((lp->solvecount == 0) && (turnon ^ lp->matA->is_roworder)) + return( mat_transpose(lp->matA) ); + else +- return( FALSE ); ++ return( FFALSE ); + } + + MYBOOL __WINAPI is_add_rowmode(lprec *lp) +@@ -3071,7 +3071,7 @@ + { + if((rownr < 0) || (rownr > lp->rows)) { + report(lp, IMPORTANT, "set_row: Row %d out of range\n", rownr); +- return( FALSE ); ++ return( FFALSE ); + } + if(rownr == 0) + return( set_obj_fn(lp, row) ); +@@ -3083,7 +3083,7 @@ + { + if((rownr < 0) || (rownr > lp->rows)) { + report(lp, IMPORTANT, "set_rowex: Row %d out of range\n", rownr); +- return( FALSE ); ++ return( FFALSE ); + } + if(rownr == 0) + return( set_obj_fnex(lp, count, row, colno) ); +@@ -3094,7 +3094,7 @@ + MYBOOL __WINAPI add_constraintex(lprec *lp, int count, REAL *row, int *colno, int constr_type, REAL rh) + { + int n; +- MYBOOL status = FALSE; ++ MYBOOL status = FFALSE; + + if(!(constr_type == LE || constr_type == GE || constr_type == EQ)) { + report(lp, IMPORTANT, "add_constraintex: Invalid %d constraint type\n", constr_type); +@@ -3155,9 +3155,9 @@ + int i; + char *p, *newp; + REAL *aRow; +- MYBOOL status = FALSE; ++ MYBOOL status = FFALSE; + +- allocREAL(lp, &aRow, lp->columns + 1, FALSE); ++ allocREAL(lp, &aRow, lp->columns + 1, FFALSE); + p = row_string; + + for(i = 1; i <= lp->columns; i++) { +@@ -3215,12 +3215,12 @@ + rownr = -rownr; + if((rownr < 1) || (rownr > lp->rows)) { + report(lp, IMPORTANT, "del_constraint: Attempt to delete non-existing constraint %d\n", rownr); +- return(FALSE); ++ return(FFALSE); + } + /* + if(lp->matA->is_roworder) { + report(lp, IMPORTANT, "del_constraint: Cannot delete constraint while in row entry mode.\n"); +- return(FALSE); ++ return(FFALSE); + } + */ + +@@ -3278,10 +3278,10 @@ + sign = -1; + else { + report(lp, IMPORTANT, "add_lag_con: Constraint type %d not implemented\n", con_type); +- return(FALSE); ++ return(FFALSE); + } + +- inc_lag_space(lp, 1, FALSE); ++ inc_lag_space(lp, 1, FFALSE); + + k = get_Lrows(lp); + lp->lag_rhs[k] = rhs * sign; +@@ -3299,7 +3299,7 @@ + REAL *a_row; + char *p, *new_p; + +- allocREAL(lp, &a_row, lp->columns + 1, FALSE); ++ allocREAL(lp, &a_row, lp->columns + 1, FFALSE); + p = row_string; + + for(i = 1; i <= lp->columns; i++) { +@@ -3307,7 +3307,7 @@ + if(p == new_p) { + report(lp, IMPORTANT, "str_add_lag_con: Bad string '%s'\n", p); + lp->spx_status = DATAIGNORED; +- ret = FALSE; ++ ret = FFALSE; + break; + } + else +@@ -3376,7 +3376,7 @@ + NB! If the column has only one entry, this should be handled as + a bound, but this currently is not the case */ + { +- MYBOOL status = FALSE; ++ MYBOOL status = FFALSE; + + /* Prepare and shift column vectors */ + if(!append_columns(lp, 1)) +@@ -3418,7 +3418,7 @@ + REAL *aCol; + char *p, *newp; + +- allocREAL(lp, &aCol, lp->rows + 1, FALSE); ++ allocREAL(lp, &aCol, lp->rows + 1, FFALSE); + p = col_string; + + for(i = 0; i <= lp->rows; i++) { +@@ -3426,7 +3426,7 @@ + if(p == newp) { + report(lp, IMPORTANT, "str_add_column: Bad string '%s'\n", p); + lp->spx_status = DATAIGNORED; +- ret = FALSE; ++ ret = FFALSE; + break; + } + else +@@ -3507,12 +3507,12 @@ + colnr = -colnr; + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "del_column: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + /* + if(lp->matA->is_roworder) { + report(lp, IMPORTANT, "del_column: Cannot delete column while in row entry mode.\n"); +- return(FALSE); ++ return(FFALSE); + } + */ + +@@ -3565,7 +3565,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "set_upbo: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + + #ifdef DoBorderRounding +@@ -3576,7 +3576,7 @@ + if(lp->tighten_on_set) { + if(value < lp->orig_lowbo[lp->rows + colnr]) { + report(lp, IMPORTANT, "set_upbo: Upperbound must be >= lowerbound\n"); +- return(FALSE); ++ return(FFALSE); + } + if(value < lp->orig_upbo[lp->rows + colnr]) { + set_action(&lp->spx_action, ACTION_REBASE); +@@ -3613,7 +3613,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "set_lowbo: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + + #ifdef DoBorderRounding +@@ -3624,7 +3624,7 @@ + if(lp->tighten_on_set) { + if(value > lp->orig_upbo[lp->rows + colnr]) { + report(lp, IMPORTANT, "set_lowbo: Upper bound must be >= lower bound\n"); +- return(FALSE); ++ return(FFALSE); + } + if((value < 0) || (value > lp->orig_lowbo[lp->rows + colnr])) { + set_action(&lp->spx_action, ACTION_REBASE); +@@ -3661,7 +3661,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "set_bounds: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + if(fabs(upper - lower) < lp->epsvalue) { + if(lower < 0) +@@ -3672,7 +3672,7 @@ + else if(lower > upper) { + report(lp, IMPORTANT, "set_bounds: Column %d upper bound must be >= lower bound\n", + colnr); +- return( FALSE ); ++ return( FFALSE ); + } + + colnr += lp->rows; +@@ -3706,7 +3706,7 @@ + { + if((column > lp->columns) || (column < 1)) { + report(lp, IMPORTANT, "get_bounds: Column %d out of range", column); +- return(FALSE); ++ return(FFALSE); + } + + if(lower != NULL) +@@ -3721,7 +3721,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "set_int: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + + if((lp->var_type[colnr] & ISINTEGER) != 0) { +@@ -3741,7 +3741,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "is_int: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + + return((lp->var_type[colnr] & ISINTEGER) != 0); +@@ -3751,7 +3751,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "is_SOS_var: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + + return((lp->var_type[colnr] & ISSOS) != 0); +@@ -3798,7 +3798,7 @@ + #ifdef Paranoia + if(count < 0) { + report(lp, IMPORTANT, "add_GUB: Invalid GUB member count %d\n", count); +- return(FALSE); ++ return(FFALSE); + } + #endif + +@@ -3816,7 +3816,7 @@ + + MYBOOL __WINAPI set_binary(lprec *lp, int colnr, MYBOOL must_be_bin) + { +- MYBOOL status = FALSE; ++ MYBOOL status = FFALSE; + + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "set_binary: Column %d out of range\n", colnr); +@@ -3833,7 +3833,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "is_binary: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + + return((MYBOOL) (((lp->var_type[colnr] & ISINTEGER) != 0) && +@@ -3845,7 +3845,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "set_unbounded: Column %d out of range\n", colnr); +- return( FALSE ); ++ return( FFALSE ); + } + + return( set_bounds(lp, colnr, -lp->infinite, lp->infinite) ); +@@ -3857,7 +3857,7 @@ + + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "is_unbounded: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + + test = is_splitvar(lp, colnr); +@@ -3873,7 +3873,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "is_negative: Column %d out of range\n", colnr); +- return( FALSE ); ++ return( FFALSE ); + } + + colnr += lp->rows; +@@ -3888,11 +3888,11 @@ + } + if(weights != NULL) { + int n; +- allocINT(lp, &lp->var_priority, lp->columns_alloc, FALSE); ++ allocINT(lp, &lp->var_priority, lp->columns_alloc, FFALSE); + for(n = 0; n < lp->columns; n++) { + lp->var_priority[n] = n+1; + } +- n = sortByREAL(lp->var_priority, weights, lp->columns, 0, FALSE); ++ n = sortByREAL(lp->var_priority, weights, lp->columns, 0, FFALSE); + } + return(TRUE); + } +@@ -3900,7 +3900,7 @@ + MYBOOL __WINAPI set_var_priority(lprec *lp) + /* Experimental automatic variable ordering/priority setting */ + { +- MYBOOL status = FALSE; ++ MYBOOL status = FFALSE; + + if(is_bb_mode(lp, NODE_AUTOORDER) && + (lp->var_priority == NULL) && +@@ -3909,7 +3909,7 @@ + REAL *rcost = NULL; + int i, j, *colorder = NULL; + +- allocINT(lp, &colorder, lp->columns+1, FALSE); ++ allocINT(lp, &colorder, lp->columns+1, FFALSE); + + /* Create an "optimal" B&B variable ordering; this MDO-based routine + returns column indeces in an increasing order of co-dependency. +@@ -3919,10 +3919,10 @@ + colorder[0] = lp->columns; + for(j = 1; j <= lp->columns; j++) + colorder[j] = lp->rows+j; +- i = getMDO(lp, NULL, colorder, NULL, FALSE); ++ i = getMDO(lp, NULL, colorder, NULL, FFALSE); + + /* Map to variable weight */ +- allocREAL(lp, &rcost, lp->columns+1, FALSE); ++ allocREAL(lp, &rcost, lp->columns+1, FFALSE); + for(j = lp->columns; j > 0; j--) { + i = colorder[j]-lp->rows; + rcost[i] = -j; +@@ -3943,7 +3943,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "get_var_priority: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + + if(lp->var_priority == NULL) +@@ -3956,7 +3956,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "set_semicont: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + + if(lp->sc_lobound[colnr] != 0) { +@@ -3975,7 +3975,7 @@ + { + if((colnr > lp->columns) || (colnr < 1)) { + report(lp, IMPORTANT, "is_semicont: Column %d out of range\n", colnr); +- return(FALSE); ++ return(FFALSE); + } + + return((lp->var_type[colnr] & ISSEMI) != 0); +@@ -3985,7 +3985,7 @@ + { + if((rownr > lp->rows) || (rownr < 0)) { + report(lp, IMPORTANT, "set_rh: Row %d out of range\n", rownr); +- return(FALSE); ++ return(FFALSE); + } + + if(((rownr == 0) && (!is_maxim(lp))) || +@@ -4061,7 +4061,7 @@ + { + if(rownr > lp->rows || rownr < 1) { + report(lp, IMPORTANT, "set_rh_upper: Row %d out of range", rownr); +- return(FALSE); ++ return(FFALSE); + } + + /* First scale the value */ +@@ -4077,7 +4077,7 @@ + if(value + lp->orig_rhs[rownr] < 0) { + report(lp, SEVERE, "set_rh_upper: Invalid negative range in row %d\n", + rownr); +- return(FALSE); ++ return(FFALSE); + } + #endif + #ifdef DoBorderRounding +@@ -4106,7 +4106,7 @@ + { + if(rownr > lp->rows || rownr < 1) { + report(lp, IMPORTANT, "set_rh_lower: Row %d out of range", rownr); +- return(FALSE); ++ return(FFALSE); + } + + /* First scale the value */ +@@ -4122,7 +4122,7 @@ + if(lp->orig_rhs[rownr] - value < 0) { + report(lp, SEVERE, "set_rh_lower: Invalid negative range in row %d\n", + rownr); +- return(FALSE); ++ return(FFALSE); + } + #endif + #ifdef DoBorderRounding +@@ -4152,7 +4152,7 @@ + { + if((rownr > lp->rows) || (rownr < 1)) { + report(lp, IMPORTANT, "set_rh_range: Row %d out of range", rownr); +- return(FALSE); ++ return(FFALSE); + } + + deltavalue = scaled_value(lp, deltavalue, rownr); +@@ -4189,7 +4189,7 @@ + { + if((rownr > lp->rows) || (rownr < 0)) { + report(lp, IMPORTANT, "get_rh_range: row %d out of range\n", rownr); +- return(FALSE); ++ return(FFALSE); + } + + if(lp->orig_upbo[rownr] >= lp->infinite) +@@ -4228,7 +4228,7 @@ + if(p == newp) { + report(lp, IMPORTANT, "str_set_rh_vec: Bad string %s\n", p); + lp->spx_status = DATAIGNORED; +- ret = FALSE; ++ ret = FFALSE; + break; + } + else +@@ -4242,7 +4242,7 @@ + + void __WINAPI set_sense(lprec *lp, MYBOOL maximize) + { +- maximize = (MYBOOL) (maximize != FALSE); ++ maximize = (MYBOOL) (maximize != FFALSE); + if(is_maxim(lp) != maximize) { + int i; + if(is_infinite(lp, lp->bb_heuristicOF)) +@@ -4267,7 +4267,7 @@ + + void __WINAPI set_minim(lprec *lp) + { +- set_sense(lp, FALSE); ++ set_sense(lp, FFALSE); + } + + MYBOOL __WINAPI is_maxim(lprec *lp) +@@ -4282,12 +4282,12 @@ + + if(rownr > lp->rows+1 || rownr < 1) { + report(lp, IMPORTANT, "set_constr_type: Row %d out of range\n", rownr); +- return( FALSE ); ++ return( FFALSE ); + } + + /* Prepare for a new row */ + if((rownr > lp->rows) && !append_rows(lp, rownr-lp->rows)) +- return( FALSE ); ++ return( FFALSE ); + + /* Update the constraint type data */ + if(is_constr_type(lp, rownr, EQ)) +@@ -4302,7 +4302,7 @@ + else { + report(lp, IMPORTANT, "set_constr_type: Constraint type %d not implemented (row %d)\n", + con_type, rownr); +- return( FALSE ); ++ return( FFALSE ); + } + + /* Change the signs of the row, if necessary */ +@@ -4315,7 +4315,7 @@ + MATrec *mat = lp->matA; + + if(mat->is_roworder) +- mat_multcol(mat, rownr, -1, FALSE); ++ mat_multcol(mat, rownr, -1, FFALSE); + else + mat_multrow(mat, rownr, -1); + if(lp->orig_rhs[rownr] != 0) +@@ -4326,7 +4326,7 @@ + lp->orig_rhs[rownr] = lp->infinite; + + set_action(&lp->spx_action, ACTION_REINVERT); +- lp->basis_valid = FALSE; ++ lp->basis_valid = FFALSE; + + return( TRUE ); + } +@@ -4340,7 +4340,7 @@ + { + if((rownr < 0) || (rownr > lp->rows)) { + report(lp, IMPORTANT, "is_constr_type: Row %d out of range\n", rownr); +- return( FALSE ); ++ return( FFALSE ); + } + return( (MYBOOL) ((lp->row_type[rownr] & ROWTYPE_CONSTRAINT) == mask)); + } +@@ -4590,7 +4590,7 @@ + } + } + else { +- MYBOOL chsign = FALSE; ++ MYBOOL chsign = FFALSE; + int ie, i; + MATrec *mat = lp->matA; + +@@ -4616,7 +4616,7 @@ + chsign = is_chsign(lp, rownr); + for(; i < ie; i++) { + j = ROW_MAT_COLNR(i); +- a = get_mat_byindex(lp, i, TRUE, FALSE); ++ a = get_mat_byindex(lp, i, TRUE, FFALSE); + if(lp->matA->is_roworder) + chsign = is_chsign(lp, j); + a = my_chsign(chsign, a); +@@ -4732,13 +4732,13 @@ + #ifndef Phase1EliminateRedundant + if(lp->P1extraDim < 0) { + if(index > lp->sum + lp->P1extraDim) +- accept = FALSE; ++ accept = FFALSE; + } + else + #endif + if((index <= lp->sum - lp->P1extraDim) || (mult == 0)) { + if((mult == 0) || (lp->bigM == 0)) +- accept = FALSE; ++ accept = FFALSE; + else + (*ofValue) /= lp->bigM; + } +@@ -4766,7 +4766,7 @@ + (*ofValue) *= mult; + if(fabs(*ofValue) < lp->epsmachine) { + (*ofValue) = 0; +- accept = FALSE; ++ accept = FFALSE; + } + } + else +@@ -5212,7 +5212,7 @@ + MYBOOL __WINAPI is_nativeBFP(lprec *lp) + { + #ifdef ExcludeNativeInverse +- return( FALSE ); ++ return( FFALSE ); + #elif LoadInverseLib == TRUE + return( (MYBOOL) (lp->hBFP == NULL) ); + #else +@@ -5242,7 +5242,7 @@ + + if(filename == NULL) { + if(!is_nativeBFP(lp)) +- return( FALSE ); ++ return( FFALSE ); + #ifndef ExcludeNativeInverse + lp->bfp_name = bfp_name; + lp->bfp_compatible = bfp_compatible; +@@ -5566,7 +5566,7 @@ + MYBOOL __WINAPI is_nativeXLI(lprec *lp) + { + #ifdef ExcludeNativeLanguage +- return( FALSE ); ++ return( FFALSE ); + #elif LoadLanguageLib == TRUE + return( (MYBOOL) (lp->hXLI == NULL) ); + #else +@@ -5592,7 +5592,7 @@ + + if(filename == NULL) { + if(!is_nativeXLI(lp)) +- return( FALSE ); ++ return( FFALSE ); + #ifndef ExcludeNativeLanguage + lp->xli_name = xli_name; + lp->xli_compatible = xli_compatible; +@@ -5798,7 +5798,7 @@ + ; + else if(!lp->basis_valid) { + report(lp, CRITICAL, "get_primal_solution: Not a valid basis"); +- return(FALSE); ++ return(FFALSE); + } + + MEMCOPY(pv, lp->best_solution, lp->sum + 1); +@@ -5818,7 +5818,7 @@ + + if(!lp->basis_valid) { + report(lp, CRITICAL, "get_dual_solution: Not a valid basis"); +- return(FALSE); ++ return(FFALSE); + } + + ret = get_ptr_sensitivity_rhs(lp, &duals, NULL, NULL); +@@ -5853,7 +5853,7 @@ + { + if(!lp->basis_valid || (get_Lrows(lp) == 0)) { + report(lp, CRITICAL, "get_lambda: Not a valid basis"); +- return(FALSE); ++ return(FFALSE); + } + + MEMCOPY(lambda, lp->lambda+1, get_Lrows(lp)); +@@ -5898,7 +5898,7 @@ + if(values[i - lp->rows] < unscaled_value(lp, lp->orig_lowbo[i], i) + || values[i - lp->rows] > unscaled_value(lp, lp->orig_upbo[i], i)) { + if(!((lp->sc_lobound[i - lp->rows]>0) && (values[i - lp->rows]==0))) +- return(FALSE); ++ return(FFALSE); + } + } + +@@ -5918,10 +5918,10 @@ + my_roundzero(dist, threshold); + if((lp->orig_upbo[i] == 0 && dist != 0) ||( dist < 0)) { + FREE(this_rhs); +- return(FALSE); ++ return(FFALSE); + } + } +- mempool_releaseVector(lp->workarrays, (char *) this_rhs, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) this_rhs, FFALSE); + /* FREE(this_rhs); */ + return(TRUE); + } +@@ -6034,24 +6034,24 @@ + int __WINAPI get_nameindex(lprec *lp, char *varname, MYBOOL isrow) + { + if(isrow) +- return( find_row(lp, varname, FALSE) ); ++ return( find_row(lp, varname, FFALSE) ); + else +- return( find_var(lp, varname, FALSE) ); ++ return( find_var(lp, varname, FFALSE) ); + } + + MYBOOL __WINAPI set_row_name(lprec *lp, int rownr, char *new_name) + { + if((rownr < 0) || (rownr > lp->rows+1)) { + report(lp, IMPORTANT, "set_row_name: Row %d out of range", rownr); +- return(FALSE); ++ return(FFALSE); + } + + /* Prepare for a new row */ + if((rownr > lp->rows) && !append_rows(lp, rownr-lp->rows)) +- return( FALSE ); ++ return( FFALSE ); + if(!lp->names_used) { + if(!init_rowcol_names(lp)) +- return(FALSE); ++ return(FFALSE); + } + rename_var(lp, rownr, new_name, lp->row_name, &lp->rowname_hashtab); + +@@ -6100,7 +6100,7 @@ + } + else { + if(lp->rowcol_name == NULL) +- if (!allocCHAR(lp, &lp->rowcol_name, 20, FALSE)) ++ if (!allocCHAR(lp, &lp->rowcol_name, 20, FFALSE)) + return(NULL); + ptr = lp->rowcol_name; + if(newrow) +@@ -6118,7 +6118,7 @@ + } + + if((colnr > lp->columns) && !append_columns(lp, colnr-lp->columns)) +- return(FALSE); ++ return(FFALSE); + + if(!lp->names_used) + init_rowcol_names(lp); +@@ -6168,7 +6168,7 @@ + } + else { + if(lp->rowcol_name == NULL) +- if (!allocCHAR(lp, &lp->rowcol_name, 20, FALSE)) ++ if (!allocCHAR(lp, &lp->rowcol_name, 20, FFALSE)) + return(NULL); + ptr = lp->rowcol_name; + if(newcol) +@@ -6320,14 +6320,14 @@ + + /* Define variable target list and compute the reduced costs */ + coltarget = (int *) mempool_obtainVector(lp->workarrays, lp->columns+1, sizeof(*coltarget)); +- if(!get_colIndexA(lp, target, coltarget, FALSE)) { +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); +- return(FALSE); ++ if(!get_colIndexA(lp, target, coltarget, FFALSE)) { ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); ++ return(FFALSE); + } + bsolve(lp, 0, *duals, NULL, lp->epsmachine*DOUBLEROUND, 1.0); + prod_xA(lp, coltarget, *duals, NULL, lp->epsmachine, 1.0, + *duals, *nzduals, MAT_ROUNDDEFAULT | MAT_ROUNDRC); +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); + + /* Compute sum or maximum infeasibility as specified */ + for(i = 1; i <= (*nzduals)[0]; i++) { +@@ -6465,7 +6465,7 @@ + if(rownr == 0) + *pivcolval = unscaled_mat(lp, lp->orig_obj[jb], 0, jb); + else +- *pivcolval = get_mat_byindex(lp, jb, TRUE, FALSE); ++ *pivcolval = get_mat_byindex(lp, jb, TRUE, FFALSE); + continue; + } + if(!is_int(lp, jj)) +@@ -6478,7 +6478,7 @@ + if(rownr == 0) + rowval = unscaled_mat(lp, lp->orig_obj[jb], 0, jb); + else +- rowval = get_mat_byindex(lp, jb, TRUE, FALSE); ++ rowval = get_mat_byindex(lp, jb, TRUE, FFALSE); + if(rowval > 0) + (*plucount)++; + +@@ -6740,11 +6740,11 @@ + if(rownr == 0) + rowval = unscaled_mat(lp, obj_orig[jj], 0, jj); + else +- rowval = get_mat_byindex(lp, j, TRUE, FALSE); ++ rowval = get_mat_byindex(lp, j, TRUE, FFALSE); + + /* Allocate array of coefficients to be sorted */ + if(n == 0) +- allocREAL(lp, &obj_sort, je-jb, FALSE); ++ allocREAL(lp, &obj_sort, je-jb, FFALSE); + + obj_sort[n++] = rowval; + } +@@ -6767,7 +6767,7 @@ + while(n > 0) { + + /* Sort the coefficients in ascending order */ +- qsortex(obj_sort, n, 0, sizeof(*obj_sort), FALSE, compareREAL, NULL, 0); ++ qsortex(obj_sort, n, 0, sizeof(*obj_sort), FFALSE, compareREAL, NULL, 0); + + /* Eliminate array duplicates (could consider applying an eps) */ + j = 0; jb = 1; +@@ -6925,7 +6925,7 @@ + (fabs(lp->upbo[varindex]-lp->rhs[basisvar]) < lp->epsprimal)) + return( TRUE ); + else +- return( FALSE ); ++ return( FFALSE ); + } + + STATIC int findBasicFixedvar(lprec *lp, int afternr, MYBOOL slacksonly) +@@ -6958,15 +6958,15 @@ + int col; + REAL x; + MYBOOL Ok = TRUE; +- MYBOOL doSC = FALSE; ++ MYBOOL doSC = FFALSE; + + col = lp->var_basic[basis_row]; + x = lp->rhs[basis_row]; /* The current solution of basic variables stored here! */ + if((x < -tol) || (x > lp->upbo[col]+tol)) +- Ok = FALSE; ++ Ok = FFALSE; + else if(doSC && (col > lp->rows) && (fabs(lp->sc_lobound[col - lp->rows]) > 0)) { + if((x > tol) && (x < fabs(lp->sc_lobound[col - lp->rows])-tol)) +- Ok = FALSE; ++ Ok = FFALSE; + } + return( Ok ); + } +@@ -6993,7 +6993,7 @@ + feasible = TRUE; + /* if(((*rhsptr) < lp->lowbo[*idxptr]-tol) || ((*rhsptr) > lp->upbo[*idxptr]+tol)) */ + if(((*rhsptr) < -tol) || ((*rhsptr) > lp->upbo[*idxptr]+tol)) +- feasible = FALSE; ++ feasible = FFALSE; + #endif + if(!feasible) { + if(infeasibles == NULL) +@@ -7008,7 +7008,7 @@ + if(feasible) + *feasibilitygap = 0.0; + else +- *feasibilitygap = feasibilityOffset(lp, FALSE); ++ *feasibilitygap = feasibilityOffset(lp, FFALSE); + } + + return(feasible); +@@ -7033,7 +7033,7 @@ + int *nzdcol = NULL; + REAL d, *dcol = NULL; + +- f = compute_dualslacks(lp, target, &dcol, &nzdcol, FALSE); ++ f = compute_dualslacks(lp, target, &dcol, &nzdcol, FFALSE); + if(nzdcol != NULL) + for(i = 1; i <= nzdcol[0]; i++) { + varnr = nzdcol[i]; +@@ -7073,7 +7073,7 @@ + } + } + else +- f = compute_dualslacks(lp, target, NULL, NULL, FALSE); ++ f = compute_dualslacks(lp, target, NULL, NULL, FFALSE); + /* f = feasibilityOffset(lp, TRUE); */ /* Safe legacy mode */ + + /* Do an extra scan to see if there are bounded variables in the OF not present in any constraint; +@@ -7125,7 +7125,7 @@ + /* Set user variables at their lower bound, including the + dummy slack for the objective "constraint" */ + for(; i <= lp->sum; i++) { +- lp->is_basic[i] = FALSE; ++ lp->is_basic[i] = FFALSE; + lp->is_lower[i] = TRUE; + } + lp->is_lower[0] = TRUE; +@@ -7151,7 +7151,7 @@ + /* Make sure we are consistent */ + if(lp->wasPresolved && ((lp->rows != lp->presolve_undo->orig_rows) || + (lp->columns != lp->presolve_undo->orig_columns))) +- return( FALSE ); ++ return( FFALSE ); + + /* Initialize (lp->is_basic is set in preprocess); Note that as of v5 and before + it is an lp_solve convention that basic variables are at their lower bounds! +@@ -7160,10 +7160,10 @@ + lp->is_lower[0] = TRUE; + for(i = 1; i <= lp->sum; i++) { + lp->is_lower[i] = TRUE; +- lp->is_basic[i] = FALSE; ++ lp->is_basic[i] = FFALSE; + } + for(i = 1; i <= lp->rows; i++) +- lp->var_basic[i] = FALSE; ++ lp->var_basic[i] = FFALSE; + + /* Set basic and optionally non-basic variables; + negative index means at lower bound, positive at upper bound */ +@@ -7175,29 +7175,29 @@ + s = bascolumn[i]; + k = abs(s); + if(k <= 0 || k > lp->sum) +- return( FALSE ); ++ return( FFALSE ); + if(i <= lp->rows) { + lp->var_basic[i] = k; + lp->is_basic[k] = TRUE; + } + else /* Remove this test if basic variables can be upper-bounded */ + if(s > 0) +- lp->is_lower[k] = FALSE; ++ lp->is_lower[k] = FFALSE; + } + if(!verify_basis(lp)) +- return( FALSE ); ++ return( FFALSE ); + + /* Invalidate basis */ + set_action(&lp->spx_action, ACTION_REBASE | ACTION_REINVERT | ACTION_RECOMPUTE); + lp->basis_valid = TRUE; /* Do not re-initialize basis on entering Solve */ +- lp->var_basic[0] = FALSE; /* Set to signal that this is a non-default basis */ ++ lp->var_basic[0] = FFALSE; /* Set to signal that this is a non-default basis */ + + return( TRUE ); + } + + void __WINAPI reset_basis(lprec *lp) + { +- lp->basis_valid = FALSE; /* Causes reinversion at next opportunity */ ++ lp->basis_valid = FFALSE; /* Causes reinversion at next opportunity */ + } + + MYBOOL __WINAPI get_basis(lprec *lp, int *bascolumn, MYBOOL nonbasic) +@@ -7207,7 +7207,7 @@ + if(!lp->basis_valid || + (lp->rows != lp->presolve_undo->orig_rows) || + (lp->columns != lp->presolve_undo->orig_columns)) +- return( FALSE ); ++ return( FFALSE ); + + *bascolumn = 0; + +@@ -7262,7 +7262,7 @@ + STATIC MYBOOL verify_basis(lprec *lp) + { + int i, ii, k = 0; +- MYBOOL result = FALSE; ++ MYBOOL result = FFALSE; + + for(i = 1; i <= lp->rows; i++) { + ii = lp->var_basic[i]; +@@ -7315,9 +7315,9 @@ + enteringCol, (double) get_total_iter(lp)); + #endif + +- lp->var_basic[0] = FALSE; /* Set to signal that this is a non-default basis */ ++ lp->var_basic[0] = FFALSE; /* Set to signal that this is a non-default basis */ + lp->var_basic[basisPos] = enteringCol; +- lp->is_basic[leavingCol] = FALSE; ++ lp->is_basic[leavingCol] = FFALSE; + lp->is_basic[enteringCol] = TRUE; + if(lp->bb_basis != NULL) + lp->bb_basis->pivots++; +@@ -7397,7 +7397,7 @@ + if((lowbo != NULL) && (lowbo != lp->lowbo)) + MEMCOPY(lp->lowbo, lowbo, lp->sum + 1); + if(lp->bb_bounds != NULL) +- lp->bb_bounds->UBzerobased = FALSE; ++ lp->bb_bounds->UBzerobased = FFALSE; + set_action(&lp->spx_action, ACTION_REBASE); + } + set_action(&lp->spx_action, ACTION_RECOMPUTE); +@@ -7442,14 +7442,14 @@ + newbasis = (basisrec *) calloc(sizeof(*newbasis), 1); + if((newbasis != NULL) && + #if LowerStorageModel == 0 +- allocMYBOOL(lp, &newbasis->is_lower, sum, FALSE) && ++ allocMYBOOL(lp, &newbasis->is_lower, sum, FFALSE) && + #else + allocMYBOOL(lp, &newbasis->is_lower, (sum + 8) / 8, TRUE) && + #endif + #if BasisStorageModel == 0 +- allocMYBOOL(lp, &newbasis->is_basic, sum, FALSE) && ++ allocMYBOOL(lp, &newbasis->is_basic, sum, FFALSE) && + #endif +- allocINT(lp, &newbasis->var_basic, lp->rows + 1, FALSE)) { ++ allocINT(lp, &newbasis->var_basic, lp->rows + 1, FFALSE)) { + + if(islower == NULL) + islower = lp->is_lower; +@@ -7489,7 +7489,7 @@ + MYBOOL same_basis = TRUE; + + if(lp->bb_basis == NULL) +- return( FALSE ); ++ return( FFALSE ); + + /* Loop over basis variables until a mismatch (order can be different) */ + i = 1; +@@ -7744,7 +7744,7 @@ + i, k); + #endif + j = lp->rows + i; +- if(!SOS_is_marked(lp->SOS, 0, i) && !SOS_is_full(lp->SOS, 0, i, FALSE)) { ++ if(!SOS_is_marked(lp->SOS, 0, i) && !SOS_is_full(lp->SOS, 0, i, FFALSE)) { + /* if(!SOS_is_marked(lp->SOS, 0, i) && !SOS_is_full(lp->SOS, 0, i, TRUE)) { */ + if(!intsos || is_int(lp, i)) { + (*count)++; +@@ -7788,16 +7788,16 @@ + depthfirstmode = is_bb_mode(lp, NODE_DEPTHFIRSTMODE); + breadthfirstmode = is_bb_mode(lp, NODE_BREADTHFIRSTMODE) && + (MYBOOL) (lp->bb_level <= lp->int_vars); +- rcostmode = (MYBOOL) /* FALSE */ (BB->lp->solutioncount > 0) && is_bb_mode(lp, NODE_RCOSTFIXING) ; /* 5/2/08 peno disabled NODE_RCOSTFIXING because it results in non-optimal solutions with some models */ /* 15/2/8 peno enabled NODE_RCOSTFIXING again because a fix is found. See lp_simplex.c NODE__RCOSTFIXING fix */ ++ rcostmode = (MYBOOL) /* FFALSE */ (BB->lp->solutioncount > 0) && is_bb_mode(lp, NODE_RCOSTFIXING) ; /* 5/2/08 peno disabled NODE_RCOSTFIXING because it results in non-optimal solutions with some models */ /* 15/2/8 peno enabled NODE_RCOSTFIXING again because a fix is found. See lp_simplex.c NODE__RCOSTFIXING fix */ + pseudocostmode = is_bb_mode(lp, NODE_PSEUDOCOSTMODE); + pseudocostsel = is_bb_rule(lp, NODE_PSEUDOCOSTSELECT) || + is_bb_rule(lp, NODE_PSEUDONONINTSELECT) || + is_bb_rule(lp, NODE_PSEUDORATIOSELECT); +- pseudostrong = FALSE && ++ pseudostrong = FFALSE && + pseudocostsel && !rcostmode && is_bb_mode(lp, NODE_STRONGINIT); + + /* Fill list of non-ints */ +- allocINT(lp, &nonint, lp->columns + 1, FALSE); ++ allocINT(lp, &nonint, lp->columns + 1, FFALSE); + n = 0; + depthmax = -1; + if(isfeasible != NULL) +@@ -7820,7 +7820,7 @@ + } + else { + +- valINT = solution_is_int(lp, i, FALSE); ++ valINT = solution_is_int(lp, i, FFALSE); + + /* Skip already fixed variables */ + if(lowbo[i] == upbo[i]) { +@@ -7871,7 +7871,7 @@ + for(i = 1; (i <= lp->rows) && (BB->lastrcf == 0); i++) { + /* Skip already fixed slacks (equalities) */ + if(lowbo[i] < upbo[i]) { +- bestvar = rcfbound_BB(BB, i, FALSE, NULL, isfeasible); ++ bestvar = rcfbound_BB(BB, i, FFALSE, NULL, isfeasible); + if(bestvar != FR) + BB->lastrcf++; + } +@@ -7893,7 +7893,7 @@ + int *depths = NULL; + + /* Fill attribute array and make sure ordinal order breaks ties during sort */ +- allocINT(lp, &depths, n + 1, FALSE); ++ allocINT(lp, &depths, n + 1, FFALSE); + for(i = 1; i <= n; i++) + depths[i] = (depthfirstmode ? n+1-i : i) + (n+1)*lp->bb_varactive[nonint[i]]; + hpsortex(depths, n, 1, sizeof(*nonint), depthfirstmode, compareINT, nonint); +@@ -8076,7 +8076,7 @@ + int i; + + if((lp->bb_PseudoCost == NULL) || ((clower == NULL) && (cupper == NULL))) +- return(FALSE); ++ return(FFALSE); + for(i = 1; i <= lp->columns; i++) { + if(clower != NULL) + lp->bb_PseudoCost->LOcost[i].value = clower[i]; +@@ -8093,7 +8093,7 @@ + int i; + + if((lp->bb_PseudoCost == NULL) || ((clower == NULL) && (cupper == NULL))) +- return(FALSE); ++ return(FFALSE); + for(i = 1; i <= lp->columns; i++) { + if(clower != NULL) + clower[i] = lp->bb_PseudoCost->LOcost[i].value; +@@ -8296,9 +8296,9 @@ + { + int varout; + REAL pivot, epsmargin, leavingValue, leavingUB, enteringUB; +- MYBOOL leavingToUB = FALSE, enteringFromUB, enteringIsFixed, leavingIsFixed; ++ MYBOOL leavingToUB = FFALSE, enteringFromUB, enteringIsFixed, leavingIsFixed; + MYBOOL *islower = &(lp->is_lower[varin]); +- MYBOOL minitNow = FALSE, minitStatus = ITERATE_MAJORMAJOR; ++ MYBOOL minitNow = FFALSE, minitStatus = ITERATE_MAJORMAJOR; + LREAL deltatheta = theta; + + if(userabort(lp, MSG_ITERATION)) +@@ -8309,7 +8309,7 @@ + if (lp->spx_trace) + report(lp, IMPORTANT, "performiteration: Numeric instability encountered!\n"); + lp->spx_status = NUMFAILURE; +- return( FALSE ); ++ return( FFALSE ); + } + #endif + varout = lp->var_basic[rownr]; +@@ -8453,7 +8453,7 @@ + lp->rhs[0], (double) get_total_iter(lp)); + + #if 0 +- if(verify_solution(lp, FALSE, my_if(minitNow, "MINOR", "MAJOR")) >= 0) { ++ if(verify_solution(lp, FFALSE, my_if(minitNow, "MINOR", "MAJOR")) >= 0) { + if(minitNow) + pivot = get_obj_active(lp, varin); + else +@@ -8562,7 +8562,7 @@ + else + return(TRUE); + } +- return(FALSE); ++ return(FFALSE); + #endif + } /* solution_is_int */ + +@@ -8760,7 +8760,7 @@ + case OF_DUALLIMIT: refvalue = lp->bb_limitOF; + break; + default : report(lp, SEVERE, "bb_better: Passed invalid test target '%d'\n", target); +- return( FALSE ); ++ return( FFALSE ); + } + + /* Adjust the test value for the desired acceptability window */ +@@ -8968,7 +8968,7 @@ + + /* Find the signed sums and the largest absolute product in the matrix (exclude the OF for speed) */ + #ifdef UseMaxValueInCheck +- allocREAL(lp, &maxvalue, lp->rows + 1, FALSE); ++ allocREAL(lp, &maxvalue, lp->rows + 1, FFALSE); + for(i = 0; i <= lp->rows; i++) + maxvalue[i] = fabs(get_rh(lp, i)); + #elif !defined RelativeAccuracyCheck +@@ -9280,18 +9280,18 @@ + if(is_action(lp->spx_action, ACTION_REBASE) || + is_action(lp->spx_action, ACTION_REINVERT) || (!lp->basis_valid) || + !allocREAL(lp, &(lp->duals), lp->sum + 1, AUTOMATIC)) +- return(FALSE); ++ return(FFALSE); + + /* Initialize */ + coltarget = (int *) mempool_obtainVector(lp->workarrays, lp->columns+1, sizeof(*coltarget)); +- if(!get_colIndexA(lp, SCAN_USERVARS+USE_NONBASICVARS, coltarget, FALSE)) { +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); +- return(FALSE); ++ if(!get_colIndexA(lp, SCAN_USERVARS+USE_NONBASICVARS, coltarget, FFALSE)) { ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); ++ return(FFALSE); + } + bsolve(lp, 0, lp->duals, NULL, lp->epsmachine*DOUBLEROUND, 1.0); + prod_xA(lp, coltarget, lp->duals, NULL, lp->epsmachine, 1.0, + lp->duals, NULL, MAT_ROUNDDEFAULT | MAT_ROUNDRC); +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); + + + /* The (Lagrangean) dual values are the reduced costs of the primal slacks; +@@ -9329,7 +9329,7 @@ + #endif + lp->full_duals[i] = lp->duals[ix]; + } +- presolve_rebuildUndo(lp, FALSE); ++ presolve_rebuildUndo(lp, FFALSE); + } + + /* Calculate the dual OF and do scaling adjustments to the duals */ +@@ -9384,7 +9384,7 @@ + FREE(lp->objfromvalue); + FREE(lp->dualsfrom); + FREE(lp->dualstill); +- ok = FALSE; ++ ok = FFALSE; + } + else { + infinite=lp->infinite; +@@ -9394,8 +9394,8 @@ + till=infinite; + objfromvalue=infinite; + if (!lp->is_basic[varnr]) { +- if (!fsolve(lp, varnr, pcol, workINT, epsvalue, 1.0, FALSE)) { /* construct one column of the tableau */ +- ok = FALSE; ++ if (!fsolve(lp, varnr, pcol, workINT, epsvalue, 1.0, FFALSE)) { /* construct one column of the tableau */ ++ ok = FFALSE; + break; + } + /* Search for the rows(s) which first result in further iterations */ +@@ -9470,7 +9470,7 @@ + FREE(lp->objfrom); + FREE(lp->objtill); + if(!allocREAL(lp, &drow, lp->sum + 1, TRUE) || +- !allocREAL(lp, &OrigObj, lp->columns + 1, FALSE) || ++ !allocREAL(lp, &OrigObj, lp->columns + 1, FFALSE) || + !allocREAL(lp, &prow, lp->sum + 1, TRUE) || + !allocREAL(lp, &lp->objfrom, lp->columns + 1, AUTOMATIC) || + !allocREAL(lp, &lp->objtill, lp->columns + 1, AUTOMATIC)) { +@@ -9480,7 +9480,7 @@ + FREE(prow); + FREE(lp->objfrom); + FREE(lp->objtill); +- ok = FALSE; ++ ok = FFALSE; + } + else { + int *coltarget; +@@ -9489,8 +9489,8 @@ + epsvalue=lp->epsmachine; + + coltarget = (int *) mempool_obtainVector(lp->workarrays, lp->columns+1, sizeof(*coltarget)); +- if(!get_colIndexA(lp, SCAN_USERVARS+USE_NONBASICVARS, coltarget, FALSE)) { +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); ++ if(!get_colIndexA(lp, SCAN_USERVARS+USE_NONBASICVARS, coltarget, FFALSE)) { ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); + goto Abandon; + } + bsolve(lp, 0, drow, NULL, epsvalue*DOUBLEROUND, 1.0); +@@ -9510,7 +9510,7 @@ + a = -a; + if ((!sensrejvar) && (lp->upbo[varnr] == 0.0)) + /* ignore, because this case doesn't results in further iterations */ ; +- else if(((lp->is_lower[varnr] != 0) == (is_maxim(lp) == FALSE)) && (a > -epsvalue)) ++ else if(((lp->is_lower[varnr] != 0) == (is_maxim(lp) == FFALSE)) && (a > -epsvalue)) + from = OrigObj[i] - a; /* less than this value gives further iterations */ + else + till = OrigObj[i] - a; /* bigger than this value gives further iterations */ +@@ -9542,7 +9542,7 @@ + min2 = a; + } + } +- if ((lp->is_lower[varnr] == 0) == (is_maxim(lp) == FALSE)) { ++ if ((lp->is_lower[varnr] == 0) == (is_maxim(lp) == FFALSE)) { + a = min1; + min1 = min2; + min2 = a; +@@ -9569,7 +9569,7 @@ + lp->objfrom[i]=from; + lp->objtill[i]=till; + } +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); + } + FREE(prow); + FREE(OrigObj); +@@ -9586,7 +9586,7 @@ + else if (pivcount < 2*DEF_MAXPIVOTRETRY) + return( TRUE ); + else +- return( FALSE ); ++ return( FFALSE ); + } + + STATIC MYBOOL check_if_less(lprec *lp, REAL x, REAL y, int variable) +@@ -9595,7 +9595,7 @@ + if(lp->bb_trace) + report(lp, NORMAL, "check_if_less: Invalid new bound %g should be < %g for %s\n", + x, y, get_col_name(lp, variable)); +- return(FALSE); ++ return(FFALSE); + } + else + return(TRUE); +@@ -9631,7 +9631,7 @@ + + out = var_basic[rownr]; + var_basic[rownr] = var; +- is_basic[out] = FALSE; ++ is_basic[out] = FFALSE; + is_basic[var] = TRUE; + } + +@@ -9803,15 +9803,15 @@ + int i, ii, n, *oldmap, *newmap, *refmap = NULL; + REAL *oldrhs, err, errmax; + +- allocINT(lp, &oldmap, lp->rows+1, FALSE); +- allocINT(lp, &newmap, lp->rows+1, FALSE); +- allocREAL(lp, &oldrhs, lp->rows+1, FALSE); ++ allocINT(lp, &oldmap, lp->rows+1, FFALSE); ++ allocINT(lp, &newmap, lp->rows+1, FFALSE); ++ allocREAL(lp, &oldrhs, lp->rows+1, FFALSE); + + /* Get sorted mapping of the old basis */ + for(i = 0; i <= lp->rows; i++) + oldmap[i] = i; + if(reinvert) { +- allocINT(lp, &refmap, lp->rows+1, FALSE); ++ allocINT(lp, &refmap, lp->rows+1, FFALSE); + MEMCOPY(refmap, lp->var_basic, lp->rows+1); + sortByINT(oldmap, refmap, lp->rows, 1, TRUE); + } +@@ -9819,7 +9819,7 @@ + /* Save old and calculate the new RHS vector */ + MEMCOPY(oldrhs, lp->rhs, lp->rows+1); + if(reinvert) +- invert(lp, INITSOL_USEZERO, FALSE); ++ invert(lp, INITSOL_USEZERO, FFALSE); + else + recompute_solution(lp, INITSOL_USEZERO); + +@@ -9905,7 +9905,7 @@ + if(knint > 1) + break; + +- mv = get_mat_byindex(lp, jb, TRUE, FALSE); ++ mv = get_mat_byindex(lp, jb, TRUE, FFALSE); + if(fabs(my_reldiff(mv, rh)) > lp->epsprimal) + break; + +@@ -10006,7 +10006,7 @@ + if(lp->constraintOF) { + del_constraint(lp, lp->rows); + if(is_BasisReady(lp) && !verify_basis(lp)) +- return( FALSE ); ++ return( FFALSE ); + } + */ + #endif +@@ -10035,16 +10035,16 @@ + doPP = is_piv_mode(lp, PRICE_PARTIAL | PRICE_AUTOPARTIAL); + /* doPP &= (MYBOOL) (lp->columns / 2 > lp->rows); */ + if(doPP) { +- i = partial_findBlocks(lp, FALSE, FALSE); ++ i = partial_findBlocks(lp, FFALSE, FFALSE); + if(i < 4) + i = (int) (5 * log((REAL) lp->columns / lp->rows)); + report(lp, NORMAL, "The model is %s to have %d column blocks/stages.\n", + (i > 1 ? "estimated" : "set"), i); +- set_partialprice(lp, i, NULL, FALSE); ++ set_partialprice(lp, i, NULL, FFALSE); + } + /* doPP &= (MYBOOL) (lp->rows / 4 > lp->columns); */ + if(doPP) { +- i = partial_findBlocks(lp, FALSE, TRUE); ++ i = partial_findBlocks(lp, FFALSE, TRUE); + if(i < 4) + i = (int) (5 * log((REAL) lp->rows / lp->columns)); + report(lp, NORMAL, "The model is %s to have %d row blocks/stages.\n", +@@ -10114,7 +10114,7 @@ + (hold < -lp->negrange) && + (lp->orig_lowbo[i] <= lp->negrange)) ) { + */ +-#define fullybounded FALSE ++#define fullybounded FFALSE + if( ((hold < lp->infinite) && my_infinite(lp, lp->orig_lowbo[i])) || + (!fullybounded && !my_infinite(lp, lp->negrange) && + (hold < -lp->negrange) && (lp->orig_lowbo[i] <= lp->negrange)) ) { +@@ -10125,7 +10125,7 @@ + mat_multcol(lp->matA, j, -1, TRUE); + if(lp->var_is_free == NULL) { + if(!allocINT(lp, &lp->var_is_free, MAX(lp->columns, lp->columns_alloc) + 1, TRUE)) +- return(FALSE); ++ return(FFALSE); + } + lp->var_is_free[j] = -j; /* Indicator UB and LB are switched, with no helper variable added */ + lp->orig_upbo[i] = my_flipsign(lp->orig_lowbo[i]); +@@ -10140,7 +10140,7 @@ + else if((lp->orig_lowbo[i] <= lp->negrange) && (hold >= -lp->negrange)) { + if(lp->var_is_free == NULL) { + if(!allocINT(lp, &lp->var_is_free, MAX(lp->columns,lp->columns_alloc) + 1, TRUE)) +- return(FALSE); ++ return(FFALSE); + } + if(lp->var_is_free[j] <= 0) { /* If this variable wasn't split yet ... */ + if(SOS_is_member(lp->SOS, 0, i - lp->rows)) { /* Added */ +@@ -10150,9 +10150,9 @@ + continue; + } + if(new_column == NULL) { +- if(!allocREAL(lp, &new_column, lp->rows + 1, FALSE) || +- !allocINT(lp, &new_index, lp->rows + 1, FALSE)) { +- ok = FALSE; ++ if(!allocREAL(lp, &new_column, lp->rows + 1, FFALSE) || ++ !allocINT(lp, &new_index, lp->rows + 1, FFALSE)) { ++ ok = FFALSE; + break; + } + } +@@ -10160,10 +10160,10 @@ + /* in get_column and add_column operations; also make sure that */ + /* full scaling information is preserved */ + scaled = lp->scaling_used; +- lp->scaling_used = FALSE; ++ lp->scaling_used = FFALSE; + k = get_columnex(lp, j, new_column, new_index); + if(!add_columnex(lp, k, new_column, new_index)) { +- ok = FALSE; ++ ok = FFALSE; + break; + } + mat_multcol(lp->matA, lp->columns, -1, TRUE); +@@ -10179,7 +10179,7 @@ + sprintf(fieldn, "__AntiBodyOf(%d)__", j); + if(!set_col_name(lp, lp->columns, fieldn)) { + /* if (!set_col_name(lp, lp->columns, get_col_name(lp, j))) { */ +- ok = FALSE; ++ ok = FFALSE; + break; + } + } +@@ -10318,6 +10318,6 @@ + + } + +- lp->wasPreprocessed = FALSE; ++ lp->wasPreprocessed = FFALSE; + } + +diff -ru lp_solve_5.5.orig/lp_matrix.c lp_solve_5.5/lp_matrix.c +--- lp_solve_5.5.orig/lp_matrix.c 2019-02-19 10:42:21.372737063 -0600 ++++ lp_solve_5.5/lp_matrix.c 2019-02-19 11:57:43.416862191 -0600 +@@ -99,7 +99,7 @@ + #else + (rowextra < 0) || (colextra < 0) || (nzextra < 0)) + #endif +- return( FALSE ); ++ return( FFALSE ); + + mat->rows_alloc = MIN(mat->rows_alloc, mat->rows + rowextra); + mat->columns_alloc = MIN(mat->columns_alloc, mat->columns + colextra); +@@ -209,7 +209,7 @@ + + /* Update row pointers */ + status = allocINT(mat->lp, &mat->row_end, rowsum, AUTOMATIC); +- mat->row_end_valid = FALSE; ++ mat->row_end_valid = FFALSE; + } + return( status ); + } +@@ -235,7 +235,7 @@ + mat->col_end[0] = 0; + for(i = MIN(oldcolsalloc, mat->columns) + 1; i < colsum; i++) + mat->col_end[i] = mat->col_end[i-1]; +- mat->row_end_valid = FALSE; ++ mat->row_end_valid = FFALSE; + } + return( status ); + } +@@ -266,9 +266,9 @@ + { + #ifdef Paranoia + if(isrow && ((index < 0) || (index > mat->rows))) +- return( FALSE ); ++ return( FFALSE ); + else if(!isrow && ((index < 1) || (index > mat->columns))) +- return( FALSE ); ++ return( FFALSE ); + #endif + + if(isrow && mat_validate(mat)) { +@@ -288,7 +288,7 @@ + STATIC int mat_shiftrows(MATrec *mat, int *bbase, int delta, LLrec *varmap) + { + int j, k, i, ii, thisrow, *colend, base; +- MYBOOL preparecompact = FALSE; ++ MYBOOL preparecompact = FFALSE; + int *rownr; + + if(delta == 0) +@@ -320,7 +320,7 @@ + if(preparecompact) { + /* Create the offset array */ + int *newrowidx = NULL; +- allocINT(mat->lp, &newrowidx, mat->rows+1, FALSE); ++ allocINT(mat->lp, &newrowidx, mat->rows+1, FFALSE); + newrowidx[0] = 0; + delta = 0; + for(j = 1; j <= mat->rows; j++) { +@@ -420,15 +420,15 @@ + /* Create map and sort by increasing index in "mat" */ + if(mat2 != NULL) { + jj = mat2->col_tag[0]; +- allocINT(lp, &indirect, jj+1, FALSE); ++ allocINT(lp, &indirect, jj+1, FFALSE); + indirect[0] = jj; + for(i = 1; i <= jj; i++) + indirect[i] = i; +- hpsortex(mat2->col_tag, jj, 1, sizeof(*indirect), FALSE, compareINT, indirect); ++ hpsortex(mat2->col_tag, jj, 1, sizeof(*indirect), FFALSE, compareINT, indirect); + } + + /* Do the compacting */ +- mat->row_end_valid = FALSE; ++ mat->row_end_valid = FFALSE; + nz = mat->col_end[mat->columns]; + ie = 0; + ii = 0; +@@ -781,7 +781,7 @@ + for(xa = 0; xa < na; xa++, rownr += matRowColStep, colnr += matRowColStep, value += matValueStep) { + if((isActiveLink(colmap, *colnr) ^ negated) && + (isActiveLink(rowmap, *rownr) ^ negated)) +- mat_setvalue(newmat, *rownr, *colnr, *value, FALSE); ++ mat_setvalue(newmat, *rownr, *colnr, *value, FFALSE); + } + + /* Return the populated new matrix */ +@@ -798,7 +798,7 @@ + /* Check if we are in row order mode and should add as row instead; + the matrix will be transposed at a later stage */ + if(checkrowmode && mat->is_roworder) +- return( mat_setrow(mat, colno, count, column, rowno, doscale, FALSE) ); ++ return( mat_setrow(mat, colno, count, column, rowno, doscale, FFALSE) ); + + /* Initialize and validate */ + isA = (MYBOOL) (mat == mat->lp->matA); +@@ -806,12 +806,12 @@ + if(!isNZ) + count = mat->lp->rows; + else if((count < 0) || (count > mat->rows+((mat->is_roworder) ? 0 : 1))) +- return( FALSE ); ++ return( FFALSE ); + if(isNZ && (count > 0)) { + if(count > 1) + sortREALByINT(column, rowno, count, 0, TRUE); + if((rowno[0] < 0) || (rowno[count-1] > mat->rows)) +- return( FALSE ); ++ return( FFALSE ); + } + + /* Capture OF definition in column mode */ +@@ -856,7 +856,7 @@ + else { + newnr = 0; + if(!allocMYBOOL(lp, &addto, mat->rows + 1, TRUE)) { +- return( FALSE ); ++ return( FFALSE ); + } + for(i = mat->rows; i >= 0; i--) { + if(fabs(column[i]) > mat->epsvalue) { +@@ -931,7 +931,7 @@ + jj++; + } + } +- mat->row_end_valid = FALSE; ++ mat->row_end_valid = FFALSE; + + /* Finish and return */ + Done: +@@ -948,15 +948,15 @@ + int i, ix, iy, n, *colmap = NULL; + REAL *colvalue = NULL; + +- if((target->rows < source->rows) || !allocREAL(lp, &colvalue, target->rows+1, FALSE)) +- return( FALSE ); ++ if((target->rows < source->rows) || !allocREAL(lp, &colvalue, target->rows+1, FFALSE)) ++ return( FFALSE ); + + if(usecolmap) { + n = source->col_tag[0]; +- allocINT(lp, &colmap, n+1, FALSE); ++ allocINT(lp, &colmap, n+1, FFALSE); + for(i = 1; i <= n; i++) + colmap[i] = i; +- hpsortex(source->col_tag, n, 1, sizeof(*colmap), FALSE, compareINT, colmap); ++ hpsortex(source->col_tag, n, 1, sizeof(*colmap), FFALSE, compareINT, colmap); + } + else + n = source->columns; +@@ -973,8 +973,8 @@ + } + else + ix = iy = i; +- mat_expandcolumn(source, ix, colvalue, NULL, FALSE); +- mat_setcol(target, iy, 0, colvalue, NULL, FALSE, FALSE); ++ mat_expandcolumn(source, ix, colvalue, NULL, FFALSE); ++ mat_setcol(target, iy, 0, colvalue, NULL, FFALSE, FFALSE); + } + + FREE( colvalue ); +@@ -1000,22 +1000,22 @@ + /* Check if we are in row order mode and should add as column instead; + the matrix will be transposed at a later stage */ + if(checkrowmode && mat->is_roworder) +- return( mat_setcol(mat, rowno, count, row, colno, doscale, FALSE) ); ++ return( mat_setcol(mat, rowno, count, row, colno, doscale, FFALSE) ); + + /* Do initialization and validation */ + if(!mat_validate(mat)) +- return( FALSE ); ++ return( FFALSE ); + isA = (MYBOOL) (mat == lp->matA); + isNZ = (MYBOOL) (colno != NULL); + if(!isNZ) + count = mat->columns; + else if((count < 0) || (count > mat->columns)) +- return( FALSE ); ++ return( FFALSE ); + if(isNZ && (count > 0)) { + if(count > 1) + sortREALByINT(row, (int *) colno, count, 0, TRUE); + if((colno[0] < 1) || (colno[count-1] > mat->columns)) +- return( FALSE ); ++ return( FFALSE ); + } + + /* Capture OF definition in row mode */ +@@ -1130,7 +1130,7 @@ + else { + if(addto == NULL) { + if(!allocMYBOOL(lp, &addto, mat->columns + 1, TRUE)) +- return( FALSE ); ++ return( FFALSE ); + firstcol = k; + } + addto[k] = TRUE; +@@ -1140,7 +1140,7 @@ + } + } + if(newnr == 0) +- if (FALSE) ++ if (FFALSE) + return( TRUE ); + + /* Make sure we have enough matrix space */ +@@ -1201,7 +1201,7 @@ + if(jj_j > 0) { + if(!inc_mat_space(mat, jj_j)) { + FREE(addto); +- return( FALSE ); ++ return( FFALSE ); + } + if(orignr-jj > 0) { + COL_MAT_MOVE(jj+jj_j, jj, orignr-jj); +@@ -1371,7 +1371,7 @@ + /* Compact in the case that we added zeros and set flag for row index update */ + if(matz > 0) + mat_zerocompact(mat); +- mat->row_end_valid = FALSE; ++ mat->row_end_valid = FFALSE; + + Done: + if(saved != 0) +@@ -1396,18 +1396,18 @@ + /* Check if we are in row order mode and should add as column instead; + the matrix will be transposed at a later stage */ + if(checkrowmode && mat->is_roworder) +- return( mat_setcol(mat, rowno, count, row, colno, doscale, FALSE) ); ++ return( mat_setcol(mat, rowno, count, row, colno, doscale, FFALSE) ); + + /* Do initialization and validation */ + if(!mat_validate(mat)) +- return( FALSE ); ++ return( FFALSE ); + isA = (MYBOOL) (mat == lp->matA); + if(doscale && isA && !lp->scaling_used) +- doscale = FALSE; ++ doscale = FFALSE; + isNZ = (MYBOOL) (colno != NULL); + lendense = (mat->is_roworder ? lp->rows : lp->columns); + if((count < 0) || (count > lendense)) +- return( FALSE ); ++ return( FFALSE ); + colnr1 = lendense + 1; + + /* Capture OF definition in row mode */ +@@ -1437,14 +1437,14 @@ + /* Make local working data copies */ + if(!isNZ) { + REAL *tmprow = NULL; +- if(!allocINT(lp, &colno, lendense+1, FALSE)) +- return( FALSE ); ++ if(!allocINT(lp, &colno, lendense+1, FFALSE)) ++ return( FFALSE ); + newnz = 0; + for(i = 1; i <= lendense; i++) + if((value = row[i]) != 0) { +- if((tmprow == NULL) && !allocREAL(lp, &tmprow, lendense-i+1, FALSE)) { ++ if((tmprow == NULL) && !allocREAL(lp, &tmprow, lendense-i+1, FFALSE)) { + FREE(colno); +- return( FALSE ); ++ return( FFALSE ); + } + tmprow[newnz] = value; + colno[newnz++] = i; +@@ -1454,8 +1454,8 @@ + } + else { + int *tmpcolno = NULL; +- if(!allocINT(lp, &tmpcolno, lendense, FALSE)) +- return( FALSE ); ++ if(!allocINT(lp, &tmpcolno, lendense, FFALSE)) ++ return( FFALSE ); + newnz = count; + MEMCOPY(tmpcolno, colno, newnz); + colno = tmpcolno; +@@ -1464,7 +1464,7 @@ + if((newnz > 0) && ((colno[0] < 0) || (colno[newnz-1] > lendense))) { + FREE(colno); + newnz = 0; +- return( FALSE ); ++ return( FFALSE ); + } + } + +@@ -1609,7 +1609,7 @@ + jj_j = origidx - j; + for(; k <= lendense; k++) + mat->col_end[k] = jj_j; +- mat->row_end_valid = FALSE; ++ mat->row_end_valid = FFALSE; + + Done: + if(!isNZ) +@@ -1630,7 +1630,7 @@ + /* Check if we are in row order mode and should add as column instead; + the matrix will be transposed at a later stage */ + if(checkrowmode && mat->is_roworder) +- return( mat_appendcol(mat, count, row, colno, mult, FALSE) ); ++ return( mat_appendcol(mat, count, row, colno, mult, FFALSE) ); + + /* Do initialization and validation */ + isA = (MYBOOL) (mat == lp->matA); +@@ -1765,7 +1765,7 @@ + /* Check if we are in row order mode and should add as row instead; + the matrix will be transposed at a later stage */ + if(checkrowmode && mat->is_roworder) +- return( mat_appendrow(mat, count, column, rowno, mult, FALSE) ); ++ return( mat_appendrow(mat, count, column, rowno, mult, FFALSE) ); + + /* Make sure we have enough space */ + /* +@@ -1929,7 +1929,7 @@ + report(mat->lp, SEVERE, "mat_validate: Matrix value storage error row %d [0..%d], column %d [1..%d]\n", + *rownr, mat->rows, *colnr, mat->columns); + mat->lp->spx_status = UNKNOWNERROR; +- return(FALSE); ++ return(FFALSE); + } + #endif + *colnr = i; +@@ -2197,14 +2197,14 @@ + } + else { + mat_setitem(mat, row, column, delta); +- return( FALSE ); ++ return( FFALSE ); + } + } + } + + STATIC MYBOOL mat_setitem(MATrec *mat, int row, int column, REAL value) + { +- return( mat_setvalue(mat, row, column, value, FALSE) ); ++ return( mat_setvalue(mat, row, column, value, FFALSE) ); + } + + STATIC void mat_multrow(MATrec *mat, int row_nr, REAL mult) +@@ -2329,9 +2329,9 @@ + } + + /* Find out if we already have such an entry, or return insertion point */ +- i = mat_findins(mat, Row, Column, &elmnr, FALSE); ++ i = mat_findins(mat, Row, Column, &elmnr, FFALSE); + if(i == -1) +- return(FALSE); ++ return(FFALSE); + + if(isA) + set_action(&mat->lp->spx_action, ACTION_REBASE | ACTION_RECOMPUTE | ACTION_REINVERT); +@@ -2363,14 +2363,14 @@ + for(i = Column; i <= mat->columns; i++) + mat->col_end[i]--; + +- mat->row_end_valid = FALSE; ++ mat->row_end_valid = FFALSE; + } + } + else if(fabs(Value) > mat->epsvalue) { + /* no existing entry. make new one only if not nearly zero */ + /* check if more space is needed for matrix */ + if(!inc_mat_space(mat, 1)) +- return(FALSE); ++ return(FFALSE); + + if(Column > mat->columns) { + i = mat->columns + 1; +@@ -2403,7 +2403,7 @@ + for(i = Column; i <= mat->columns; i++) + mat->col_end[i]++; + +- mat->row_end_valid = FALSE; ++ mat->row_end_valid = FFALSE; + } + + if(isA && (mat->lp->var_is_free != NULL) && (mat->lp->var_is_free[ColumnA] > 0)) +@@ -2425,13 +2425,13 @@ + + /* Check if more space is needed for matrix */ + if(!inc_mat_space(mat, 1)) +- return(FALSE); ++ return(FFALSE); + + #ifdef Paranoia + /* Check valid indeces */ + if((Row < 0) || (Row > mat->rows)) { + report(mat->lp, SEVERE, "mat_appendvalue: Invalid row index %d specified\n", Row); +- return(FALSE); ++ return(FFALSE); + } + #endif + +@@ -2441,14 +2441,14 @@ + + /* Update column count */ + (*elmnr)++; +- mat->row_end_valid = FALSE; ++ mat->row_end_valid = FFALSE; + + return(TRUE); + } + + STATIC MYBOOL mat_equalRows(MATrec *mat, int baserow, int comprow) + { +- MYBOOL status = FALSE; ++ MYBOOL status = FFALSE; + + if(mat_validate(mat)) { + int bj1 = 0, ej1, bj2 = 0, ej2; +@@ -2469,7 +2469,7 @@ + if(COL_MAT_COLNR(bj1) != COL_MAT_COLNR(bj2)) + break; + #if 1 +- if(fabs(get_mat_byindex(mat->lp, bj1, TRUE, FALSE)-get_mat_byindex(mat->lp, bj2, TRUE, FALSE)) > mat->lp->epsprimal) ++ if(fabs(get_mat_byindex(mat->lp, bj1, TRUE, FFALSE)-get_mat_byindex(mat->lp, bj2, TRUE, FFALSE)) > mat->lp->epsprimal) + #else + if(fabs(COL_MAT_VALUE(bj1)-COL_MAT_VALUE(bj2)) > mat->lp->epsprimal) + #endif +@@ -2537,7 +2537,7 @@ + /* Prepare arrays */ + if(!allocREAL(mat->lp, &mat->colmax, mat->columns_alloc+1, AUTOMATIC) || + !allocREAL(mat->lp, &mat->rowmax, mat->rows_alloc+1, AUTOMATIC)) +- return( FALSE ); ++ return( FFALSE ); + MEMCLEAR(mat->colmax, mat->columns+1); + MEMCLEAR(mat->rowmax, mat->rows+1); + +@@ -2600,8 +2600,8 @@ + #else /*if MatrixColAccess==CAM_Vector*/ + REAL *newValue = NULL; + int *newRownr = NULL; +- allocREAL(mat->lp, &newValue, mat->mat_alloc, FALSE); +- allocINT(mat->lp, &newRownr, mat->mat_alloc, FALSE); ++ allocREAL(mat->lp, &newValue, mat->mat_alloc, FFALSE); ++ allocINT(mat->lp, &newRownr, mat->mat_alloc, FFALSE); + + j = mat->row_end[0]; + for(i = nz-1; i >= j ; i--) { +@@ -2640,7 +2640,7 @@ + + /* Finally set current storage mode */ + mat->is_roworder = (MYBOOL) !mat->is_roworder; +- mat->row_end_valid = FALSE; ++ mat->row_end_valid = FFALSE; + } + return(status); + } +@@ -2731,7 +2731,7 @@ + STATIC MYBOOL freeUndoLadder(DeltaVrec **DV) + { + if((DV == NULL) || (*DV == NULL)) +- return(FALSE); ++ return(FFALSE); + + mat_free(&((*DV)->tracker)); + FREE(*DV); +@@ -2759,19 +2759,19 @@ + + /* Do normal user variable case */ + if(colnrDep <= lp->columns) +- mat_setvalue(mat, colnrDep, ix, beta, FALSE); ++ mat_setvalue(mat, colnrDep, ix, beta, FFALSE); + + /* Handle case where a slack variable is referenced */ + else { + int ipos, jx = mat->col_tag[ix]; +- mat_setvalue(mat, jx, ix, beta, FALSE); +- jx = mat_findins(mat, jx, ix, &ipos, FALSE); ++ mat_setvalue(mat, jx, ix, beta, FFALSE); ++ jx = mat_findins(mat, jx, ix, &ipos, FFALSE); + COL_MAT_ROWNR(ipos) = colnrDep; + } + return( TRUE ); + } + else +- return( FALSE ); ++ return( FFALSE ); + } + STATIC MYBOOL addUndoPresolve(lprec *lp, MYBOOL isprimal, int colnrElim, REAL alpha, REAL beta, int colnrDep) + { +@@ -2787,7 +2787,7 @@ + *DV = createUndoLadder(lp, lp->columns+1, lp->columns); + mat = (*DV)->tracker; + mat->epsvalue = lp->matA->epsvalue; +- allocINT(lp, &(mat->col_tag), lp->columns+1, FALSE); ++ allocINT(lp, &(mat->col_tag), lp->columns+1, FFALSE); + mat->col_tag[0] = 0; + } + } +@@ -2797,7 +2797,7 @@ + *DV = createUndoLadder(lp, lp->rows+1, lp->rows); + mat = (*DV)->tracker; + mat->epsvalue = lp->matA->epsvalue; +- allocINT(lp, &(mat->col_tag), lp->rows+1, FALSE); ++ allocINT(lp, &(mat->col_tag), lp->rows+1, FFALSE); + mat->col_tag[0] = 0; + } + } +@@ -2810,13 +2810,13 @@ + ix = mat->col_tag[0] = incrementUndoLadder(*DV); + mat->col_tag[ix] = colnrElim; + if(alpha != 0) +- mat_setvalue(mat, 0, ix, alpha, FALSE); ++ mat_setvalue(mat, 0, ix, alpha, FFALSE); + /* mat_appendvalue(*mat, 0, alpha);*/ + if((colnrDep > 0) && (beta != 0)) { + if(colnrDep > lp->columns) + return( appendUndoPresolve(lp, isprimal, beta, colnrDep) ); + else +- mat_setvalue(mat, colnrDep, ix, beta, FALSE); ++ mat_setvalue(mat, colnrDep, ix, beta, FFALSE); + } + + return( TRUE ); +@@ -2957,7 +2957,7 @@ + /* Make sure the tags are correct */ + if(!mat_validate(lp->matA)) { + lp->spx_status = INFEASIBLE; +- return(FALSE); ++ return(FFALSE); + } + + /* Create the inverse management object at the first call to invert() */ +@@ -2970,7 +2970,7 @@ + /* Must save spx_status since it is used to carry information about + the presence and handling of singular columns in the matrix */ + if(userabort(lp, MSG_INVERT)) +- return(FALSE); ++ return(FFALSE); + + #ifdef Paranoia + if(lp->spx_trace) +@@ -2982,7 +2982,7 @@ + the basis is I; in this case take the easy way out */ + if(!allocMYBOOL(lp, &usedpos, lp->sum + 1, TRUE)) { + lp->bb_break = TRUE; +- return(FALSE); ++ return(FFALSE); + } + usedpos[0] = TRUE; + usercolB = 0; +@@ -3008,7 +3008,7 @@ + if(resetbasis) { + j = lp->var_basic[i]; + if(j > lp->rows) +- lp->is_basic[j] = FALSE; ++ lp->is_basic[j] = FFALSE; + lp->var_basic[i] = i; + lp->is_basic[i] = TRUE; + } +@@ -3036,7 +3036,7 @@ + + Cleanup: + /* Check for numerical instability indicated by frequent refactorizations */ +- test = get_refactfrequency(lp, FALSE); ++ test = get_refactfrequency(lp, FFALSE); + if(test < MIN_REFACTFREQUENCY) { + test = get_refactfrequency(lp, TRUE); + report(lp, NORMAL, "invert: Refactorization frequency %.1g indicates numeric instability.\n", +@@ -3055,9 +3055,9 @@ + int j; + MYBOOL Ok = TRUE; + +- allocREAL(lp, &errors, lp->rows + 1, FALSE); ++ allocREAL(lp, &errors, lp->rows + 1, FFALSE); + if(errors == NULL) { +- Ok = FALSE; ++ Ok = FFALSE; + return(Ok); + } + MEMCOPY(errors, pcol, lp->rows + 1); +@@ -3087,9 +3087,9 @@ + REAL *errors, err, maxerr; + MYBOOL Ok = TRUE; + +- allocREAL(lp, &errors, lp->sum + 1, FALSE); ++ allocREAL(lp, &errors, lp->sum + 1, FFALSE); + if(errors == NULL) { +- Ok = FALSE; ++ Ok = FFALSE; + return(Ok); + } + MEMCOPY(errors, rhsvector, lp->sum + 1); +@@ -3193,7 +3193,7 @@ + int n; + + if((densevector == NULL) || (nzindex == NULL) || (startpos > endpos)) +- return( FALSE ); ++ return( FFALSE ); + + n = 0; + densevector += startpos; +@@ -3265,15 +3265,15 @@ + + /* Adjust for partial pricing */ + if(varset & SCAN_PARTIALBLOCK) { +- SETMAX(vb, partial_blockStart(lp, FALSE)); +- SETMIN(ve, partial_blockEnd(lp, FALSE)); ++ SETMAX(vb, partial_blockStart(lp, FFALSE)); ++ SETMIN(ve, partial_blockEnd(lp, FFALSE)); + } + + /* Determine exclusion columns */ + omitfixed = (MYBOOL) ((varset & OMIT_FIXED) != 0); + omitnonfixed = (MYBOOL) ((varset & OMIT_NONFIXED) != 0); + if(omitfixed && omitnonfixed) +- return(FALSE); ++ return(FFALSE); + + /* Scan the target colums */ + if(append) +@@ -3323,7 +3323,7 @@ + /* prod_Ax is only used in fimprove; note that it is NOT VALIDATED/verified as of 20030801 - KE */ + { + int j, colnr, ib, ie, vb, ve; +- MYBOOL localset, localnz = FALSE, isRC; ++ MYBOOL localset, localnz = FFALSE, isRC; + MATrec *mat = lp->matA; + REAL sdp; + REAL *value; +@@ -3339,9 +3339,9 @@ + if(isRC && is_piv_mode(lp, PRICE_PARTIAL) && !is_piv_mode(lp, PRICE_FORCEFULL)) + varset |= SCAN_PARTIALBLOCK; + coltarget = (int *) mempool_obtainVector(lp->workarrays, lp->sum+1, sizeof(*coltarget)); +- if(!get_colIndexA(lp, varset, coltarget, FALSE)) { +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); +- return(FALSE); ++ if(!get_colIndexA(lp, varset, coltarget, FFALSE)) { ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); ++ return(FFALSE); + } + } + localnz = (MYBOOL) (nzinput == NULL); +@@ -3377,9 +3377,9 @@ + + /* Clean up and return */ + if(localset) +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); + if(localnz) +- mempool_releaseVector(lp->workarrays, (char *) nzinput, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) nzinput, FFALSE); + + return(TRUE); + } +@@ -3392,7 +3392,7 @@ + the same vector as input, without overwriting the [0..rows] elements. */ + { + int colnr, rownr, varnr, ib, ie, vb, ve, nrows = lp->rows; +- MYBOOL localset, localnz = FALSE, includeOF, isRC; ++ MYBOOL localset, localnz = FFALSE, includeOF, isRC; + REALXP vmax; + register REALXP v; + int inz, *rowin, countNZ = 0; +@@ -3418,9 +3418,9 @@ + if(isRC && is_piv_mode(lp, PRICE_PARTIAL) && !is_piv_mode(lp, PRICE_FORCEFULL)) + varset |= SCAN_PARTIALBLOCK; + coltarget = (int *) mempool_obtainVector(lp->workarrays, lp->sum+1, sizeof(*coltarget)); +- if(!get_colIndexA(lp, varset, coltarget, FALSE)) { +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); +- return(FALSE); ++ if(!get_colIndexA(lp, varset, coltarget, FFALSE)) { ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); ++ return(FFALSE); + } + } + /*#define UseLocalNZ*/ +@@ -3589,9 +3589,9 @@ + + /* Clean up and return */ + if(localset) +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); + if(localnz) +- mempool_releaseVector(lp->workarrays, (char *) nzinput, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) nzinput, FFALSE); + + if(nzoutput != NULL) + *nzoutput = countNZ; +@@ -3621,9 +3621,9 @@ + /*SCAN_PARTIALBLOCK+*/ + USE_NONBASICVARS+OMIT_FIXED; + coltarget = (int *) mempool_obtainVector(lp->workarrays, lp->sum+1, sizeof(*coltarget)); +- if(!get_colIndexA(lp, varset, coltarget, FALSE)) { +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); +- return(FALSE); ++ if(!get_colIndexA(lp, varset, coltarget, FFALSE)) { ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); ++ return(FFALSE); + } + } + +@@ -3768,7 +3768,7 @@ + + /* Clean up and return */ + if(localset) +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); + return( TRUE ); + } + +diff -ru lp_solve_5.5.orig/lp_MDO.c lp_solve_5.5/lp_MDO.c +--- lp_solve_5.5.orig/lp_MDO.c 2019-02-19 10:42:21.372737063 -0600 ++++ lp_solve_5.5/lp_MDO.c 2019-02-19 11:54:51.568857436 -0600 +@@ -46,7 +46,7 @@ + return( test != TRUE ); + #else + test = test & TRUE; +- return( test == FALSE ); ++ return( test == FFALSE ); + #endif + } + } +@@ -156,7 +156,7 @@ + + int __WINAPI getMDO(lprec *lp, MYBOOL *usedpos, int *colorder, int *size, MYBOOL symmetric) + { +- int error = FALSE; ++ int error = FFALSE; + int nrows = lp->rows+1, ncols = colorder[0]; + int i, j, kk, n; + int *col_end, *row_map = NULL; +@@ -166,7 +166,7 @@ + + /* Tally the non-zero counts of the unused columns/rows of the + basis matrix and store corresponding "net" starting positions */ +- allocINT(lp, &col_end, ncols+1, FALSE); ++ allocINT(lp, &col_end, ncols+1, FFALSE); + n = prepareMDO(lp, usedpos, colorder, col_end, NULL); + Bnz = col_end[ncols]; + +@@ -175,7 +175,7 @@ + goto Transfer; + + /* Get net number of rows and fill mapper */ +- allocINT(lp, &row_map, nrows, FALSE); ++ allocINT(lp, &row_map, nrows, FFALSE); + nrows = 0; + for(i = 0; i <= lp->rows; i++) { + row_map[i] = i-nrows; +@@ -187,7 +187,7 @@ + + /* Store row indeces of non-zero values in the basic columns */ + Blen = colamd_recommended(Bnz, nrows, ncols); +- allocINT(lp, &Brows, Blen, FALSE); ++ allocINT(lp, &Brows, Blen, FFALSE); + prepareMDO(lp, usedpos, colorder, Brows, row_map); + #ifdef Paranoia + verifyMDO(lp, col_end, Brows, nrows, ncols); +diff -ru lp_solve_5.5.orig/lp_mipbb.c lp_solve_5.5/lp_mipbb.c +--- lp_solve_5.5.orig/lp_mipbb.c 2019-02-19 10:42:21.372737063 -0600 ++++ lp_solve_5.5/lp_mipbb.c 2019-02-19 11:58:25.340863351 -0600 +@@ -48,14 +48,14 @@ + if(newBB != NULL) { + + if(parentBB == NULL) { +- allocREAL(lp, &newBB->upbo, lp->sum + 1, FALSE); +- allocREAL(lp, &newBB->lowbo, lp->sum + 1, FALSE); ++ allocREAL(lp, &newBB->upbo, lp->sum + 1, FFALSE); ++ allocREAL(lp, &newBB->lowbo, lp->sum + 1, FFALSE); + MEMCOPY(newBB->upbo, lp->orig_upbo, lp->sum + 1); + MEMCOPY(newBB->lowbo, lp->orig_lowbo, lp->sum + 1); + } + else if(dofullcopy) { +- allocREAL(lp, &newBB->upbo, lp->sum + 1, FALSE); +- allocREAL(lp, &newBB->lowbo, lp->sum + 1, FALSE); ++ allocREAL(lp, &newBB->upbo, lp->sum + 1, FFALSE); ++ allocREAL(lp, &newBB->lowbo, lp->sum + 1, FFALSE); + MEMCOPY(newBB->upbo, parentBB->upbo, lp->sum + 1); + MEMCOPY(newBB->lowbo, parentBB->lowbo, lp->sum + 1); + } +@@ -85,7 +85,7 @@ + /* Do initialization and updates */ + if(parentBB == NULL) + parentBB = lp->bb_bounds; +- newBB = create_BB(lp, parentBB, FALSE); ++ newBB = create_BB(lp, parentBB, FFALSE); + if(newBB != NULL) { + + newBB->varno = varno; +@@ -105,7 +105,7 @@ + for(k = 1; k <= lp->nzdrow[0]; k++) { + ii = lp->nzdrow[k]; + #ifdef UseMilpSlacksRCF /* Check if we should include ranged constraints */ +- isINT = FALSE; ++ isINT = FFALSE; + #else + if(ii <= lp->rows) + continue; +@@ -168,7 +168,7 @@ + + STATIC MYBOOL free_BB(BBrec **BB) + { +- MYBOOL parentreturned = FALSE; ++ MYBOOL parentreturned = FFALSE; + + if((BB != NULL) && (*BB != NULL)) { + BBrec *parent = (*BB)->parent; +@@ -237,7 +237,7 @@ + } + if(lp->int_vars+lp->sc_vars > 0) + free_pseudocost(lp); +- pop_basis(lp, FALSE); ++ pop_basis(lp, FFALSE); + lp->rootbounds = NULL; + } + else +@@ -256,7 +256,7 @@ + /* Pop the associated basis */ + #if 1 + /* Original version that does not restore previous basis */ +- pop_basis(lp, FALSE); ++ pop_basis(lp, FFALSE); + #else + /* Experimental version that restores previous basis */ + pop_basis(lp, BB->isSOS); +@@ -388,7 +388,7 @@ + /* Set direction by pseudocost (normally used in tandem with NODE_PSEUDOxxxSELECT) */ + else if(is_bb_mode(lp, NODE_PSEUDOCOSTMODE)) { + BB->isfloor = (MYBOOL) (get_pseudobranchcost(lp->bb_PseudoCost, k, TRUE) > +- get_pseudobranchcost(lp->bb_PseudoCost, k, FALSE)); ++ get_pseudobranchcost(lp->bb_PseudoCost, k, FFALSE)); + if(is_maxim(lp)) + BB->isfloor = !BB->isfloor; + } +@@ -432,7 +432,7 @@ + REAL ult_upbo, ult_lowbo; + REAL new_bound, SC_bound, intmargin = BB->lp->epsprimal; + lprec *lp = BB->lp; +- MYBOOL OKstatus = FALSE; ++ MYBOOL OKstatus = FFALSE; + + if(lp->bb_break || userabort(lp, MSG_MILPSTRATEGY)) + return( OKstatus ); +@@ -602,7 +602,7 @@ + if((BB->vartype != BB_SOS) && (fabs(BB->LObound-BB->UPbound) < intmargin)) { + BB->nodesleft--; + if(fabs(BB->lowbo[K]-BB->LObound) < intmargin) +- BB->isfloor = FALSE; ++ BB->isfloor = FFALSE; + else if(fabs(BB->upbo[K]-BB->UPbound) < intmargin) + BB->isfloor = TRUE; + else { +@@ -638,7 +638,7 @@ + { + int k; + lprec *lp = BB->lp; +- MYBOOL OKstatus = FALSE; ++ MYBOOL OKstatus = FFALSE; + + /* Undo the most recently imposed B&B bounds using the data + in the last level of change tracker; this code handles changes +@@ -652,7 +652,7 @@ + /* Handle the special case of B&B restart; + (typically used with the restart after pseudocost initialization) */ + if((lp->bb_level == 1) && (lp->bb_break == AUTOMATIC)) { +- lp->bb_break = FALSE; ++ lp->bb_break = FFALSE; + OKstatus = TRUE; + } + return( OKstatus ); +@@ -797,7 +797,7 @@ + /* Copy user-specified entering bounds into lp_solve working bounds and run */ + status = spx_run(lp, (MYBOOL) (tilted+restored > 0)); + lp->bb_status = status; +- lp->spx_perturbed = FALSE; ++ lp->spx_perturbed = FFALSE; + + if(tilted < 0) + break; +@@ -817,7 +817,7 @@ + else + impose_bounds(lp, perturbed->upbo, perturbed->lowbo); + set_action(&lp->spx_action, ACTION_REBASE | ACTION_RECOMPUTE); +- BB->UBzerobased = FALSE; ++ BB->UBzerobased = FFALSE; + if(lp->bb_totalnodes == 0) + lp->real_solution = lp->infinite; + status = RUNNING; +@@ -845,11 +845,11 @@ + #if 1 + perturb_bounds(lp, perturbed, TRUE, TRUE, TRUE); + #else +- perturb_bounds(lp, perturbed, TRUE, TRUE, FALSE); ++ perturb_bounds(lp, perturbed, TRUE, TRUE, FFALSE); + #endif + impose_bounds(lp, perturbed->upbo, perturbed->lowbo); + set_action(&lp->spx_action, ACTION_REBASE | ACTION_RECOMPUTE); +- BB->UBzerobased = FALSE; ++ BB->UBzerobased = FFALSE; + status = RUNNING; + tilted++; + lp->perturb_count++; +@@ -1025,7 +1025,7 @@ + + /* Check and set feasibility status */ + if((isfeasible != NULL) && (upbo - lowbo < -lp->epsprimal)) +- *isfeasible = FALSE; ++ *isfeasible = FFALSE; + + /* Flag that we can fix the variable by returning the relation code negated */ + else if(fabs(upbo - lowbo) < lp->epsprimal) +@@ -1045,7 +1045,7 @@ + { + int countsossc, countnint, k, reasonmsg = MSG_NONE; + REAL varsol; +- MYBOOL is_better = FALSE, is_equal = FALSE, is_feasible = TRUE; ++ MYBOOL is_better = FFALSE, is_equal = FFALSE, is_feasible = TRUE; + lprec *lp = BB->lp; + + /* Initialize result and return variables */ +@@ -1066,13 +1066,13 @@ + 2) B&B level relative to the "B&B order" (bb_limitlevel < 0). */ + countsossc = lp->sos_vars + lp->sc_vars; + if((lp->bb_limitlevel > 0) && (lp->bb_level > lp->bb_limitlevel+countsossc)) +- return( FALSE ); ++ return( FFALSE ); + else if((lp->bb_limitlevel < 0) && + (lp->bb_level > 2*(lp->int_vars+countsossc)*abs(lp->bb_limitlevel))) { + if(lp->bb_limitlevel == DEF_BB_LIMITLEVEL) + report(lp, IMPORTANT, "findnode_BB: Default B&B limit reached at %d; optionally change strategy or limit.\n\n", + lp->bb_level); +- return( FALSE ); ++ return( FFALSE ); + } + + /* First initialize or update pseudo-costs from previous optimal solution */ +@@ -1093,7 +1093,7 @@ + if(lp->bb_trace) + report(lp, IMPORTANT, "findnode_BB: Simplex failure due to loss of numeric accuracy\n"); + lp->spx_status = NUMFAILURE; +- return( FALSE ); ++ return( FFALSE ); + } + + /* Abandon this branch if the solution is "worse" than a heuristically +@@ -1102,7 +1102,7 @@ + ((lp->solutioncount > 0) && + (!bb_better(lp, OF_INCUMBENT | OF_DELTA, OF_TEST_BE | OF_TEST_RELGAP) || + !bb_better(lp, OF_INCUMBENT | OF_DELTA, OF_TEST_BE)))) { +- return( FALSE ); ++ return( FFALSE ); + } + + /* Collect violated SC variables (since they can also be real-valued); the +@@ -1115,7 +1115,7 @@ + + /* Look among SOS variables if no SC candidate was found */ + if((SOS_count(lp) > 0) && (*varno == 0)) { +- *varno = find_sos_bbvar(lp, &countnint, FALSE); ++ *varno = find_sos_bbvar(lp, &countnint, FFALSE); + if(*varno < 0) + *varno = 0; + else if(*varno > 0) +@@ -1129,7 +1129,7 @@ + *vartype = BB_INT; + if((countnint == 1) && !is_feasible) { + BB->lastrcf = 0; +- return( FALSE ); ++ return( FFALSE ); + } + } + } +@@ -1146,7 +1146,7 @@ + */ + /* set_action(&lp->nomessage, NOMSG_BBLIMIT); */ + /* } */ +- return( FALSE ); ++ return( FFALSE ); + } + #endif + +@@ -1191,7 +1191,7 @@ + } + + if(lp->bb_trace || +- ((lp->verbose >= NORMAL) && (lp->print_sol == FALSE) && (lp->lag_status != RUNNING))) { ++ ((lp->verbose >= NORMAL) && (lp->print_sol == FFALSE) && (lp->lag_status != RUNNING))) { + report(lp, IMPORTANT, + "%s solution " RESULTVALUEMASK " after %10.0f iter, %9.0f nodes (gap %.1f%%)\n", + (lp->bb_improvements == 0) ? "Feasible" : "Improved", +@@ -1232,7 +1232,7 @@ + lp->spx_status = NUMFAILURE; + lp->bb_status = lp->spx_status; + lp->bb_break = TRUE; +- return( FALSE ); ++ return( FFALSE ); + } + #endif + transfer_solution(lp, (MYBOOL) ((lp->do_presolve & PRESOLVE_LASTMASKMODE) != PRESOLVE_NONE)); +@@ -1247,7 +1247,7 @@ + if((reasonmsg != MSG_NONE) && (lp->msgmask & reasonmsg) && (lp->usermessage != NULL)) + lp->usermessage(lp, lp->msghandle, reasonmsg); + +- if(lp->print_sol != FALSE) { ++ if(lp->print_sol != FFALSE) { + print_objective(lp); + print_solution(lp, 1); + } +@@ -1259,7 +1259,7 @@ + if((countnint == 0) && (lp->solutioncount == 1) && (lp->solutionlimit == 1) && + (bb_better(lp, OF_DUALLIMIT, OF_TEST_BE) || bb_better(lp, OF_USERBREAK, OF_TEST_BE | OF_TEST_RELGAP))) { + lp->bb_break = (MYBOOL) (countnint == 0); +- return( FALSE ); ++ return( FFALSE ); + } + else if(lp->bb_level > 0) { + #ifdef MIPboundWithOF +@@ -1273,7 +1273,7 @@ + return( (MYBOOL) (*varno > 0)); + } + else +- return( FALSE ); ++ return( FFALSE ); + + } + +@@ -1322,7 +1322,7 @@ + /* Routine to compute a "strong" pseudo-cost update for a node */ + STATIC MYBOOL strongbranch_BB(lprec *lp, BBrec *BB, int varno, int vartype, int varcus) + { +- MYBOOL success = FALSE; ++ MYBOOL success = FFALSE; + int i; + BBrec *strongBB; + +@@ -1346,7 +1346,7 @@ + /* Compute new count of non-ints */ + strongBB->lastvarcus = 0; + for(i = 1; i <= lp->columns; i++) { +- if(is_int(lp, i) && !solution_is_int(lp, lp->rows+i, FALSE)) ++ if(is_int(lp, i) && !solution_is_int(lp, lp->rows+i, FFALSE)) + strongBB->lastvarcus++; + } + +@@ -1364,7 +1364,7 @@ + pop_basis(lp, TRUE); + set_action(&lp->spx_action, ACTION_REBASE | ACTION_REINVERT | ACTION_RECOMPUTE); + +- lp->is_strongbranch = FALSE; ++ lp->is_strongbranch = FFALSE; + + return( success ); + } +diff -ru lp_solve_5.5.orig/lp_MPS.c lp_solve_5.5/lp_MPS.c +--- lp_solve_5.5.orig/lp_MPS.c 2019-02-19 10:42:21.372737063 -0600 ++++ lp_solve_5.5/lp_MPS.c 2019-02-19 11:59:02.500864379 -0600 +@@ -464,7 +464,7 @@ + set_bounds(lp, lp->columns, 10.0 / DEF_INFINITE, DEF_INFINITE / 10.0); + } + } +- *Column_ready = FALSE; ++ *Column_ready = FFALSE; + *count = 0; + return(ok); + } +@@ -475,7 +475,7 @@ + int i = *count; + + if(rowValue[i] == 0) +- return( FALSE ); ++ return( FFALSE ); + + while((i > 0) && (rowIndex[i] < rowIndex[i-1])) { + swapINT (rowIndex+i, rowIndex+i-1); +@@ -493,7 +493,7 @@ + + /* Check for non-negativity of the index */ + if(rowIndex[i] < 0) +- return( FALSE ); ++ return( FFALSE ); + + /* Move the element so that the index list is sorted ascending */ + while((i > 0) && (rowIndex[i] < rowIndex[i-1])) { +@@ -521,7 +521,7 @@ + + MYBOOL MPS_readfile(lprec **newlp, char *filename, int typeMPS, int verbose) + { +- MYBOOL status = FALSE; ++ MYBOOL status = FFALSE; + FILE *fpin; + + fpin = fopen(filename, "r"); +@@ -549,7 +549,7 @@ + int items, row, Lineno, var, + section = MPSUNDEF, variant = 0, NZ = 0, SOS = 0; + MYBOOL Int_section, Column_ready, Column_ready1, +- Unconstrained_rows_found = FALSE, OF_found = FALSE, CompleteStatus = FALSE; ++ Unconstrained_rows_found = FFALSE, OF_found = FFALSE, CompleteStatus = FFALSE; + double field4, field6; + REAL *Last_column = NULL; + int count = 0, *Last_columnno = NULL; +@@ -581,8 +581,8 @@ + lp->verbose = verbose; + strcpy(Last_col_name, ""); + strcpy(OBJNAME, ""); +- Int_section = FALSE; +- Column_ready = FALSE; ++ Int_section = FFALSE; ++ Column_ready = FFALSE; + Lineno = 0; + + /* let's initialize line to all zero's */ +@@ -758,7 +758,7 @@ + else if(*field2) { + Column_ready1 = (MYBOOL) (strcmp(field2, Last_col_name) != 0); + if(Column_ready1) { +- if (find_var(lp, field2, FALSE) >= 0) { ++ if (find_var(lp, field2, FFALSE) >= 0) { + report(lp, SEVERE, "Variable name (%s) is already used!\n", field2); + break; + } +@@ -783,7 +783,7 @@ + report(lp, FULL, "Switching to integer section\n"); + } + else if(strcmp(field5, "'INTEND'") == 0) { +- Int_section = FALSE; ++ Int_section = FFALSE; + report(lp, FULL, "Switching to non-integer section\n"); + } + else +@@ -861,10 +861,10 @@ + report(lp, FULL, "BOUNDS line: %s %s %s %g\n", + field1, field2, field3, field4); + +- var = find_var(lp, field3, FALSE); ++ var = find_var(lp, field3, FFALSE); + if(var < 0){ /* bound on undefined var in COLUMNS section ... */ + Column_ready = TRUE; +- if (!addmpscolumn(lp, FALSE, typeMPS, &Column_ready, &count, Last_column, Last_columnno, field3)) ++ if (!addmpscolumn(lp, FFALSE, typeMPS, &Column_ready, &count, Last_column, Last_columnno, field3)) + break; + Column_ready = TRUE; + var = find_var(lp, field3, TRUE); +@@ -1112,10 +1112,10 @@ + else { + char *field = (items == 3) ? field3 /* Native lp_solve and XPRESS formats */ : field2 /* CPLEX format */; + +- var = find_var(lp, field, FALSE); /* Native lp_solve and XPRESS formats */ ++ var = find_var(lp, field, FFALSE); /* Native lp_solve and XPRESS formats */ + if(var < 0){ /* SOS on undefined var in COLUMNS section ... */ + Column_ready = TRUE; +- if (!addmpscolumn(lp, FALSE, typeMPS, &Column_ready, &count, Last_column, Last_columnno, field)) ++ if (!addmpscolumn(lp, FFALSE, typeMPS, &Column_ready, &count, Last_column, Last_columnno, field)) + break; + Column_ready = TRUE; + var = find_var(lp, field, TRUE); +@@ -1137,10 +1137,10 @@ + if((*OBJNAME) && (!OF_found)) { + report(lp, IMPORTANT, + "Error: Objective function specified by OBJNAME card not found\n"); +- CompleteStatus = FALSE; ++ CompleteStatus = FFALSE; + } + +- if(CompleteStatus == FALSE) { ++ if(CompleteStatus == FFALSE) { + if (*newlp == NULL) + delete_lp(lp); + } +@@ -1299,7 +1299,7 @@ + + MYBOOL __WINAPI MPS_writefileex(lprec *lp, int typeMPS, void *userhandle, write_modeldata_func write_modeldata) + { +- int i, j, jj, je, k, marker, putheader, ChangeSignObj = FALSE, *idx, *idx1; ++ int i, j, jj, je, k, marker, putheader, ChangeSignObj = FFALSE, *idx, *idx1; + MYBOOL ok = TRUE, names_used; + REAL a, *val, *val1; + char * (*MPSname)(char *name0, char *name); +@@ -1315,7 +1315,7 @@ + } + else { + report(lp, IMPORTANT, "MPS_writefile: unrecognized MPS name type.\n"); +- return(FALSE); ++ return(FFALSE); + } + + names_used = lp->names_used; +@@ -1328,11 +1328,11 @@ + for(j = 1; (j < i) && (ok); j++) + if((lp->col_name[j] != NULL) && (lp->col_name[j]->name != NULL) && (!is_splitvar(lp, j))) + if(strncmp(lp->col_name[i]->name, lp->col_name[j]->name, 8) == 0) +- ok = FALSE; ++ ok = FFALSE; + } + + if(!ok) { +- lp->names_used = FALSE; ++ lp->names_used = FFALSE; + ok = TRUE; + } + +@@ -1452,7 +1452,7 @@ + if(a) { + if(putheader) { + write_data(userhandle, write_modeldata, "RANGES\n"); +- putheader = FALSE; ++ putheader = FFALSE; + } + a = unscaled_value(lp, a, i); + k = 1 - k; +@@ -1479,7 +1479,7 @@ + a = unscaled_value(lp, a, i); + if(putheader) { + write_data(userhandle, write_modeldata, "BOUNDS\n"); +- putheader = FALSE; ++ putheader = FFALSE; + } + write_data(userhandle, write_modeldata, " FX BND %s %s\n", + MPSname(name0, get_col_name(lp, j)), +@@ -1488,7 +1488,7 @@ + else if(is_binary(lp, j)) { + if(putheader) { + write_data(userhandle, write_modeldata, "BOUNDS\n"); +- putheader = FALSE; ++ putheader = FFALSE; + } + write_data(userhandle, write_modeldata, " BV BND %s\n", + MPSname(name0, get_col_name(lp, j))); +@@ -1496,7 +1496,7 @@ + else if(is_unbounded(lp, j)) { + if(putheader) { + write_data(userhandle, write_modeldata, "BOUNDS\n"); +- putheader = FALSE; ++ putheader = FFALSE; + } + write_data(userhandle, write_modeldata, " FR BND %s\n", + MPSname(name0, get_col_name(lp, j))); +@@ -1507,7 +1507,7 @@ + a = unscaled_value(lp, a, i); + if(putheader) { + write_data(userhandle, write_modeldata, "BOUNDS\n"); +- putheader = FALSE; ++ putheader = FFALSE; + } + if(lp->orig_lowbo[i] != -lp->infinite) + write_data(userhandle, write_modeldata, " LO BND %s %s\n", +@@ -1524,7 +1524,7 @@ + a = unscaled_value(lp, a, i); + if(putheader) { + write_data(userhandle, write_modeldata, "BOUNDS\n"); +- putheader = FALSE; ++ putheader = FFALSE; + } + if(is_semicont(lp, j)) { + if(is_int(lp, j)) +@@ -1551,7 +1551,7 @@ + + if(putheader) { + write_data(userhandle, write_modeldata, "SOS\n"); +- putheader = FALSE; ++ putheader = FFALSE; + } + write_data(userhandle, write_modeldata, " S%1d SOS %s %s\n", + SOS->sos_list[i]->type, +@@ -1682,7 +1682,7 @@ + scan_line = scan_lineFREE; + else { + report(lp, IMPORTANT, "MPS_readBAS: unrecognized MPS line type.\n"); +- return(FALSE); ++ return(FFALSE); + } + + ok = (MYBOOL) ((filename != NULL) && ((input = fopen(filename,"r")) != NULL)); +@@ -1692,7 +1692,7 @@ + + /* Let's initialize line to all zero's */ + MEMCLEAR(line, BUFSIZ); +- ok = FALSE; ++ ok = FFALSE; + while(fgets(line, BUFSIZ - 1, input)) { + Lineno++; + +@@ -1738,7 +1738,7 @@ + break; + } + /* find first variable index value */ +- in = MPS_getnameidx(lp, field2, FALSE); ++ in = MPS_getnameidx(lp, field2, FFALSE); + #ifdef OldNameMatch + if(in < 0) + in = MPS_getnameidx(lp, field2, TRUE); +@@ -1752,7 +1752,7 @@ + if(field1[0] == 'X') { + /* find second variable index value */ + ib = in; +- in = MPS_getnameidx(lp, field3, FALSE); ++ in = MPS_getnameidx(lp, field3, FFALSE); + #ifdef OldNameMatch + if(in < 0) + in = MPS_getnameidx(lp, field3, TRUE); +@@ -1768,7 +1768,7 @@ + else + lp->is_lower[in] = (MYBOOL) (field1[0] == 'L'); + +- lp->is_basic[in] = FALSE; ++ lp->is_basic[in] = FFALSE; + + } + } +@@ -1801,7 +1801,7 @@ + MPSname = MPSnameFREE; + else { + report(lp, IMPORTANT, "MPS_writeBAS: unrecognized MPS name type.\n"); +- return(FALSE); ++ return(FFALSE); + } + + /* Open the file for writing */ +diff -ru lp_solve_5.5.orig/lp_params.c lp_solve_5.5/lp_params.c +--- lp_solve_5.5.orig/lp_params.c 2019-02-19 10:42:21.372737063 -0600 ++++ lp_solve_5.5/lp_params.c 2019-02-19 11:59:35.984865306 -0600 +@@ -130,7 +130,7 @@ + + static REAL __WINAPI get_mip_gap_rel(lprec *lp) + { +- return(get_mip_gap(lp, FALSE)); ++ return(get_mip_gap(lp, FFALSE)); + } + + static void __WINAPI set_mip_gap_abs(lprec *lp, REAL mip_gap) +@@ -140,7 +140,7 @@ + + static void __WINAPI set_mip_gap_rel(lprec *lp, REAL mip_gap) + { +- set_mip_gap(lp, FALSE, mip_gap); ++ set_mip_gap(lp, FFALSE, mip_gap); + } + + static struct _values pivoting[] = +@@ -219,7 +219,7 @@ + + static struct _values print_sol[] = + { +- { FALSE, "0" }, ++ { FFALSE, "0" }, + { TRUE, "1" }, + { setvalue(AUTOMATIC) }, + }; +@@ -442,15 +442,15 @@ + case EACCES: /* File or directory specified by newname already exists or could not be created (invalid path); or oldname is a directory and newname specifies a different path. */ + FREE(filename0); + FREE(header); +- return(FALSE); ++ return(FFALSE); + break; + } + } + + if((fp = ini_create(filename)) == NULL) +- ret = FALSE; ++ ret = FFALSE; + else { +- params_written = FALSE; ++ params_written = FFALSE; + newline = TRUE; + if(filename0 != NULL) { + fp0 = ini_open(filename0); +@@ -458,13 +458,13 @@ + rename(filename0, filename); + FREE(filename0); + FREE(header); +- return(FALSE); ++ return(FFALSE); + } + looping = TRUE; + while(looping) { + switch(ini_readdata(fp0, buf, sizeof(buf), TRUE)) { + case 0: /* End of file */ +- looping = FALSE; ++ looping = FFALSE; + break; + case 1: /* header */ + ptr1 = strdup(buf); +@@ -525,7 +525,7 @@ + char buf[4096], *header = NULL, *ptr, *ptr1, *ptr2; + + if((fp = ini_open(filename)) == NULL) +- ret = FALSE; ++ ret = FFALSE; + else { + /* create hashtable of all callable commands to find them quickly */ + hashfunctions = create_hash_table(sizeof(functions) / sizeof(*functions), 0); +@@ -553,9 +553,9 @@ + line = 0; + while((ret) && (looping)) { + line++; +- switch(ini_readdata(fp, buf, sizeof(buf), FALSE)) { ++ switch(ini_readdata(fp, buf, sizeof(buf), FFALSE)) { + case 0: /* End of file */ +- looping = FALSE; ++ looping = FFALSE; + break; + case 1: /* header */ + switch(state) { +@@ -565,7 +565,7 @@ + state = 1; + break; + case 1: +- looping = FALSE; ++ looping = FFALSE; + break; + } + break; +@@ -580,7 +580,7 @@ + ptr = strchr(buf, '='); + if(ptr == NULL) { + report(lp, IMPORTANT, "read_params: No equal sign on line %d\n", line); +- ret = FALSE; ++ ret = FFALSE; + } + else { + *ptr = 0; +@@ -588,14 +588,14 @@ + for(ptr2 = ptr - 1; (ptr2 >= ptr1) && (isspace(*ptr2)); ptr2--); + if(ptr2 <= ptr1) { + report(lp, IMPORTANT, "read_params: No parameter name before equal sign on line %d\n", line); +- ret = FALSE; ++ ret = FFALSE; + } + else { + ptr2[1] = 0; + hp = findhash(ptr1, hashfunctions); + if(hp == NULL) { + report(lp, IMPORTANT, "read_params: Unknown parameter name (%s) before equal sign on line %d\n", ptr1, line); +- ret = FALSE; ++ ret = FFALSE; + } + else { + i = hp->index; +@@ -612,7 +612,7 @@ + ptr2++; + if(*ptr2) { + report(lp, IMPORTANT, "read_params: Invalid integer value on line %d\n", line); +- ret = FALSE; ++ ret = FFALSE; + } + break; + case REALfunction: +@@ -621,7 +621,7 @@ + ptr2++; + if(*ptr2) { + report(lp, IMPORTANT, "read_params: Invalid real value on line %d\n", line); +- ret = FALSE; ++ ret = FFALSE; + } + break; + } +@@ -640,14 +640,14 @@ + hp = findhash(ptr1, hashparameters); + if (hp == NULL) { + report(lp, IMPORTANT, "read_params: Invalid parameter name (%s) on line %d\n", ptr1, line); +- ret = FALSE; ++ ret = FFALSE; + } + else { + j = hp->index; + if((j >= functions[i].elements) || + (strcmp(functions[i].values[j].svalue, ptr1))) { + report(lp, IMPORTANT, "read_params: Inappropriate parameter name (%s) on line %d\n", ptr1, line); +- ret = FALSE; ++ ret = FFALSE; + } + else { + intvalue += functions[i].values[j].value; +diff -ru lp_solve_5.5.orig/lp_presolve.c lp_solve_5.5/lp_presolve.c +--- lp_solve_5.5.orig/lp_presolve.c 2019-02-19 10:42:21.372737063 -0600 ++++ lp_solve_5.5/lp_presolve.c 2019-02-19 12:01:01.680867677 -0600 +@@ -80,7 +80,7 @@ + lp->presolve_undo = (presolveundorec *) calloc(1, sizeof(presolveundorec)); + lp->presolve_undo->lp = lp; + if(lp->presolve_undo == NULL) +- return( FALSE ); ++ return( FFALSE ); + return( TRUE ); + } + STATIC MYBOOL inc_presolve_space(lprec *lp, int delta, MYBOOL isrows) +@@ -129,12 +129,12 @@ + presolveundorec *psundo = lp->presolve_undo; + + if(psundo == NULL) +- return( FALSE ); ++ return( FFALSE ); + psundo->orig_rows = orig_rows; + psundo->orig_columns = orig_cols; + psundo->orig_sum = orig_rows + orig_cols; + if(lp->wasPresolved) +- presolve_fillUndo(lp, orig_rows, orig_cols, FALSE); ++ presolve_fillUndo(lp, orig_rows, orig_cols, FFALSE); + return( TRUE ); + } + STATIC MYBOOL presolve_fillUndo(lprec *lp, int orig_rows, int orig_cols, MYBOOL setOrig) +@@ -178,7 +178,7 @@ + slacks = lp->full_duals + lp->presolve_undo->orig_rows; + } + if(mat == NULL) +- return( FALSE ); ++ return( FFALSE ); + + /* Loop backward over the undo chain */ + for(j = mat->col_tag[0]; j > 0; j--) { +@@ -224,7 +224,7 @@ + presolveundorec *psundo = lp->presolve_undo; + + if(psundo == NULL) +- return( FALSE ); ++ return( FFALSE ); + FREE(psundo->orig_to_var); + FREE(psundo->var_to_orig); + FREE(psundo->fixed_rhs); +@@ -242,7 +242,7 @@ + STATIC void presolve_storeDualUndo(presolverec *psdata, int rownr, int colnr) + { + lprec *lp = psdata->lp; +- MYBOOL firstdone = FALSE; ++ MYBOOL firstdone = FFALSE; + int ix, iix, item; + REAL Aij = get_mat(lp, rownr, colnr); + MATrec *mat = lp->matA; +@@ -258,10 +258,10 @@ + if(iix == rownr) + continue; + if(!firstdone) +- firstdone = addUndoPresolve(lp, FALSE, rownr, get_mat(lp, 0, colnr)/Aij, +- get_mat_byindex(lp, ix, FALSE, TRUE)/Aij, iix); ++ firstdone = addUndoPresolve(lp, FFALSE, rownr, get_mat(lp, 0, colnr)/Aij, ++ get_mat_byindex(lp, ix, FFALSE, TRUE)/Aij, iix); + else +- appendUndoPresolve(lp, FALSE, get_mat_byindex(lp, ix, FALSE, TRUE)/Aij, iix); ++ appendUndoPresolve(lp, FFALSE, get_mat_byindex(lp, ix, FFALSE, TRUE)/Aij, iix); + } + } + +@@ -400,14 +400,14 @@ + + INLINE void presolve_range(lprec *lp, int rownr, psrec *ps, REAL *loValue, REAL *hiValue) + { +- *loValue = presolve_sumplumin(lp, rownr, ps, FALSE); ++ *loValue = presolve_sumplumin(lp, rownr, ps, FFALSE); + *hiValue = presolve_sumplumin(lp, rownr, ps, TRUE); + } + + STATIC void presolve_rangeorig(lprec *lp, int rownr, psrec *ps, REAL *loValue, REAL *hiValue, REAL delta) + { + delta = my_chsign(is_chsign(lp, rownr), lp->presolve_undo->fixed_rhs[rownr] + delta); +- *loValue = presolve_sumplumin(lp, rownr, ps, FALSE) + delta; ++ *loValue = presolve_sumplumin(lp, rownr, ps, FFALSE) + delta; + *hiValue = presolve_sumplumin(lp, rownr, ps, TRUE) + delta; + } + +@@ -435,17 +435,17 @@ + if(rownr != origrownr) + report(lp, NORMAL, " ... Input row base used for testing was %s\n", + get_row_name(lp, origrownr)); +- status = FALSE; ++ status = FFALSE; + } + + /* Check the upper bound */ +- value = presolve_sumplumin(lp, rownr, psdata->rows, FALSE); ++ value = presolve_sumplumin(lp, rownr, psdata->rows, FFALSE); + RHS = get_rh_upper(lp, rownr); + if(value > RHS+lp->epssolution) { + contype = get_constr_type(lp, rownr); + report(lp, NORMAL, "presolve_rowfeasible: Upper bound infeasibility in %s row %s (%g >> %g)\n", + get_str_constr_type(lp, contype), get_row_name(lp, rownr), value, RHS); +- status = FALSE; ++ status = FFALSE; + } + if(userowmap) + rownr = nextActiveLink(psdata->rows->varmap, rownr); +@@ -461,7 +461,7 @@ + MATrec *mat = lp->matA; + int colnr, ix, ie, nx, jx, je, *cols, *rows, n; + int nz = mat->col_end[lp->columns] - 1; +- MYBOOL status = FALSE; ++ MYBOOL status = FFALSE; + + for(colnr = 1; colnr <= lp->columns; colnr++) { + rows = psdata->cols->next[colnr]; +@@ -774,7 +774,7 @@ + #if 1 + my_roundzero(lp->orig_rhs[rownr], epsvalue); + #else +- lp->orig_rhs[rownr] = presolve_roundrhs(lp, lp->orig_rhs[rownr], FALSE); ++ lp->orig_rhs[rownr] = presolve_roundrhs(lp, lp->orig_rhs[rownr], FFALSE); + #endif + lp->presolve_undo->fixed_rhs[rownr] += fixdelta; + } +@@ -792,7 +792,7 @@ + n = list[0]; + for(i = 1; i <= n; i++) + if(isActiveLink(psdata->rows->varmap, list[i])) { +- presolve_rowremove(psdata, list[i], FALSE); ++ presolve_rowremove(psdata, list[i], FFALSE); + countR++; + } + if(nConRemove != NULL) +@@ -812,7 +812,7 @@ + status = presolve_setstatus(psdata, INFEASIBLE); + break; + } +- presolve_colremove(psdata, ix, FALSE); ++ presolve_colremove(psdata, ix, FFALSE); + countC++; + } + else if(SOS_is_member(SOS, 0, ix)) +@@ -968,7 +968,7 @@ + return( status ); + + /* Allocate working member list */ +- if(!allocINT(lp, &fixed, lp->columns+1, FALSE) ) ++ if(!allocINT(lp, &fixed, lp->columns+1, FFALSE) ) + return( lp->spx_status ); + + /* Check if we have SOS'es that are already satisfied or fixable/satisfiable */ +@@ -1007,7 +1007,7 @@ + } + } + /* Remove the SOS */ +- delete_SOSrec(lp->SOS, i /* , FALSE */); ++ delete_SOSrec(lp->SOS, i /* , FFALSE */); + } + /* Otherwise, try to fix variables outside the SOS type window */ + else if(fixed[0] > 0) { +@@ -1054,11 +1054,11 @@ + int i, k, j; + SOSrec *SOS; + REAL newvalue; +- MYBOOL *fixed = NULL, status = FALSE; ++ MYBOOL *fixed = NULL, status = FFALSE; + + /* Allocate working member list */ + if(!allocMYBOOL(lp, &fixed, lp->columns+1, TRUE) ) +- return(FALSE); ++ return(FFALSE); + + /* Fix variables in SOS's where colnr is a member */ + i = SOS_count(lp); +@@ -1100,7 +1100,7 @@ + if(SOS_is_member(lp->SOS, i, colnr)) { + /* Always delete SOS1's */ + if(SOS->type == SOS1) +- delete_SOSrec(lp->SOS, i /* , FALSE */); ++ delete_SOSrec(lp->SOS, i /* , FFALSE */); + /* Only delete leading or trailing SOS members in higher-order SOS'es that are fixed at 0; + (note that this section of the code will never be called in the current setup) */ + else { +@@ -1244,14 +1244,14 @@ + if((reflotest > refuptest + epsvalue) || + #endif + !presolve_singletonbounds(psdata, rownr, colnr, &coeff_bl, &coeff_bu, NULL)) +- return( FALSE ); ++ return( FFALSE ); + + /* Base data is Ok, now check against against each other */ + epsvalue = MAX(reflotest-coeff_bu, coeff_bl-refuptest) / epsvalue; + if(epsvalue > PRESOLVE_BOUNDSLACK) { + report(lp, NORMAL, "presolve_altsingletonvalid: Singleton variable %s in row %s infeasible (%g)\n", + get_col_name(lp, colnr), get_row_name(lp, rownr), MAX(reflotest-coeff_bu, coeff_bl-refuptest)); +- return( FALSE ); ++ return( FFALSE ); + } + else + return( TRUE ); +@@ -1261,7 +1261,7 @@ + REAL *lobound, REAL *upbound, REAL *aval, MYBOOL *rowbinds) + { + lprec *lp = psdata->lp; +- MYBOOL rowbindsvar = FALSE, status = FALSE; ++ MYBOOL rowbindsvar = FFALSE, status = FFALSE; + REAL coeff_a, LHS, RHS, netX, Xupper, Xlower, epsvalue = psdata->epsvalue; + + /* Get variable bounds for netting */ +@@ -1292,7 +1292,7 @@ + LHS -= netX-coeff_a*Xlower; + LHS /= coeff_a; + if(LHS < Xupper - epsvalue) { +- Xupper = presolve_roundrhs(lp, LHS, FALSE); ++ Xupper = presolve_roundrhs(lp, LHS, FFALSE); + status = AUTOMATIC; + } + else if(LHS < Xupper + epsvalue) +@@ -1300,7 +1300,7 @@ + } + } + +- netX = presolve_sumplumin(lp, rownr, psdata->rows, FALSE); ++ netX = presolve_sumplumin(lp, rownr, psdata->rows, FFALSE); + if(!my_infinite(lp, RHS) && !my_infinite(lp, netX)) { + if(coeff_a < 0) { + if(!my_infinite(lp, Xupper)) { +@@ -1318,7 +1318,7 @@ + RHS -= netX-coeff_a*Xlower; + RHS /= coeff_a; + if(RHS < Xupper - epsvalue) { +- Xupper = presolve_roundrhs(lp, RHS, FALSE); ++ Xupper = presolve_roundrhs(lp, RHS, FFALSE); + status |= AUTOMATIC; + } + else if(RHS < Xupper + epsvalue) +@@ -1343,10 +1343,10 @@ + { + if(psdata->forceupdate) { + presolve_updatesums(psdata); +- psdata->forceupdate = FALSE; ++ psdata->forceupdate = FFALSE; + } + if(!presolve_rowfeasible(psdata, 0, TRUE)) +- return( FALSE ); ++ return( FFALSE ); + else + return( TRUE ); + } +@@ -1375,7 +1375,7 @@ + #ifdef Paranoia + if(((LOold > LOnew) && !is_semicont(lp, colnr)) || (UPold < UPnew)) { + report(lp, SEVERE, "presolve_coltighten: Inconsistent new bounds requested for column %d\n", colnr); +- return( FALSE ); ++ return( FFALSE ); + } + #endif + if(count != NULL) +@@ -1487,7 +1487,7 @@ + else { + report(lp, NORMAL, "presolve_coltighten: Found column %s with LB %g > UB %g\n", + get_col_name(lp, colnr), LOnew, UPnew); +- return( FALSE ); ++ return( FFALSE ); + } + } + if(lp->spx_trace || (lp->verbose > DETAILED)) +@@ -1588,7 +1588,7 @@ + { + lprec *lp = psdata->lp; + int i, ix, ie; +- MYBOOL isneg, lofinite, upfinite, doupdate = FALSE, chsign = is_chsign(lp, rownr); ++ MYBOOL isneg, lofinite, upfinite, doupdate = FFALSE, chsign = is_chsign(lp, rownr); + REAL lobound, upbound, lovalue, upvalue, + Value, fixvalue, fixprod, mult; + MATrec *mat = lp->matA; +@@ -1612,7 +1612,7 @@ + } + set_dv_bounds(psdata, rownr, fixvalue, fixvalue); + if(fixvalue != 0) +- addUndoPresolve(lp, FALSE, rownr, fixvalue, 0, 0); ++ addUndoPresolve(lp, FFALSE, rownr, fixvalue, 0, 0); + mult = -1; + } + else { +@@ -1673,7 +1673,7 @@ + if(isneg) { + if((ps->negupper[i] < lp->infinite) && lofinite) { + ps->negupper[i] += mult*lovalue; +- ps->negupper[i] = presolve_roundrhs(lp, ps->negupper[i], FALSE); ++ ps->negupper[i] = presolve_roundrhs(lp, ps->negupper[i], FFALSE); + } + else if(remove && !lofinite) + doupdate = TRUE; +@@ -1683,7 +1683,7 @@ + else { + if((ps->pluupper[i] < lp->infinite) && upfinite) { + ps->pluupper[i] += mult*upvalue; +- ps->pluupper[i] = presolve_roundrhs(lp, ps->pluupper[i], FALSE); ++ ps->pluupper[i] = presolve_roundrhs(lp, ps->pluupper[i], FFALSE); + } + else if(remove && !upfinite) + doupdate = TRUE; +@@ -1721,7 +1721,7 @@ + (lovalue > Value)) { + report(lp, IMPORTANT, "presolve: Row %s (%g << %g) infeasibility in column %s (OF=%g)\n", + get_row_name(lp, rownr), lovalue, upvalue, get_col_name(lp, i), Value); +- return( FALSE ); ++ return( FFALSE ); + } + } + } +@@ -1775,7 +1775,7 @@ + { + lprec *lp = psdata->lp; + int i, ix, ie; +- MYBOOL isneg, lofinite, upfinite, doupdate = FALSE, doOF = TRUE; ++ MYBOOL isneg, lofinite, upfinite, doupdate = FFALSE, doOF = TRUE; + REAL lobound, upbound, lovalue, upvalue, + Value, fixvalue, mult; + MATrec *mat = lp->matA; +@@ -1882,7 +1882,7 @@ + if(isneg) { + if((ps->negupper[i] < lp->infinite) && lofinite) { + ps->negupper[i] += mult*lovalue; +- ps->negupper[i] = presolve_roundrhs(lp, ps->negupper[i], FALSE); ++ ps->negupper[i] = presolve_roundrhs(lp, ps->negupper[i], FFALSE); + } + else if(remove && !lofinite) + doupdate = TRUE; +@@ -1892,7 +1892,7 @@ + else { + if((ps->pluupper[i] < lp->infinite) && upfinite) { + ps->pluupper[i] += mult*upvalue; +- ps->pluupper[i] = presolve_roundrhs(lp, ps->pluupper[i], FALSE); ++ ps->pluupper[i] = presolve_roundrhs(lp, ps->pluupper[i], FFALSE); + } + else if(remove && !upfinite) + doupdate = TRUE; +@@ -1943,13 +1943,13 @@ + report(lp, NORMAL, "presolve_colfix: Variable %s (%g << %g) infeasibility in row %s (%g << %g)\n", + get_col_name(lp, colnr), lovalue, upvalue, + get_row_name(lp, i), get_rh_lower(lp,i), get_rh_upper(lp, i)); +- return( FALSE ); ++ return( FFALSE ); + } + } + } + BlockEnd: + if(doOF) { +- doOF = FALSE; ++ doOF = FFALSE; + if(ix < ie) + goto Restart; + } +@@ -2001,7 +2001,7 @@ + if(((loX < 0) && (upX > 0)) || + (fabs(upX-loX) < lp->epsvalue) || + SOS_is_member_of_type(lp->SOS, colnr, SOSn)) +- return( FALSE ); ++ return( FFALSE ); + isMI = (MYBOOL) (upX <= 0); + + /* Retrieve OF (standard form assuming maximization) */ +@@ -2027,18 +2027,18 @@ + upR = get_rh_upper(lp, i); + if(!presolve_singletonbounds(psdata, i, colnr, &loR, &upR, &val)) { + *status = presolve_setstatus(psdata, INFEASIBLE); +- return( FALSE ); ++ return( FFALSE ); + } + if(loR > loX + psdata->epsvalue) + loX = presolve_roundrhs(lp, loR, TRUE); + if(upR < upX - psdata->epsvalue) +- upX = presolve_roundrhs(lp, upR, FALSE); ++ upX = presolve_roundrhs(lp, upR, FFALSE); + continue; + } + else + isDualFREE = my_infinite(lp, get_rh_range(lp, i)) || /* Explicitly free */ + ((presolve_sumplumin(lp, i, psdata->rows, TRUE)-eps <= get_rh_upper(lp, i)) && /* Implicitly free */ +- (presolve_sumplumin(lp, i, psdata->rows, FALSE)+eps >= get_rh_lower(lp, i))); ++ (presolve_sumplumin(lp, i, psdata->rows, FFALSE)+eps >= get_rh_lower(lp, i))); + if(isDualFREE) { + if(signOF == 0) /* Test on the basis of identical signs in the constraints */ + signOF = my_sign(*value); +@@ -2055,7 +2055,7 @@ + } + else if(signOF > 0) { + if(my_infinite(lp, loX)) +- isDualFREE = FALSE; ++ isDualFREE = FFALSE; + else { + if(is_int(lp, colnr)) + *fixValue = ceil(loX-PRESOLVE_EPSVALUE); +@@ -2065,7 +2065,7 @@ + } + else { + if(my_infinite(lp, upX)) +- isDualFREE = FALSE; ++ isDualFREE = FFALSE; + else { + if(is_int(lp, colnr) && (upX != 0)) + *fixValue = floor(upX+PRESOLVE_EPSVALUE); +@@ -2074,7 +2074,7 @@ + } + } + if((*fixValue != 0) && SOS_is_member(lp->SOS, 0, colnr)) +- return( FALSE ); ++ return( FFALSE ); + + } + +@@ -2088,7 +2088,7 @@ + int i, ix, item; + REAL loLim, absvalue, epsvalue = psdata->epsvalue; + MATrec *mat = lp->matA; +- MYBOOL chsign, canfix = FALSE; ++ MYBOOL chsign, canfix = FFALSE; + + if(!is_binary(lp, colnr)) + return( canfix ); +@@ -2134,7 +2134,7 @@ + int i, ix, item; + REAL loLim, upLim, range, absvalue, epsvalue = psdata->epsvalue, tolgap; + MATrec *mat = lp->matA; +- MYBOOL chsign, status = FALSE; ++ MYBOOL chsign, status = FFALSE; + + if(!is_binary(lp, colnr)) + return( status ); +@@ -2153,7 +2153,7 @@ + chsign = is_chsign(lp, i); + + /* Get the constraint value limits based on variable bounds, normalized to LE constraint */ +- loLim = presolve_sumplumin(lp, i, psdata->rows, FALSE); ++ loLim = presolve_sumplumin(lp, i, psdata->rows, FFALSE); + upLim = presolve_sumplumin(lp, i, psdata->rows, TRUE); + if(chsign) { + loLim = my_chsign(chsign, loLim); +@@ -2278,7 +2278,7 @@ + firstix = ix; + for(RT1 = 0; (ix > 0) && (RT1 < RT2) && (status == RUNNING); + ix = prevActiveLink(psdata->rows->varmap, ix), RT1++) { +- candelete = FALSE; ++ candelete = FFALSE; + if(presolve_rowlength(psdata, ix) != j) + continue; + +@@ -2292,8 +2292,8 @@ + continue; + + /* We have a candidate row; check if the entries have a fixed non-zero ratio */ +- Value1 = get_mat_byindex(lp, iix, TRUE, FALSE); +- Value2 = get_mat_byindex(lp, jjx, TRUE, FALSE); ++ Value1 = get_mat_byindex(lp, iix, TRUE, FFALSE); ++ Value2 = get_mat_byindex(lp, jjx, TRUE, FFALSE); + bound = Value1 / Value2; + Value1 = bound; + +@@ -2304,8 +2304,8 @@ + iix = presolve_nextcol(psdata, ix, &item1); + if(ROW_MAT_COLNR(iix) != ROW_MAT_COLNR(jjx)) + break; +- Value1 = get_mat_byindex(lp, iix, TRUE, FALSE); +- Value2 = get_mat_byindex(lp, jjx, TRUE, FALSE); ++ Value1 = get_mat_byindex(lp, iix, TRUE, FFALSE); ++ Value2 = get_mat_byindex(lp, jjx, TRUE, FFALSE); + + /* If the ratio is different from the reference value we have a mismatch */ + Value1 = Value1 / Value2; +@@ -2431,7 +2431,7 @@ + Rvalue = fabs(lp->orig_rhs[i]-Rvalue); + if(is_constr_type(lp, i, EQ) && (Rvalue > epsvalue)) { + report(lp, NORMAL, "presolve_reduceGCD: Infeasible equality constraint %d\n", i); +- status = FALSE; ++ status = FFALSE; + break; + } + if(!my_infinite(lp, lp->orig_upbo[i])) +@@ -2464,8 +2464,8 @@ + return( status ); + + /* Get the OF row */ +- allocINT(lp, &rownr, map->count+1, FALSE); +- allocREAL(lp, &ratio, map->count+1, FALSE); ++ allocINT(lp, &rownr, map->count+1, FFALSE); ++ allocREAL(lp, &ratio, map->count+1, FFALSE); + + /* Loop over each row trying to find equal entries in the OF */ + rownr[0] = 0; +@@ -2543,7 +2543,7 @@ + { + int jx, jjx, i = 0, item; + MATrec *mat = lp->matA; +- MYBOOL error = FALSE; ++ MYBOOL error = FFALSE; + + do { + +@@ -2608,8 +2608,8 @@ + + /* Create condensed row map */ + allocINT(lp, &rmapin, lp->rows+1, TRUE); +- allocINT(lp, &rmapout, psdata->EQmap->count+1, FALSE); +- allocINT(lp, &cmapout, lp->columns+1, FALSE); ++ allocINT(lp, &rmapout, psdata->EQmap->count+1, FFALSE); ++ allocINT(lp, &cmapout, lp->columns+1, FFALSE); + n = 0; + for(i = firstActiveLink(psdata->EQmap); i != 0; i = nextActiveLink(psdata->EQmap, i)) { + n++; +@@ -2666,8 +2666,8 @@ + + /* Tally counts */ + createLink(lp->rows, &EQ2, NULL); +- if((EQ2 == NULL) || !allocREAL(lp, &colvalue, nrows+1, FALSE) || +- !allocREAL(lp, &delvalue, nrows+1, FALSE)) ++ if((EQ2 == NULL) || !allocREAL(lp, &colvalue, nrows+1, FFALSE) || ++ !allocREAL(lp, &delvalue, nrows+1, FFALSE)) + goto Finish; + for(i = firstActiveLink(psdata->EQmap); i > 0; i = nextActiveLink(psdata->EQmap, i)) { + if(presolve_rowlength(psdata, i) == 2) +@@ -2785,11 +2785,11 @@ + if(freshupdate) + mat_expandcolumn(mat, jjx, colvalue, NULL, TRUE); + else +- mat_expandcolumn(rev, colindex[jjx], colvalue, NULL, FALSE); ++ mat_expandcolumn(rev, colindex[jjx], colvalue, NULL, FFALSE); + if((colindex == NULL) || (colindex[jx] == 0)) + mat_expandcolumn(mat, jx, delvalue, NULL, TRUE); + else +- mat_expandcolumn(rev, colindex[jx], delvalue, NULL, FALSE); ++ mat_expandcolumn(rev, colindex[jx], delvalue, NULL, FFALSE); + + /* Add variable reconstruction information */ + addUndoPresolve(lp, TRUE, jx, Value1, Value2, jjx); +@@ -2807,7 +2807,7 @@ + if(is_int(lp, jjx)) + lp->orig_upbo[k] = floor(bound + lp->epsint); + else +- lp->orig_upbo[k] = presolve_roundrhs(lp, bound, FALSE); ++ lp->orig_upbo[k] = presolve_roundrhs(lp, bound, FFALSE); + } + } + else { +@@ -2829,7 +2829,7 @@ + if(is_int(lp, jjx)) + lp->orig_upbo[k] = floor(bound + lp->epsint); + else +- lp->orig_upbo[k] = presolve_roundrhs(lp, bound, FALSE); ++ lp->orig_upbo[k] = presolve_roundrhs(lp, bound, FFALSE); + } + } + else { +@@ -2950,12 +2950,12 @@ + DV = createUndoLadder(lp, nrows, lp->columns / RESIZEFACTOR); + rev = DV->tracker; + rev->epsvalue = mat->epsvalue; +- allocINT(lp, &(rev->col_tag), mat->columns_alloc+1, FALSE); ++ allocINT(lp, &(rev->col_tag), mat->columns_alloc+1, FFALSE); + allocINT(lp, &colindex, lp->columns+1, TRUE); + rev->col_tag[0] = 0; + } + n = rev->col_tag[0] = incrementUndoLadder(DV); +- mat_setcol(rev, n, 0, colvalue, NULL, FALSE, FALSE); ++ mat_setcol(rev, n, 0, colvalue, NULL, FFALSE, FFALSE); + rev->col_tag[n] = jjx; + + /* Save index to updated vector, but specially handle case where we have +@@ -2965,7 +2965,7 @@ + colindex[jjx] = n; + + /* Delete the column dependent variable */ +- jx = presolve_colremove(psdata, jx, FALSE); ++ jx = presolve_colremove(psdata, jx, FFALSE); + iVarsFixed++; + + /* Check if we have been lucky enough to have eliminated the independent +@@ -2976,11 +2976,11 @@ + jx, jjx, get_row_name(lp, i)); + #endif + if(presolve_colfix(psdata, jjx, 0.0, TRUE, nc)) +- jjx = presolve_colremove(psdata, jjx, FALSE); ++ jjx = presolve_colremove(psdata, jjx, FFALSE); + } + + /* Delete the row */ +- presolve_rowremove(psdata, i, FALSE); ++ presolve_rowremove(psdata, i, FFALSE); + iRowsRemoved++; + } + +@@ -2989,7 +2989,7 @@ + mat_mapreplace(mat, psdata->rows->varmap, psdata->cols->varmap, rev); + presolve_validate(psdata, TRUE); + #ifdef PresolveForceUpdateMax +- mat_computemax(mat /* , FALSE */); ++ mat_computemax(mat /* , FFALSE */); + #endif + psdata->forceupdate = TRUE; + } +@@ -3016,7 +3016,7 @@ + { + int i, ix, ie; + REAL Tlower, Tupper; +- MYBOOL status, rowbinds, isfree = FALSE; ++ MYBOOL status, rowbinds, isfree = FFALSE; + MATrec *mat = lp->matA; + + if(my_infinite(lp, get_lowbo(lp, colnr)) && my_infinite(lp, get_upbo(lp, colnr))) +@@ -3039,7 +3039,7 @@ + STATIC MYBOOL presolve_impliedcolfix(presolverec *psdata, int rownr, int colnr, MYBOOL isfree) + { + lprec *lp = psdata->lp; +- MYBOOL signflip, undoadded = FALSE; ++ MYBOOL signflip, undoadded = FFALSE; + MATrec *mat = lp->matA; + int jx, i, ib, ie = mat->row_end[rownr]; + REAL varLo = 0, varHi = 0, varRange, conRange = 0, matValue = 0, dual, RHS = lp->orig_rhs[rownr], +@@ -3047,10 +3047,10 @@ + + /* We cannot have semi-continuous or non-qualifying integers */ + if(is_semicont(lp, colnr) || is_SOS_var(lp, colnr)) +- return( FALSE ); ++ return( FFALSE ); + if(is_int(lp, colnr)) { + if(!isActiveLink(psdata->INTmap, rownr) || !is_presolve(lp, PRESOLVE_KNAPSACK)) +- return( FALSE ); ++ return( FFALSE ); + /* colnr must have a coefficient equal to the smallest in the row */ + varRange = lp->infinite; + i = 0; +@@ -3069,21 +3069,21 @@ + /* Cannot accept case where result can be fractional */ + else if((pivot > dual + psdata->epsvalue) || + ((pivot > 0) && (fabs(fmod(dual, pivot)) > psdata->epsvalue))) +- return( FALSE ); ++ return( FFALSE ); + } + } + + /* Ascertain that the pivot value is large enough to preserve stability */ + pivot = matAij; + if(fabs(pivot) < psdata->epspivot*mat->colmax[colnr]) +- return( FALSE ); ++ return( FFALSE ); + + /* Must ascertain that the row variables are not SOS'es; this is because + the eliminated variable will be a function of another variable. */ + if(SOS_count(lp) > 0) { + for(ib = mat->row_end[rownr-1]; ib < ie; ib++) + if(SOS_is_member(lp->SOS, 0, ROW_MAT_COLNR(ib))) +- return( FALSE ); ++ return( FFALSE ); + } + + /* Calculate the dual value */ +@@ -3107,7 +3107,7 @@ + non-infinite. */ + if(isfree) { + SETMIN(RHS, presolve_sumplumin(lp, rownr, psdata->rows, TRUE)); +- matValue = presolve_sumplumin(lp, rownr, psdata->rows, FALSE); ++ matValue = presolve_sumplumin(lp, rownr, psdata->rows, FFALSE); + conRange = get_rh_lower(lp, rownr); + conRange = RHS - MAX(matValue, conRange); + signflip = (MYBOOL) ((dual > 0) && +@@ -3156,7 +3156,7 @@ + undoadded = addUndoPresolve(lp, TRUE, colnr, matValue, 0.0, 0); + /* Add undo information for the dual of the deleted constraint */ + if(dual != 0) +- addUndoPresolve(lp, FALSE, rownr, dual, 0.0, 0); ++ addUndoPresolve(lp, FFALSE, rownr, dual, 0.0, 0); + } + + /* Prepare for deleting implied slack variable. The following two cases are +@@ -3256,14 +3256,14 @@ + + size++; + +- allocINT(lp, &ps->empty, size, FALSE); ++ allocINT(lp, &ps->empty, size, FFALSE); + ps->empty[0] = 0; + +- allocREAL(lp, &ps->pluupper, size, FALSE); +- allocREAL(lp, &ps->negupper, size, FALSE); +- allocREAL(lp, &ps->plulower, size, FALSE); +- allocREAL(lp, &ps->neglower, size, FALSE); +- allocINT(lp, &ps->infcount, size, FALSE); ++ allocREAL(lp, &ps->pluupper, size, FFALSE); ++ allocREAL(lp, &ps->negupper, size, FFALSE); ++ allocREAL(lp, &ps->plulower, size, FFALSE); ++ allocREAL(lp, &ps->neglower, size, FFALSE); ++ allocINT(lp, &ps->infcount, size, FFALSE); + + ps->next = (int **) calloc(size, sizeof(*(ps->next))); + +@@ -3329,14 +3329,14 @@ + + /* Save incoming primal bounds */ + k = lp->sum + 1; +- allocREAL(lp, &psdata->pv_lobo, k, FALSE); ++ allocREAL(lp, &psdata->pv_lobo, k, FFALSE); + MEMCOPY(psdata->pv_lobo, lp->orig_lowbo, k); +- allocREAL(lp, &psdata->pv_upbo, k, FALSE); ++ allocREAL(lp, &psdata->pv_upbo, k, FFALSE); + MEMCOPY(psdata->pv_upbo, lp->orig_upbo, k); + + /* Create and initialize dual value (Langrangean and slack) limits */ +- allocREAL(lp, &psdata->dv_lobo, k, FALSE); +- allocREAL(lp, &psdata->dv_upbo, k, FALSE); ++ allocREAL(lp, &psdata->dv_lobo, k, FFALSE); ++ allocREAL(lp, &psdata->dv_upbo, k, FFALSE); + for(i = 0; i <= nrows; i++) { + psdata->dv_lobo[i] = (is_constr_type(lp, i, EQ) ? -lp->infinite : 0); + psdata->dv_upbo[i] = lp->infinite; +@@ -3516,7 +3516,7 @@ + /* Loop over active columns */ + for(j = firstActiveLink(psdata->cols->varmap); j != 0; + j = nextActiveLink(psdata->cols->varmap, j)) { +- presolve_colfix(psdata, j, lp->infinite, FALSE, NULL); ++ presolve_colfix(psdata, j, lp->infinite, FFALSE, NULL); + } + + #ifdef UseDualPresolve +@@ -3530,7 +3530,7 @@ + /* Loop over active rows */ + for(j = firstActiveLink(psdata->rows->varmap); j != 0; + j = nextActiveLink(psdata->rows->varmap, j)) { +- presolve_rowfix(psdata, j, lp->infinite, FALSE, NULL); ++ presolve_rowfix(psdata, j, lp->infinite, FFALSE, NULL); + } + #endif + +@@ -3540,7 +3540,7 @@ + STATIC MYBOOL presolve_finalize(presolverec *psdata) + { + lprec *lp = psdata->lp; +- MYBOOL compactvars = FALSE; ++ MYBOOL compactvars = FFALSE; + int ke, n; + + /* Save eliminated rows and columns for restoration purposes */ +@@ -3551,7 +3551,7 @@ + #endif + + /* Check if OF columns are to be deleted */ +- lp->presolve_undo->OFcolsdeleted = FALSE; ++ lp->presolve_undo->OFcolsdeleted = FFALSE; + for(n = firstInactiveLink(psdata->cols->varmap); (n != 0) && !lp->presolve_undo->OFcolsdeleted; + n = nextInactiveLink(psdata->cols->varmap, n)) + lp->presolve_undo->OFcolsdeleted = (MYBOOL) (lp->orig_obj[n] != 0); +@@ -3752,7 +3752,7 @@ + /* Let us start from the top of the list, going forward and looking + for the longest possible dominating row */ + if(!allocREAL(lp, &rowvalues, lp->columns + 1, TRUE) || +- !allocINT(lp, &coldel, lp->columns + 1, FALSE)) ++ !allocINT(lp, &coldel, lp->columns + 1, FFALSE)) + goto Finish; + + for(ib = 0; ib < n; ib++) { +@@ -3946,7 +3946,7 @@ + /* Let us start from the top of the list, going forward and looking + for the longest possible dominated column */ + if(!allocREAL(lp, &colvalues, lp->rows + 1, TRUE) || +- !allocINT(lp, &coldel, lp->columns + 1, FALSE)) ++ !allocINT(lp, &coldel, lp->columns + 1, FFALSE)) + goto Finish; + + for(ib = 0; ib < n; ib++) { +@@ -4151,8 +4151,8 @@ + /* Let us start from the top of the list, going forward and looking + for the longest possible dominated column */ + if(!allocREAL(lp, &colvalues, nrows + 1, TRUE) || +- !allocREAL(lp, &colobj, n + 1, FALSE) || +- !allocINT(lp, &coldel, n + 1, FALSE)) ++ !allocREAL(lp, &colobj, n + 1, FFALSE) || ++ !allocINT(lp, &coldel, n + 1, FFALSE)) + goto Finish; + + for(ib = 0; ib < n; ib++) { +@@ -4227,7 +4227,7 @@ + + /* Find the dominant columns, fix and delete the others */ + if(coldel[0] > 1) { +- qsortex(colobj+1, coldel[0], 0, sizeof(*colobj), FALSE, compareREAL, coldel+1, sizeof(*coldel)); ++ qsortex(colobj+1, coldel[0], 0, sizeof(*colobj), FFALSE, compareREAL, coldel+1, sizeof(*coldel)); + /* if(rhsval+lp->epsvalue < lp->infinite) { */ + jb = (NATURAL) (rhsval+lp->epsvalue); + /* printf("%f / %d\n", rhsval, jb); */ +@@ -4301,7 +4301,7 @@ + /* Let us start from the top of the list, going forward and looking + for the longest possible identical column */ + if(!allocREAL(lp, &colvalues, lp->rows + 1, TRUE) || +- !allocINT(lp, &coldel, lp->columns + 1, FALSE)) ++ !allocINT(lp, &coldel, lp->columns + 1, FFALSE)) + goto Finish; + + for(ib = 0; ib < n; ib++) { +@@ -4524,7 +4524,7 @@ + + /* Create associated sorted map of indeces to equality constraints; + note that we need to have a unit offset for compatibility. */ +- allocINT(lp, &nzidx, lp->columns + 1, FALSE); ++ allocINT(lp, &nzidx, lp->columns + 1, FFALSE); + createLink(lp->rows, &EQlist, NULL); + for(ib = 0; ib < n; ib++) { + i = QS[ib].int4.intval; +@@ -4741,11 +4741,11 @@ + + /* Let us condense the matrix if we modified the constraint matrix */ + if(iCoeffChanged > 0) { +- mat->row_end_valid = FALSE; ++ mat->row_end_valid = FFALSE; + mat_zerocompact(mat); + presolve_validate(psdata, TRUE); + #ifdef PresolveForceUpdateMax +- mat_computemax(mat /* , FALSE */); ++ mat_computemax(mat /* , FFALSE */); + #endif + psdata->forceupdate = TRUE; + } +@@ -4760,14 +4760,14 @@ + STATIC int presolve_SOS1(presolverec *psdata, int *nCoeffChanged, int *nConRemove, int *nVarFixed, int *nSOS, int *nSum) + { + lprec *lp = psdata->lp; +- MYBOOL candelete, SOS_GUBactive = FALSE; ++ MYBOOL candelete, SOS_GUBactive = FFALSE; + int iCoeffChanged = 0, iConRemove = 0, iSOS = 0, + i,ix,iix, j,jx,jjx, status = RUNNING; + REAL Value1; + MATrec *mat = lp->matA; + + for(i = lastActiveLink(psdata->rows->varmap); i > 0; ) { +- candelete = FALSE; ++ candelete = FFALSE; + Value1 = get_rh(lp, i); + jx = get_constr_type(lp, i); + if((Value1 == 1) && (presolve_rowlength(psdata, i) >= MIN_SOS1LENGTH) && +@@ -4889,9 +4889,9 @@ + + /* Clear unnecessary semicont-definitions */ + if((lp->sc_vars > 0) && (Value1 == 0) && is_semicont(lp, j)) +- set_semicont(lp, j, FALSE); ++ set_semicont(lp, j, FFALSE); + +- candelete = FALSE; ++ candelete = FFALSE; + item = 0; + ix = lp->rows + j; + +@@ -5079,7 +5079,7 @@ + else if(impliedslack && + (countNZ > 1) && + is_constr_type(lp, i, EQ) && +- presolve_impliedcolfix(psdata, i, j, FALSE)) { ++ presolve_impliedcolfix(psdata, i, j, FFALSE)) { + report(lp, DETAILED, "presolve_freeandslacks: Eliminated implied slack variable %s via row %s\n", + get_col_name(lp, j), get_row_name(lp, i)); + psdata->forceupdate = TRUE; +@@ -5120,7 +5120,7 @@ + } + else { + *target += ValueA * coeff_bu; +- *target = presolve_roundrhs(lp, *target, FALSE); ++ *target = presolve_roundrhs(lp, *target, FFALSE); + } + } + } +@@ -5144,7 +5144,7 @@ + } + else { + *target -= ValueA * coeff_bu; +- *target = presolve_roundrhs(lp, *target, FALSE); ++ *target = presolve_roundrhs(lp, *target, FFALSE); + } + } + presolve_colfix(psdata, j, coeff_bl, TRUE, &iVarFixed); +@@ -5182,7 +5182,7 @@ + #ifdef Paranoia + if(!presolve_testrow(psdata, nextActiveLink(psdata->rows->varmap, i))) { + #else +- if((j > 1) && !psdata->forceupdate && !presolve_rowfeasible(psdata, i, FALSE)) { ++ if((j > 1) && !psdata->forceupdate && !presolve_rowfeasible(psdata, i, FFALSE)) { + #endif + status = presolve_setstatus(psdata, INFEASIBLE); + break; +@@ -5209,7 +5209,7 @@ + iRangeTighten++; + } + if(upsum < uprhs-epsvalue) { +- set_rh_upper(lp, i, presolve_roundrhs(lp, upsum, FALSE)); ++ set_rh_upper(lp, i, presolve_roundrhs(lp, upsum, FFALSE)); + iRangeTighten++; + } + } +@@ -5218,7 +5218,7 @@ + if(tightenbounds && mat_validate(mat)) { + #if 1 + if(j > 1) +- status = presolve_rowtighten(psdata, i, &iBoundTighten, FALSE); ++ status = presolve_rowtighten(psdata, i, &iBoundTighten, FFALSE); + #else + if((MIP_count(lp) > 0) && (j > 1)) + status = presolve_rowtighten(psdata, i, &iBoundTighten, TRUE); +@@ -5250,14 +5250,14 @@ + + for(i = lastActiveLink(psdata->rows->varmap); (i > 0) && (status == RUNNING); ) { + +- candelete = FALSE; ++ candelete = FFALSE; + + /* First identify any full row infeasibilities + Note: Handle singletons below to ensure that conflicting multiple singleton + rows with this variable do not provoke notice of infeasibility */ + j = presolve_rowlengthex(psdata, i); + if((j > 1) && +- !psdata->forceupdate && !presolve_rowfeasible(psdata, i, FALSE)) { ++ !psdata->forceupdate && !presolve_rowfeasible(psdata, i, FFALSE)) { + status = presolve_setstatus(psdata, INFEASIBLE); + break; + } +@@ -5305,7 +5305,7 @@ + /* Proceed to fix and remove variable (if it is not a SOS member) */ + if(status == RUNNING) { + if((fabs(Value2-Value1) < epsvalue) && (fabs(Value2) > epsvalue)) { +- MYBOOL isSOS = (MYBOOL) (SOS_is_member(lp->SOS, 0, j) != FALSE), ++ MYBOOL isSOS = (MYBOOL) (SOS_is_member(lp->SOS, 0, j) != FFALSE), + deleteSOS = isSOS && presolve_candeletevar(psdata, j); + if((Value1 != 0) && deleteSOS) { + if(!presolve_fixSOS1(psdata, j, Value1, &iConRemove, &iVarFixed)) +@@ -5466,7 +5466,7 @@ + #endif + + /* Update inf norms and check for potential factorization trouble */ +- mat_computemax(mat /*, FALSE */); ++ mat_computemax(mat /*, FFALSE */); + #if 0 + Value1 = fabs(lp->negrange); + if(is_obj_in_basis(lp) && (mat->dynrange < Value1) && vec_computeext(lp->orig_obj, 1, lp->columns, TRUE, &i, &j)) { +@@ -5542,7 +5542,7 @@ + /* Accumulate constraint bounds based on bounds on individual variables. */ + j = 0; + while(presolve_statuscheck(psdata, &status) && psdata->forceupdate) { +- psdata->forceupdate = FALSE; ++ psdata->forceupdate = FFALSE; + /* Update sums, but limit iteration count to avoid possible + "endless" loops with only marginal bound improvements */ + if(presolve_updatesums(psdata) && (j < MAX_PSBOUNDTIGHTENLOOPS)) { +@@ -5627,7 +5627,7 @@ + if(presolve_statuscheck(psdata, &status) && (psdata->EQmap->count > 1) && + is_presolve(lp, PRESOLVE_LINDEP)) { + #if 0 +- REPORT_mat_mmsave(lp, "A.mtx", NULL, FALSE, "Constraint matrix A"); ++ REPORT_mat_mmsave(lp, "A.mtx", NULL, FFALSE, "Constraint matrix A"); + #endif + presolve_singularities(psdata, &iCoeffChanged, &iConRemove, &iVarFixed, &iSum); + } +@@ -5823,7 +5823,7 @@ + + /* Produce presolved model statistics */ + if(nConRemove+nVarFixed+nBoundTighten+nVarFixed+nCoeffChanged > 0) { +- REPORT_modelinfo(lp, FALSE, "REDUCED"); ++ REPORT_modelinfo(lp, FFALSE, "REDUCED"); + if(nSum > 0) { + report(lp, NORMAL, "Row-types: %7d LE, %7d GE, %7d EQ.\n", + j, jjx, jx); +@@ -5848,7 +5848,7 @@ + write_lp(lp, "test_out.lp"); /* Must put here due to variable name mapping */ + #endif + #if 0 +- REPORT_debugdump(lp, "testint2.txt", FALSE); ++ REPORT_debugdump(lp, "testint2.txt", FFALSE); + #endif + + return( status ); +@@ -5888,9 +5888,9 @@ + + /* Check if we can clear the variable map */ + if(varmap_canunlock(lp)) +- lp->varmap_locked = FALSE; ++ lp->varmap_locked = FFALSE; + #if 0 +- REPORT_mat_mmsave(lp, "basis.mtx", NULL, FALSE); /* Write the current basis matrix (no OF) */ ++ REPORT_mat_mmsave(lp, "basis.mtx", NULL, FFALSE); /* Write the current basis matrix (no OF) */ + #endif + + return( TRUE ); +diff -ru lp_solve_5.5.orig/lp_price.c lp_solve_5.5/lp_price.c +--- lp_solve_5.5.orig/lp_price.c 2019-02-19 10:42:21.372737063 -0600 ++++ lp_solve_5.5/lp_price.c 2019-02-19 12:01:35.652868617 -0600 +@@ -388,7 +388,7 @@ + + #ifdef Paranoia + if(candidate->varno <= 0) +- return( FALSE ); ++ return( FFALSE ); + else + #endif + if(fabs(candidate->pivot) >= lp->infinite) +@@ -501,7 +501,7 @@ + + Allowed variable set: Any pivot PRIMAL:larger or DUAL:smaller than threshold value of 0 */ + { +- MYBOOL Action = FALSE, ++ MYBOOL Action = FFALSE, + #ifdef ExtractedValidityTest + Accept = TRUE; + #else /* Check for validity and compare result with previous best */ +@@ -511,7 +511,7 @@ + if(candidatecount != NULL) + (*candidatecount)++; + if(collectMP) { +- if(addCandidateVar(candidate, current->lp->multivars, (findCompare_func *) compareImprovementQS, FALSE) < 0) ++ if(addCandidateVar(candidate, current->lp->multivars, (findCompare_func *) compareImprovementQS, FFALSE) < 0) + return(Action); + } + if(current->varno > 0) +@@ -537,7 +537,7 @@ + /* 1. Check for ratio and pivot validity (to have the extra flexibility that all + bound-flip candidates are also possible as basis-entering variables */ + if(!validSubstitutionVar(candidate)) +- return( FALSE ); ++ return( FFALSE ); + + /* 2. If the free-list is empty we need to see if we have a better candidate, + and for this the candidate list has to be sorted by merit */ +@@ -572,7 +572,7 @@ + + Allowed variable set: "Equal-valued" smallest thetas! */ + { +- MYBOOL Action = FALSE, ++ MYBOOL Action = FFALSE, + #ifdef ExtractedValidityTest + Accept = TRUE; + #else /* Check for validity and comparison result with previous best */ +@@ -653,7 +653,7 @@ + } + else { + *delta = 1; /* Step forwards - "right" */ +- lp->_piv_left_ = FALSE; ++ lp->_piv_left_ = FFALSE; + } + } + +@@ -788,7 +788,7 @@ + idea is to relax the tolerance to account for this and only + marginally weakening the (user-specified) tolerance. */ + if((sfeas-xfeas) < f*lp->epsprimal) +- testOK = FALSE; ++ testOK = FFALSE; + } + return( testOK ); + } +@@ -835,7 +835,7 @@ + int i, ix, iy, iz, ninfeas, nloop = 0; + REAL f, sinfeas, xinfeas, epsvalue = lp->epsdual; + pricerec current, candidate; +- MYBOOL collectMP = FALSE; ++ MYBOOL collectMP = FFALSE; + int *coltarget = NULL; + + /* Identify pivot column according to pricing strategy; set +@@ -843,9 +843,9 @@ + current.pivot = lp->epsprimal; /* Minimum acceptable improvement */ + current.varno = 0; + current.lp = lp; +- current.isdual = FALSE; ++ current.isdual = FFALSE; + candidate.lp = lp; +- candidate.isdual = FALSE; ++ candidate.isdual = FFALSE; + *candidatecount = 0; + + /* Update local value of pivot setting and determine active multiple pricing set */ +@@ -859,7 +859,7 @@ + coltarget = NULL; + } + else +- coltarget = multi_indexSet(lp->multivars, FALSE); ++ coltarget = multi_indexSet(lp->multivars, FFALSE); + } + + /* Compute reduced costs c - c*Inv(B), if necessary +@@ -869,7 +869,7 @@ + /* Recompute from scratch only at the beginning, otherwise update */ + if((lp->current_iter > 0) && (refactRecent(lp) == AUTOMATIC)) + #endif +- compute_reducedcosts(lp, FALSE, 0, coltarget, (MYBOOL) ((nloop <= 1) || (partialloop > 1)), ++ compute_reducedcosts(lp, FFALSE, 0, coltarget, (MYBOOL) ((nloop <= 1) || (partialloop > 1)), + NULL, NULL, + drow, nzdrow, + MAT_ROUNDDEFAULT); +@@ -908,7 +908,7 @@ + ninfeas++; + SETMAX(xinfeas, f); + sinfeas += f; +- candidate.pivot = normalizeEdge(lp, i, f, FALSE); ++ candidate.pivot = normalizeEdge(lp, i, f, FFALSE); + candidate.varno = i; + if(findImprovementVar(¤t, &candidate, collectMP, candidatecount)) + break; +@@ -923,8 +923,8 @@ + coltarget = multi_indexSet(lp->multivars, TRUE); + } + else if((current.varno == 0) && (lp->multivars->retries == 0)) { +- ix = partial_blockStart(lp, FALSE); +- iy = partial_blockEnd(lp, FALSE); ++ ix = partial_blockStart(lp, FFALSE); ++ iy = partial_blockEnd(lp, FFALSE); + lp->multivars->used = 0; + lp->multivars->retries++; + goto doLoop; +@@ -963,7 +963,7 @@ + LREAL f, savef; + REAL Heps, Htheta, Hlimit, epsvalue, epspivot, p = 0.0; + pricerec current, candidate; +- MYBOOL isupper = !lp->is_lower[colnr], HarrisTwoPass = FALSE; ++ MYBOOL isupper = !lp->is_lower[colnr], HarrisTwoPass = FFALSE; + + /* Update local value of pivot setting */ + lp->_piv_rule_ = get_piv_rule(lp); +@@ -1039,11 +1039,11 @@ + current.theta = lp->infinite; + current.pivot = 0; + current.varno = 0; +- current.isdual = FALSE; ++ current.isdual = FFALSE; + current.epspivot = epspivot; + current.lp = lp; + candidate.epspivot = epspivot; +- candidate.isdual = FALSE; ++ candidate.isdual = FFALSE; + candidate.lp = lp; + savef = 0; + for(; Hpass <= 2; Hpass++) { +@@ -1133,7 +1133,7 @@ + i++; + if(i > lp->rows) { /* Empty column with upper bound! */ + lp->is_lower[colnr] = !lp->is_lower[colnr]; +-/* lp->is_lower[colnr] = FALSE; */ ++/* lp->is_lower[colnr] = FFALSE; */ + lp->rhs[0] += lp->upbo[colnr]*pcol[0]; + } + else /* if(pcol[i]<0) */ +@@ -1151,7 +1151,7 @@ + + /* Return working array to pool */ + if(nzpcol == NULL) +- mempool_releaseVector(lp->workarrays, (char *) nzlist, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) nzlist, FFALSE); + + if(lp->spx_trace) + report(lp, DETAILED, "row_prim: %d, pivot size = " RESULTVALUEMASK "\n", +@@ -1172,7 +1172,7 @@ + REAL up, lo = 0, + epsvalue, sinfeas, xinfeas; + pricerec current, candidate; +- MYBOOL collectMP = FALSE; ++ MYBOOL collectMP = FFALSE; + + /* Initialize */ + if(rhvec == NULL) +@@ -1262,7 +1262,7 @@ + if(updateinfeas) + lp->suminfeas = fabs(sinfeas); + if((ninfeas > 1) && +- !verify_stability(lp, FALSE, xinfeas, sinfeas, ninfeas)) { ++ !verify_stability(lp, FFALSE, xinfeas, sinfeas, ninfeas)) { + report(lp, IMPORTANT, "rowdual: Check for reduced accuracy and tolerance settings.\n"); + current.varno = 0; + } +@@ -1294,11 +1294,11 @@ + j = 1; i = lp->rows+j; lp->upbo[i] = 0; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = 2; drow[i] = -1; + j = 2; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = -2; drow[i] = 2; + j = 3; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = 1; drow[i] = 5; +- j = 4; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FALSE; nzprow[j] = i; prow[i] = 3; drow[i] = -6; +- j = 5; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FALSE; nzprow[j] = i; prow[i] = -4; drow[i] = -2; ++ j = 4; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FFALSE; nzprow[j] = i; prow[i] = 3; drow[i] = -6; ++ j = 5; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FFALSE; nzprow[j] = i; prow[i] = -4; drow[i] = -2; + j = 6; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = -1; drow[i] = 0; +- j = 7; i = lp->rows+j; lp->upbo[i] = 2; lp->is_lower[i] = FALSE; nzprow[j] = i; prow[i] = 1; drow[i] = 0; +- j = 8; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FALSE; nzprow[j] = i; prow[i] = -2; drow[i] = 0; ++ j = 7; i = lp->rows+j; lp->upbo[i] = 2; lp->is_lower[i] = FFALSE; nzprow[j] = i; prow[i] = 1; drow[i] = 0; ++ j = 8; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FFALSE; nzprow[j] = i; prow[i] = -2; drow[i] = 0; + j = 9; i = lp->rows+j; lp->upbo[i] = 5; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = -1; drow[i] = 4; + j = 10; i = lp->rows+j; lp->upbo[i] = F; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = -2; drow[i] = 10; + nzprow[0] = i-lp->rows; +@@ -1309,13 +1309,13 @@ + else if(which == 1) { /* Maros Example-1 - presorted in correct order */ + j = 1; i = lp->rows+j; lp->upbo[i] = 0; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = 2; drow[i] = -1; + j = 2; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = 1; drow[i] = 5; +- j = 3; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FALSE; nzprow[j] = i; prow[i] = -4; drow[i] = -2; +- j = 4; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FALSE; nzprow[j] = i; prow[i] = -2; drow[i] = 0; ++ j = 3; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FFALSE; nzprow[j] = i; prow[i] = -4; drow[i] = -2; ++ j = 4; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FFALSE; nzprow[j] = i; prow[i] = -2; drow[i] = 0; + + j = 5; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = -1; drow[i] = 0; +- j = 6; i = lp->rows+j; lp->upbo[i] = 2; lp->is_lower[i] = FALSE; nzprow[j] = i; prow[i] = 1; drow[i] = 0; ++ j = 6; i = lp->rows+j; lp->upbo[i] = 2; lp->is_lower[i] = FFALSE; nzprow[j] = i; prow[i] = 1; drow[i] = 0; + j = 7; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = -2; drow[i] = 2; +- j = 8; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FALSE; nzprow[j] = i; prow[i] = 3; drow[i] = -6; ++ j = 8; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FFALSE; nzprow[j] = i; prow[i] = 3; drow[i] = -6; + j = 9; i = lp->rows+j; lp->upbo[i] = 5; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = -1; drow[i] = 4; + j = 10; i = lp->rows+j; lp->upbo[i] = F; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = -2; drow[i] = 10; + nzprow[0] = i-lp->rows; +@@ -1327,8 +1327,8 @@ + else if(which == 10) { /* Maros Example-2 - raw data */ + j = 1; i = lp->rows+j; lp->upbo[i] = 5; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = -2; drow[i] = 2; + j = 2; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = 3; drow[i] = 3; +- j = 3; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FALSE; nzprow[j] = i; prow[i] = -2; drow[i] = 0; +- j = 4; i = lp->rows+j; lp->upbo[i] = 2; lp->is_lower[i] = FALSE; nzprow[j] = i; prow[i] = -1; drow[i] = -2; ++ j = 3; i = lp->rows+j; lp->upbo[i] = 1; lp->is_lower[i] = FFALSE; nzprow[j] = i; prow[i] = -2; drow[i] = 0; ++ j = 4; i = lp->rows+j; lp->upbo[i] = 2; lp->is_lower[i] = FFALSE; nzprow[j] = i; prow[i] = -1; drow[i] = -2; + j = 5; i = lp->rows+j; lp->upbo[i] = 2; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = 1; drow[i] = 0; + j = 6; i = lp->rows+j; lp->upbo[i] = F; lp->is_lower[i] = TRUE; nzprow[j] = i; prow[i] = 3; drow[i] = 9; + nzprow[0] = i-lp->rows; +@@ -1354,7 +1354,7 @@ + REAL epsvalue = lp->epsvalue; + #endif + pricerec current, candidate; +- MYBOOL isbatch = FALSE, /* Requires that lp->longsteps->size > lp->sum */ ++ MYBOOL isbatch = FFALSE, /* Requires that lp->longsteps->size > lp->sum */ + dolongsteps = (MYBOOL) (lp->longsteps != NULL); + + /* Initialize */ +@@ -1479,7 +1479,7 @@ + /* Initialize the long-step structures if indicated */ + if(dolongsteps) { + if((nzprow[0] <= 1) || (nbound == 0)) { /* Don't bother */ +- dolongsteps = FALSE; ++ dolongsteps = FFALSE; + lp->longsteps->indexSet[0] = 0; + } + else { +@@ -1565,7 +1565,7 @@ + + blockdata = IF(isrow, lp->rowblocks, lp->colblocks); + items = IF(isrow, lp->rows, lp->columns); +- allocREAL(lp, &sum, items+1, FALSE); ++ allocREAL(lp, &sum, items+1, FFALSE); + + /* Loop over items and compute the average column index for each */ + sum[0] = 0; +@@ -1693,7 +1693,7 @@ + + blockdata = IF(isrow, lp->rowblocks, lp->colblocks); + if(blockdata == NULL) +- return( FALSE ); ++ return( FFALSE ); + else if(blockdata->blocknow < blockdata->blockcount) { + blockdata->blocknow++; + return( TRUE); +@@ -1820,8 +1820,8 @@ + int i, n = multi->used; + + multi->used = 0; +- multi->sorted = FALSE; +- multi->dirty = FALSE; ++ multi->sorted = FFALSE; ++ multi->dirty = FFALSE; + if(multi->freeList != NULL) { + for(i = 1; i <= multi->size; i++) + multi->freeList[i] = multi->size - i; +@@ -1947,8 +1947,8 @@ + } + multi->used = index; + if(multi->sorted && (index == 1)) +- multi->sorted = FALSE; +- multi->dirty = FALSE; ++ multi->sorted = FFALSE; ++ multi->dirty = FFALSE; + + /* Return TRUE if the step is now positive */ + return( (MYBOOL) (multi->step_last >= multi->epszero) ); +@@ -1965,12 +1965,12 @@ + int *coltarget = multi->indexSet; + + if(coltarget == NULL) +- return( FALSE ); ++ return( FFALSE ); + + while((i <= multi->used) && (coltarget[i] != varnr)) + i++; + if(i > multi->used) +- return( FALSE ); ++ return( FFALSE ); + + for(; i < multi->used; i++) + coltarget[i] = coltarget[i+1]; +@@ -2084,7 +2084,7 @@ + if(list == NULL) + list = &(multi->indexSet); + if((multi->used > 0) && +- ((*list != NULL) || allocINT(multi->lp, list, multi->size+1, FALSE))) { ++ ((*list != NULL) || allocINT(multi->lp, list, multi->size+1, FFALSE))) { + int i, colnr; + + for(i = 0; i < multi->used; i++) { +diff -ru lp_solve_5.5.orig/lp_pricePSE.c lp_solve_5.5/lp_pricePSE.c +--- lp_solve_5.5.orig/lp_pricePSE.c 2019-02-19 10:42:21.372737063 -0600 ++++ lp_solve_5.5/lp_pricePSE.c 2019-02-19 12:01:58.856869259 -0600 +@@ -68,7 +68,7 @@ + + /* Reallocate vector for new size */ + if(!allocREAL(lp, &(lp->edgeVector), lp->sum_alloc+1, AUTOMATIC)) +- return( FALSE ); ++ return( FFALSE ); + + /* Signal that we have not yet initialized the price vector */ + MEMCLEAR(lp->edgeVector, lp->sum_alloc+1); +@@ -80,7 +80,7 @@ + STATIC MYBOOL initPricer(lprec *lp) + { + if(!applyPricer(lp)) +- return( FALSE ); ++ return( FFALSE ); + + /* Free any pre-existing pricer */ + freePricer(lp); +@@ -171,7 +171,7 @@ + } + + /* Otherwise do the full Steepest Edge norm initialization */ +- ok = allocREAL(lp, &sEdge, m+1, FALSE); ++ ok = allocREAL(lp, &sEdge, m+1, FFALSE); + if(!ok) + return( ok ); + +@@ -203,7 +203,7 @@ + if(lp->is_basic[i]) + continue; + +- fsolve(lp, i, sEdge, NULL, 0, 0.0, FALSE); ++ fsolve(lp, i, sEdge, NULL, 0, 0.0, FFALSE); + + /* Compute the edge norm */ + seNorm = 1; +@@ -227,11 +227,11 @@ + STATIC MYBOOL formWeights(lprec *lp, int colnr, REAL *pcol, REAL **w) + /* This computes Bw = a, where B is the basis and a is a column of A */ + { +- MYBOOL ok = allocREAL(lp, w, lp->rows+1, FALSE); ++ MYBOOL ok = allocREAL(lp, w, lp->rows+1, FFALSE); + + if(ok) { + if(pcol == NULL) +- fsolve(lp, colnr, *w, NULL, 0.0, 0.0, FALSE); ++ fsolve(lp, colnr, *w, NULL, 0.0, 0.0, FFALSE); + else { + MEMCOPY(*w, pcol, lp->rows+1); + /* *w[0] = 0; */ /* Test */ +@@ -265,7 +265,7 @@ + { + REAL *vEdge = NULL, cEdge, hold, *newEdge, *w = NULL; + int i, m, n, exitcol, errlevel = DETAILED; +- MYBOOL forceRefresh = FALSE, isDual, isDEVEX, ok = FALSE; ++ MYBOOL forceRefresh = FFALSE, isDual, isDEVEX, ok = FFALSE; + + if(!applyPricer(lp)) + return(ok); +@@ -298,7 +298,7 @@ + + /* Don't need to compute cross-products with DEVEX */ + if(!isDEVEX) { +- ok = allocREAL(lp, &vEdge, m+1, FALSE); ++ ok = allocREAL(lp, &vEdge, m+1, FFALSE); + if(!ok) + return( ok ); + +@@ -385,9 +385,9 @@ + + /* Initialize column target array */ + coltarget = (int *) mempool_obtainVector(lp->workarrays, lp->sum+1, sizeof(*coltarget)); +- ok = get_colIndexA(lp, SCAN_SLACKVARS+SCAN_USERVARS+USE_NONBASICVARS, coltarget, FALSE); ++ ok = get_colIndexA(lp, SCAN_SLACKVARS+SCAN_USERVARS+USE_NONBASICVARS, coltarget, FFALSE); + if(!ok) { +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); + return( ok ); + } + +@@ -410,7 +410,7 @@ + vTemp[0] = 0; + prod_xA(lp, coltarget, vTemp, NULL, lp->epsmachine, 0.0, + vAlpha, NULL, MAT_ROUNDDEFAULT); +- mempool_releaseVector(lp->workarrays, (char *) coltarget, FALSE); ++ mempool_releaseVector(lp->workarrays, (char *) coltarget, FFALSE); + + /* Update the squared steepest edge norms; first store some constants */ + cEdge = lp->edgeVector[colnr]; +@@ -494,7 +494,7 @@ + + if(!ok) + return( ok ); +- ok = FALSE; ++ ok = FFALSE; + + /* Verify */ + if(lp->edgeVector == NULL) +diff -ru lp_solve_5.5.orig/lp_scale.c lp_solve_5.5/lp_scale.c +--- lp_solve_5.5.orig/lp_scale.c 2019-02-19 10:42:21.372737063 -0600 ++++ lp_solve_5.5/lp_scale.c 2019-02-19 12:02:23.228869934 -0600 +@@ -76,7 +76,7 @@ + } + + /* Compute the scale factor by the formulae: +- FALSE: SUM (log |Aij|) ^ 2 ++ FFALSE: SUM (log |Aij|) ^ 2 + TRUE: SUM (log |Aij| - RowScale[i] - ColScale[j]) ^ 2 */ + REAL CurtisReidMeasure(lprec *lp, MYBOOL _Advanced, REAL *FRowScale, REAL *FColScale) + { +@@ -171,8 +171,8 @@ + allocINT(lp, &ColCount, colMax+1, TRUE); + allocREAL(lp, &residual_even, colMax+1, TRUE); + +- allocREAL(lp, &RowScalem2, lp->rows+1, FALSE); +- allocREAL(lp, &ColScalem2, colMax+1, FALSE); ++ allocREAL(lp, &RowScalem2, lp->rows+1, FFALSE); ++ allocREAL(lp, &ColScalem2, colMax+1, FFALSE); + + /* Set origin for row scaling */ + for(i = 1; i <= colMax; i++) { +@@ -362,7 +362,7 @@ + } + + /* Do validation, if indicated */ +- if(FALSE && mat_validate(mat)){ ++ if(FFALSE && mat_validate(mat)){ + double check, error; + + /* CHECK: M RowScale + E ColScale = RowSum */ +@@ -445,18 +445,18 @@ + int Result; + + if(!lp->scaling_used) { +- allocREAL(lp, &lp->scalars, lp->sum_alloc + 1, FALSE); ++ allocREAL(lp, &lp->scalars, lp->sum_alloc + 1, FFALSE); + for(Result = 0; Result <= lp->sum; Result++) + lp->scalars[Result] = 1; + lp->scaling_used = TRUE; + } + + if(scaledelta == NULL) +- allocREAL(lp, &scalechange, lp->sum + 1, FALSE); ++ allocREAL(lp, &scalechange, lp->sum + 1, FFALSE); + else + scalechange = scaledelta; + +- Result=CurtisReidScales(lp, FALSE, scalechange, &scalechange[lp->rows]); ++ Result=CurtisReidScales(lp, FFALSE, scalechange, &scalechange[lp->rows]); + if(Result>0) { + + /* Do the scaling*/ +@@ -479,7 +479,7 @@ + *value = fabs(*value); + #ifdef Paranoia + if(*value < lp->epsmachine) { +- Accept = FALSE; ++ Accept = FFALSE; + report(lp, SEVERE, "transform_for_scale: A zero-valued entry was passed\n"); + } + else +@@ -558,7 +558,7 @@ + scale is used to normalize another value */ + { + long int power2; +- MYBOOL isSmall = FALSE; ++ MYBOOL isSmall = FFALSE; + + if(scale == 1) + return( scale ); +@@ -591,7 +591,7 @@ + if(fabs(scalechange[i]-1) > lp->epsprimal) + break; + if(i <= 0) +- return( FALSE ); ++ return( FFALSE ); + + /* Update the pre-existing column scalar */ + if(updateonly) +@@ -614,7 +614,7 @@ + break; + } + if(i < 0) +- return( FALSE ); ++ return( FFALSE ); + + /* Update the pre-existing row scalar */ + if(updateonly) +@@ -744,7 +744,7 @@ + return(0.0); + + if(!lp->scaling_used) { +- allocREAL(lp, &lp->scalars, lp->sum_alloc + 1, FALSE); ++ allocREAL(lp, &lp->scalars, lp->sum_alloc + 1, FFALSE); + for(i = 0; i <= lp->sum; i++) { + lp->scalars[i] = 1; + } +@@ -758,7 +758,7 @@ + } + #endif + if(scaledelta == NULL) +- allocREAL(lp, &scalechange, lp->sum + 1, FALSE); ++ allocREAL(lp, &scalechange, lp->sum + 1, FFALSE); + else + scalechange = scaledelta; + +@@ -768,7 +768,7 @@ + + row_count = lp->rows; + allocREAL(lp, &row_max, row_count + 1, TRUE); +- allocREAL(lp, &row_min, row_count + 1, FALSE); ++ allocREAL(lp, &row_min, row_count + 1, FFALSE); + + /* Initialise min and max values of rows */ + for(i = 0; i <= row_count; i++) { +@@ -926,7 +926,7 @@ + /* Allocate array for incremental scaling if appropriate */ + if((lp->solvecount > 1) && (lp->bb_level < 1) && + ((lp->scalemode & SCALE_DYNUPDATE) != 0)) +- allocREAL(lp, &scalenew, lp->sum + 1, FALSE); ++ allocREAL(lp, &scalenew, lp->sum + 1, FFALSE); + + if(is_scaletype(lp, SCALE_CURTISREID)) { + scalingmetric = scaleCR(lp, scalenew); +@@ -974,8 +974,8 @@ + if(lp->scalars != NULL) { + FREE(lp->scalars); + } +- lp->scaling_used = FALSE; +- lp->columns_scaled = FALSE; ++ lp->scaling_used = FFALSE; ++ lp->columns_scaled = FFALSE; + } + if(scalenew != NULL) + FREE(scalenew); +@@ -1019,7 +1019,7 @@ + for(i = lp->rows + 1; i<= lp->sum; i++) + lp->scalars[i] = 1; + +- lp->columns_scaled = FALSE; ++ lp->columns_scaled = FFALSE; + set_action(&lp->spx_action, ACTION_REBASE | ACTION_REINVERT | ACTION_RECOMPUTE); + } + +@@ -1066,8 +1066,8 @@ + } + + FREE(lp->scalars); +- lp->scaling_used = FALSE; +- lp->columns_scaled = FALSE; ++ lp->scaling_used = FFALSE; ++ lp->columns_scaled = FFALSE; + + set_action(&lp->spx_action, ACTION_REBASE | ACTION_REINVERT | ACTION_RECOMPUTE); + } +diff -ru lp_solve_5.5.orig/lp_simplex.c lp_solve_5.5/lp_simplex.c +--- lp_solve_5.5.orig/lp_simplex.c 2019-02-19 10:42:21.372737063 -0600 ++++ lp_solve_5.5/lp_simplex.c 2019-02-19 12:03:59.848872607 -0600 +@@ -67,7 +67,7 @@ + return( (MYBOOL) (deltaOF < monitor->epsvalue) ); + } + else +- return( FALSE ); ++ return( FFALSE ); + } + + STATIC MYBOOL stallMonitor_shortSteps(lprec *lp) +@@ -81,7 +81,7 @@ + return( (MYBOOL) (deltaOF > monitor->limitstall[TRUE]) ); + } + else +- return( FALSE ); ++ return( FFALSE ); + } + + STATIC void stallMonitor_reset(lprec *lp) +@@ -103,11 +103,11 @@ + { + OBJmonrec *monitor = NULL; + if(lp->monitor != NULL) +- return( FALSE ); ++ return( FFALSE ); + + monitor = (OBJmonrec *) calloc(sizeof(*monitor), 1); + if(monitor == NULL) +- return( FALSE ); ++ return( FFALSE ); + + monitor->lp = lp; + strcpy(monitor->spxfunc, funcname); +@@ -116,14 +116,14 @@ + monitor->oldpivstrategy = lp->piv_strategy; + monitor->oldpivrule = get_piv_rule(lp); + if(MAX_STALLCOUNT <= 1) +- monitor->limitstall[FALSE] = 0; ++ monitor->limitstall[FFALSE] = 0; + else +- monitor->limitstall[FALSE] = MAX(MAX_STALLCOUNT, ++ monitor->limitstall[FFALSE] = MAX(MAX_STALLCOUNT, + (int) pow((REAL) (lp->rows+lp->columns)/2, 0.667)); + #if 1 +- monitor->limitstall[FALSE] *= 2+2; /* Expand degeneracy/stalling tolerance range */ ++ monitor->limitstall[FFALSE] *= 2+2; /* Expand degeneracy/stalling tolerance range */ + #endif +- monitor->limitstall[TRUE] = monitor->limitstall[FALSE]; ++ monitor->limitstall[TRUE] = monitor->limitstall[FFALSE]; + if(monitor->oldpivrule == PRICER_DEVEX) /* Increase tolerance since primal Steepest Edge is expensive */ + monitor->limitstall[TRUE] *= 2; + if(MAX_RULESWITCH <= 0) +@@ -152,7 +152,7 @@ + REAL deltaobj = lp->suminfeas; + + /* Accept unconditionally if this is the first or second call */ +- monitor->active = FALSE; ++ monitor->active = FFALSE; + if(monitor->Icount <= 1) { + if(monitor->Icount == 1) { + monitor->prevobj = lp->rhs[0]; +@@ -211,7 +211,7 @@ + #endif + + #if 1 +- isCreeping = FALSE; ++ isCreeping = FFALSE; + #else + isCreeping |= stallMonitor_creepingObj(lp); + /* isCreeping |= stallMonitor_shortSteps(lp); */ +@@ -256,7 +256,7 @@ + lp->spx_status = DEGENERATE; + report(lp, msglevel, "%s: Stalling at iter %10.0f; no alternative strategy left.\n", + monitor->spxfunc, (double) get_total_iter(lp)); +- acceptance = FALSE; ++ acceptance = FFALSE; + return( acceptance ); + } + +@@ -293,7 +293,7 @@ + else { + report(lp, msglevel, "%s: Stalling at iter %10.0f; proceed to bound relaxation.\n", + monitor->spxfunc, (double) get_total_iter(lp)); +- acceptance = FALSE; ++ acceptance = FFALSE; + lp->spx_status = DEGENERATE; + return( acceptance ); + } +@@ -405,11 +405,11 @@ + + /* Create temporary sparse array storage */ + if(nzarray == NULL) +- allocREAL(lp, &avalue, 2, FALSE); ++ allocREAL(lp, &avalue, 2, FFALSE); + else + avalue = nzarray; + if(idxarray == NULL) +- allocINT(lp, &rownr, 2, FALSE); ++ allocINT(lp, &rownr, 2, FFALSE); + else + rownr = idxarray; + +@@ -437,7 +437,7 @@ + else { + report(lp, CRITICAL, "add_artificial: Could not find replacement basis variable for row %d\n", + forrownr); +- lp->basis_valid = FALSE; ++ lp->basis_valid = FFALSE; + } + + } +@@ -515,7 +515,7 @@ + rownr = get_artificialRow(lp, j); + colnr = find_rowReplacement(lp, rownr, prow, NULL); + #if 0 +- performiteration(lp, rownr, colnr, 0.0, TRUE, FALSE, prow, NULL, ++ performiteration(lp, rownr, colnr, 0.0, TRUE, FFALSE, prow, NULL, + NULL, NULL, NULL); + #else + set_basisvar(lp, rownr, colnr); +@@ -562,7 +562,7 @@ + + STATIC int primloop(lprec *lp, MYBOOL primalfeasible, REAL primaloffset) + { +- MYBOOL primal = TRUE, bfpfinal = FALSE, changedphase = FALSE, forceoutEQ = AUTOMATIC, ++ MYBOOL primal = TRUE, bfpfinal = FFALSE, changedphase = FFALSE, forceoutEQ = AUTOMATIC, + primalphase1, pricerCanChange, minit, stallaccept, pendingunbounded; + int i, j, k, colnr = 0, rownr = 0, lastnr = 0, + candidatecount = 0, minitcount = 0, ok = TRUE; +@@ -628,13 +628,13 @@ + } + + /* Create work arrays and optionally the multiple pricing structure */ +- ok = allocREAL(lp, &(lp->bsolveVal), lp->rows + 1, FALSE) && ++ ok = allocREAL(lp, &(lp->bsolveVal), lp->rows + 1, FFALSE) && + allocREAL(lp, &prow, lp->sum + 1, TRUE) && + allocREAL(lp, &pcol, lp->rows + 1, TRUE); + if(is_piv_mode(lp, PRICE_MULTIPLE) && (lp->multiblockdiv > 1)) { +- lp->multivars = multi_create(lp, FALSE); ++ lp->multivars = multi_create(lp, FFALSE); + ok &= (lp->multivars != NULL) && +- multi_resize(lp->multivars, lp->sum / lp->multiblockdiv, 2, FALSE, TRUE); ++ multi_resize(lp->multivars, lp->sum / lp->multiblockdiv, 2, FFALSE, TRUE); + } + if(!ok) + goto Finish; +@@ -643,9 +643,9 @@ + lp->spx_status = RUNNING; + minit = ITERATE_MAJORMAJOR; + epsvalue = lp->epspivot; +- pendingunbounded = FALSE; ++ pendingunbounded = FFALSE; + +- ok = stallMonitor_create(lp, FALSE, "primloop"); ++ ok = stallMonitor_create(lp, FFALSE, "primloop"); + if(!ok) + goto Finish; + +@@ -667,7 +667,7 @@ + /* Find best column to enter the basis */ + RetryCol: + #if 0 +- if(verify_solution(lp, FALSE, "spx_loop") > 0) ++ if(verify_solution(lp, FFALSE, "spx_loop") > 0) + i = 1; /* This is just a debug trap */ + #endif + if(!changedphase) { +@@ -700,14 +700,14 @@ + colnr = lp->rejectpivot[1]; + rownr = 0; + lp->rejectpivot[0] = 0; +- ok = FALSE; ++ ok = FFALSE; + break; + } + #endif + + /* Check if we found an entering variable (indicating that we are still dual infeasible) */ + if(colnr > 0) { +- changedphase = FALSE; ++ changedphase = FFALSE; + fsolve(lp, colnr, pcol, NULL, lp->epsmachine, 1.0, TRUE); /* Solve entering column for Pi */ + + /* Do special anti-degeneracy column selection, if specified */ +@@ -748,7 +748,7 @@ + rownr = findAnti_artificial(lp, colnr); + + if(rownr > 0) { +- pendingunbounded = FALSE; ++ pendingunbounded = FFALSE; + lp->rejectpivot[0] = 0; + set_action(&lp->spx_action, ACTION_ITERATE); + if(!lp->obj_in_basis) /* We must manually copy the reduced cost for RHS update */ +@@ -801,7 +801,7 @@ + if((lp->usermessage != NULL) && (lp->msgmask & MSG_LPFEASIBLE)) + lp->usermessage(lp, lp->msghandle, MSG_LPFEASIBLE); + } +- changedphase = FALSE; ++ changedphase = FFALSE; + primalfeasible = TRUE; + lp->simplex_mode = SIMPLEX_Phase2_PRIMAL; + set_OF_p1extra(lp, 0.0); +@@ -830,7 +830,7 @@ + + /* Delete row before column due to basis "compensation logic" */ + if(lp->is_basic[k]) { +- lp->is_basic[lp->rows+j] = FALSE; ++ lp->is_basic[lp->rows+j] = FFALSE; + del_constraint(lp, k); + } + else +@@ -874,7 +874,7 @@ + is not necessary after the relaxed problem has been solved satisfactorily. */ + if((lp->bb_level <= 1) || (lp->improve & IMPROVE_BBSIMPLEX) /* || (lp->bb_rule & NODE_RCOSTFIXING) */) { /* NODE_RCOSTFIXING fix */ + set_action(&lp->piv_strategy, PRICE_FORCEFULL); +- i = rowdual(lp, lp->rhs, FALSE, FALSE, NULL); ++ i = rowdual(lp, lp->rhs, FFALSE, FFALSE, NULL); + clear_action(&lp->piv_strategy, PRICE_FORCEFULL); + if(i > 0) { + lp->spx_status = LOSTFEAS; +@@ -943,7 +943,7 @@ + #endif + if(!invert(lp, INITSOL_USEZERO, bfpfinal)) + lp->spx_status = SINGULAR_BASIS; +- bfpfinal = FALSE; ++ bfpfinal = FFALSE; + } + } + +@@ -983,9 +983,9 @@ + + STATIC int dualloop(lprec *lp, MYBOOL dualfeasible, int dualinfeasibles[], REAL dualoffset) + { +- MYBOOL primal = FALSE, inP1extra, dualphase1 = FALSE, changedphase = TRUE, ++ MYBOOL primal = FFALSE, inP1extra, dualphase1 = FFALSE, changedphase = TRUE, + pricerCanChange, minit, stallaccept, longsteps, +- forceoutEQ = FALSE, bfpfinal = FALSE; ++ forceoutEQ = FFALSE, bfpfinal = FFALSE; + int i, colnr = 0, rownr = 0, lastnr = 0, + candidatecount = 0, minitcount = 0, + #ifdef FixInaccurateDualMinit +@@ -1006,7 +1006,7 @@ + + /* Allocate work arrays */ + ok = allocREAL(lp, &prow, lp->sum + 1, TRUE) && +- allocINT (lp, &nzprow, lp->sum + 1, FALSE) && ++ allocINT (lp, &nzprow, lp->sum + 1, FFALSE) && + allocREAL(lp, &pcol, lp->rows + 1, TRUE); + if(!ok) + goto Finish; +@@ -1033,7 +1033,7 @@ + #elif 0 + longsteps = (MYBOOL) ((MIP_count(lp) > 0) && (lp->solutioncount >= 1)); + #else +- longsteps = FALSE; ++ longsteps = FFALSE; + #endif + #ifdef UseLongStepDualPhase1 + longsteps = !dualfeasible && (MYBOOL) (dualinfeasibles != NULL); +@@ -1048,7 +1048,7 @@ + #ifdef UseLongStepPruning + lp->longsteps->objcheck = TRUE; + #endif +- boundswaps = multi_indexSet(lp->longsteps, FALSE); ++ boundswaps = multi_indexSet(lp->longsteps, FFALSE); + } + + /* Do regular dual simplex variable initializations */ +@@ -1082,7 +1082,7 @@ + #if 1 + if(is_anti_degen(lp, ANTIDEGEN_DYNAMIC) && (bin_count(lp, TRUE)*2 > lp->columns)) { + switch (forceoutEQ) { +- case FALSE: forceoutEQ = AUTOMATIC; ++ case FFALSE: forceoutEQ = AUTOMATIC; + break; + /* case AUTOMATIC: forceoutEQ = TRUE; + break; +@@ -1100,7 +1100,7 @@ + break; + + /* Store current LP index for reference at next iteration */ +- changedphase = FALSE; ++ changedphase = FFALSE; + + /* Compute (pure) dual phase1 offsets / reduced costs if appropriate */ + dualphase1 &= (MYBOOL) (lp->simplex_mode == SIMPLEX_Phase1_DUAL); +@@ -1137,7 +1137,7 @@ + rownr = lp->rejectpivot[1]; + colnr = 0; + lp->rejectpivot[0] = 0; +- ok = FALSE; ++ ok = FFALSE; + break; + } + #endif +@@ -1196,13 +1196,13 @@ + if(!refactRecent(lp)) { + report(lp, DETAILED, "...trying to recover by refactorizing basis.\n"); + set_action(&lp->spx_action, ACTION_REINVERT); +- bfpfinal = FALSE; ++ bfpfinal = FFALSE; + } + else { + if(lp->bb_totalnodes == 0) + report(lp, DETAILED, "...cannot recover by refactorizing basis.\n"); + lp->spx_status = NUMFAILURE; +- ok = FALSE; ++ ok = FFALSE; + } + } + else { +@@ -1277,7 +1277,7 @@ + if((lp->spx_trace && (lp->bb_totalnodes == 0)) || + (lp->bb_trace && (lp->bb_totalnodes > 0))) + report(lp, DETAILED, "dualloop: Model lost dual feasibility.\n"); +- ok = FALSE; ++ ok = FFALSE; + break; + } + +@@ -1297,7 +1297,7 @@ + (lp->bb_trace && (lp->bb_totalnodes > 0))) + report(lp, DETAILED, "The model is primal infeasible.\n"); + } +- ok = FALSE; ++ ok = FFALSE; + break; + } + } +@@ -1330,7 +1330,7 @@ + colnr = find_rowReplacement(lp, rownr, prow, nzprow); + if(colnr > 0) { + theta = 0; +- performiteration(lp, rownr, colnr, theta, TRUE, FALSE, prow, NULL, ++ performiteration(lp, rownr, colnr, theta, TRUE, FFALSE, prow, NULL, + NULL, NULL, NULL); + lp->fixedvars--; + } +@@ -1348,11 +1348,11 @@ + report(lp, DETAILED, "The model is primal infeasible and dual unbounded.\n"); + } + set_OF_p1extra(lp, 0); +- inP1extra = FALSE; ++ inP1extra = FFALSE; + set_action(&lp->spx_action, ACTION_REINVERT); + lp->spx_status = INFEASIBLE; + lp->simplex_mode = SIMPLEX_UNDEFINED; +- ok = FALSE; ++ ok = FFALSE; + } + + /* Check if we are FEASIBLE (and possibly also optimal) for the case that the +@@ -1368,7 +1368,7 @@ + lp->usermessage(lp, lp->msghandle, MSG_LPFEASIBLE); + } + set_OF_p1extra(lp, 0); +- inP1extra = FALSE; ++ inP1extra = FFALSE; + set_action(&lp->spx_action, ACTION_REINVERT); + + #if 1 +@@ -1406,7 +1406,7 @@ + colnr = 0; + if((dualoffset != 0) || (lp->bb_level <= 1) || (lp->improve & IMPROVE_BBSIMPLEX) || (lp->bb_rule & NODE_RCOSTFIXING)) { /* NODE_RCOSTFIXING fix */ + set_action(&lp->piv_strategy, PRICE_FORCEFULL); +- colnr = colprim(lp, drow, nzdrow, FALSE, 1, &candidatecount, FALSE, NULL); ++ colnr = colprim(lp, drow, nzdrow, FFALSE, 1, &candidatecount, FFALSE, NULL); + clear_action(&lp->piv_strategy, PRICE_FORCEFULL); + if((dualoffset == 0) && (colnr > 0)) { + lp->spx_status = LOSTFEAS; +@@ -1456,7 +1456,7 @@ + if(!lp->is_strongbranch && (lp->solutioncount >= 1) && !lp->spx_perturbed && !inP1extra && + bb_better(lp, OF_WORKING, OF_TEST_WE)) { + lp->spx_status = FATHOMED; +- ok = FALSE; ++ ok = FFALSE; + break; + } + +@@ -1467,7 +1467,7 @@ + if(longsteps && dualphase1 && !inP1extra) { + dualfeasible = isDualFeasible(lp, lp->epsprimal, NULL, dualinfeasibles, NULL); + if(dualfeasible) { +- dualphase1 = FALSE; ++ dualphase1 = FFALSE; + changedphase = TRUE; + lp->simplex_mode = SIMPLEX_Phase2_DUAL; + } +@@ -1492,7 +1492,7 @@ + if(!isDualFeasible(lp, lp->epsdual, &colnr, NULL, NULL)) { + #else + set_action(&lp->piv_strategy, PRICE_FORCEFULL); +- colnr = colprim(lp, drow, nzdrow, FALSE, 1, &candidatecount, FALSE, NULL); ++ colnr = colprim(lp, drow, nzdrow, FFALSE, 1, &candidatecount, FFALSE, NULL); + clear_action(&lp->piv_strategy, PRICE_FORCEFULL); + if(colnr > 0) { + #endif +@@ -1502,7 +1502,7 @@ + } + #endif + +- bfpfinal = FALSE; ++ bfpfinal = FFALSE; + #ifdef ResetMinitOnReinvert + minit = ITERATE_MAJORMAJOR; + #endif +@@ -1536,7 +1536,7 @@ + set_OF_p1extra(lp, 0); + singular_count = 0; + lost_feas_count = 0; +- lost_feas_state = FALSE; ++ lost_feas_state = FFALSE; + lp->simplex_mode = SIMPLEX_DYNAMIC; + + /* Compute the number of fixed basic and bounded variables (used in long duals) */ +@@ -1554,7 +1554,7 @@ + lp->boundedvars++; + } + #ifdef UseLongStepDualPhase1 +- allocINT(lp, &infeasibles, lp->columns + 1, FALSE); ++ allocINT(lp, &infeasibles, lp->columns + 1, FFALSE); + infeasibles[0] = 0; + #endif + +@@ -1649,7 +1649,7 @@ + + /* Check for outcomes that may involve trying another simplex loop */ + if(lp->spx_status == SINGULAR_BASIS) { +- lost_feas_state = FALSE; ++ lost_feas_state = FFALSE; + singular_count++; + if(singular_count >= DEF_MAXSINGULARITIES) { + report(lp, IMPORTANT, "spx_run: Failure due to too many singular bases.\n"); +@@ -1744,7 +1744,7 @@ + + status = RUNNING; + lp->bb_limitOF = my_chsign(is_maxim(lp), -lp->infinite); +- if(FALSE && (lp->int_vars > 0)) { ++ if(FFALSE && (lp->int_vars > 0)) { + + /* 1. Copy the problem into a new relaxed instance, extracting Lagrangean constraints */ + hlp = make_lag(lp); +@@ -1779,7 +1779,7 @@ + } + + /* Allocate iteration arrays */ +- if(!allocREAL(lp, &OrigObj, lp->columns + 1, FALSE) || ++ if(!allocREAL(lp, &OrigObj, lp->columns + 1, FFALSE) || + !allocREAL(lp, &ModObj, lp->columns + 1, TRUE) || + !allocREAL(lp, &SubGrad, get_Lrows(lp) + 1, TRUE) || + !allocREAL(lp, &BestFeasSol, lp->sum + 1, TRUE)) { +@@ -1803,9 +1803,9 @@ + + Phi = DEF_LAGCONTRACT; /* In the range 0-2.0 to guarantee convergence */ + /* Phi = 0.15; */ +- LagFeas = FALSE; +- Converged= FALSE; +- AnyFeas = FALSE; ++ LagFeas = FFALSE; ++ Converged= FFALSE; ++ AnyFeas = FFALSE; + citer = 0; + nochange = 0; + +@@ -1840,14 +1840,14 @@ + if(LagFeas) { + if(lp->lag_con_type[i] == EQ) { + if(fabs(hold) > lp->epsprimal) +- LagFeas = FALSE; ++ LagFeas = FFALSE; + } + else if(hold < -lp->epsprimal) +- LagFeas = FALSE; ++ LagFeas = FFALSE; + } + /* Test for convergence and update */ + if(Converged && (fabs(my_reldiff(hold , SubGrad[i])) > /* lp->lag_accept */ DEF_LAGACCEPT)) +- Converged = FALSE; ++ Converged = FFALSE; + SubGrad[i] = hold; + SqrsumSubGrad += hold * hold; + } +@@ -1961,7 +1961,7 @@ + same_basis = compare_basis(lp); + if(LagFeas && + !same_basis) { +- pop_basis(lp, FALSE); ++ pop_basis(lp, FFALSE); + push_basis(lp, NULL, NULL, NULL); + Phi *= DEF_LAGCONTRACT; + } +@@ -2022,7 +2022,7 @@ + FREE(SubGrad); + FREE(OrigObj); + FREE(ModObj); +- pop_basis(lp, FALSE); ++ pop_basis(lp, FFALSE); + + lp->do_presolve = oldpresolve; + +@@ -2041,7 +2041,7 @@ + lp->bb_totalnodes = 0; + lp->bb_improvements = 0; + lp->bb_strongbranches= 0; +- lp->is_strongbranch = FALSE; ++ lp->is_strongbranch = FFALSE; + lp->bb_level = 0; + lp->bb_solutionlevel = 0; + lp->best_solution[0] = my_chsign(is_maxim(lp), lp->infinite); +@@ -2066,7 +2066,7 @@ + lp->solutioncount = 0; + lp->real_solution = lp->infinite; + set_action(&lp->spx_action, ACTION_REBASE | ACTION_REINVERT); +- lp->bb_break = FALSE; ++ lp->bb_break = FFALSE; + + /* Do the call to the real underlying solver (note that + run_BB is replaceable with any compatible MIP solver) */ +diff -ru lp_solve_5.5.orig/lp_SOS.c lp_solve_5.5/lp_SOS.c +--- lp_solve_5.5.orig/lp_SOS.c 2019-02-19 10:42:21.376737063 -0600 ++++ lp_solve_5.5/lp_SOS.c 2019-02-19 12:04:39.152873695 -0600 +@@ -147,7 +147,7 @@ + SOS->name = NULL; + else + { +- allocCHAR(group->lp, &SOS->name, (int) (strlen(name)+1), FALSE); ++ allocCHAR(group->lp, &SOS->name, (int) (strlen(name)+1), FFALSE); + strcpy(SOS->name, name); + } + if(type < 0) +@@ -248,8 +248,8 @@ + lp->sos_vars = n; + if(lp->sos_vars > 0) /* Prevent memory loss in case of multiple solves */ + FREE(lp->sos_priority); +- allocINT(lp, &lp->sos_priority, n, FALSE); +- allocREAL(lp, &order, n, FALSE); ++ allocINT(lp, &lp->sos_priority, n, FFALSE); ++ allocREAL(lp, &order, n, FFALSE); + + /* Move variable data to the master SOS list and sort by ascending weight */ + n = 0; +@@ -263,7 +263,7 @@ + n++; + } + } +- hpsortex(order, n, 0, sizeof(*order), FALSE, compareREAL, lp->sos_priority); ++ hpsortex(order, n, 0, sizeof(*order), FFALSE, compareREAL, lp->sos_priority); + FREE(order); + + /* Remove duplicate SOS variables */ +@@ -296,7 +296,7 @@ + #ifdef Paranoia + if((sosindex <= 0) || (sosindex > group->sos_count)) { + report(group->lp, IMPORTANT, "delete_SOSrec: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + +@@ -345,7 +345,7 @@ + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(lp, IMPORTANT, "SOS_member_sortlist: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + +@@ -355,7 +355,7 @@ + if(sosindex == 0) { + for(i = 1; i <= group->sos_count; i++) { + if(!SOS_member_sortlist(group, i)) +- return(FALSE); ++ return(FFALSE); + } + } + else { +@@ -453,12 +453,12 @@ + + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(lp, IMPORTANT, "SOS_shift_col: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + else if((column < 1) || (delta == 0)) { + report(lp, IMPORTANT, "SOS_shift_col: Invalid column %d specified with delta %d\n", + column, delta); +- return(FALSE); ++ return(FFALSE); + } + #endif + +@@ -468,7 +468,7 @@ + if(sosindex == 0) { + for(i = 1; i <= group->sos_count; i++) { + if(!SOS_shift_col(group, i, column, delta, usedmap, forceresort)) +- return(FALSE); ++ return(FFALSE); + } + } + else { +@@ -629,7 +629,7 @@ + #ifdef Paranoia + if((sosindex < 1) || (sosindex > group->sos_count)) { + report(group->lp, IMPORTANT, "SOS_get_type: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + +@@ -645,7 +645,7 @@ + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(lp, IMPORTANT, "SOS_infeasible: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + +@@ -695,7 +695,7 @@ + SOS = group->sos_list[sosindex-1]; + n = SOS->members[0]; + +- n = searchFor(member, SOS->membersSorted, n, 0, FALSE); ++ n = searchFor(member, SOS->membersSorted, n, 0, FFALSE); + if(n >= 0) + n = SOS->membersMapped[n]; + +@@ -733,11 +733,11 @@ + + int SOS_is_member(SOSgroup *group, int sosindex, int column) + { +- int i, n = FALSE, *list; ++ int i, n = FFALSE, *list; + lprec *lp; + + if(group == NULL) +- return( FALSE ); ++ return( FFALSE ); + lp = group->lp; + + #ifdef Paranoia +@@ -756,7 +756,7 @@ + /* Search for the variable */ + i = SOS_member_index(group, sosindex, column); + +- /* Signal active status if found, otherwise return FALSE */ ++ /* Signal active status if found, otherwise return FFALSE */ + if(i > 0) { + list = group->sos_list[sosindex-1]->members; + if(list[i] < 0) +@@ -781,7 +781,7 @@ + ((sostype == SOSn) && (n > 2))) && SOS_is_member(group, k, column)) + return(TRUE); + } +- return(FALSE); ++ return(FFALSE); + } + + +@@ -792,7 +792,7 @@ + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(group->lp, IMPORTANT, "SOS_set_GUB: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + if((sosindex == 0) && (group->sos_count == 1)) +@@ -815,7 +815,7 @@ + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(group->lp, IMPORTANT, "SOS_is_GUB: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + +@@ -827,7 +827,7 @@ + if(SOS_is_GUB(group, i)) + return(TRUE); + } +- return(FALSE); ++ return(FFALSE); + } + else + return( group->sos_list[sosindex-1]->isGUB ); +@@ -840,18 +840,18 @@ + lprec *lp; + + if(group == NULL) +- return( FALSE ); ++ return( FFALSE ); + lp = group->lp; + + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(lp, IMPORTANT, "SOS_is_marked: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + + if(!(lp->var_type[column] & (ISSOS | ISGUB))) +- return(FALSE); ++ return(FFALSE); + + if(sosindex == 0) { + for(i = group->memberpos[column-1]; i < group->memberpos[column]; i++) { +@@ -871,7 +871,7 @@ + if(list[i] == column) + return(TRUE); + } +- return(FALSE); ++ return(FFALSE); + } + + +@@ -883,12 +883,12 @@ + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(lp, IMPORTANT, "SOS_is_active: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + + if(!(lp->var_type[column] & (ISSOS | ISGUB))) +- return(FALSE); ++ return(FFALSE); + + if(sosindex == 0) { + for(i = group->memberpos[column-1]; i < group->memberpos[column]; i++) { +@@ -909,7 +909,7 @@ + if(list[n+i] == column) + return(TRUE); + } +- return(FALSE); ++ return(FFALSE); + } + + +@@ -921,12 +921,12 @@ + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(lp, IMPORTANT, "SOS_is_full: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + + if(!(lp->var_type[column] & (ISSOS | ISGUB))) +- return(FALSE); ++ return(FFALSE); + + if(sosindex == 0) { + for(i = group->memberpos[column-1]; i < group->memberpos[column]; i++) { +@@ -959,7 +959,7 @@ + } + } + +- return(FALSE); ++ return(FFALSE); + } + + +@@ -969,25 +969,25 @@ + lprec *lp; + + if(group == NULL) +- return( FALSE ); ++ return( FFALSE ); + lp = group->lp; + + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(lp, IMPORTANT, "SOS_can_activate: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + + if(!(lp->var_type[column] & (ISSOS | ISGUB))) +- return(FALSE); ++ return(FFALSE); + + if(sosindex == 0) { + for(i = group->memberpos[column-1]; i < group->memberpos[column]; i++) { + nn = group->membership[i]; + n = SOS_can_activate(group, nn, column); +- if(n == FALSE) +- return(FALSE); ++ if(n == FFALSE) ++ return(FFALSE); + } + } + else if(SOS_is_member(group, sosindex, column)) { +@@ -1004,7 +1004,7 @@ + + /* Cannot activate a variable if the SOS is full */ + if(list[n+nn] != 0) +- return(FALSE); ++ return(FFALSE); + + /* Check if there are variables quasi-active via non-zero lower bounds */ + nz = 0; +@@ -1013,7 +1013,7 @@ + nz++; + /* Reject outright if selected column has a non-zero lower bound */ + if(list[i] == column) +- return(FALSE); ++ return(FFALSE); + } + #ifdef Paranoia + if(nz > nn) +@@ -1026,7 +1026,7 @@ + nz++; + } + if(nz == nn) +- return(FALSE); ++ return(FFALSE); + + /* Accept if the SOS is empty */ + if(list[n+1] == 0) +@@ -1042,7 +1042,7 @@ + if(list[n+i] == 0) + break; + if(list[n+i] == column) +- return(FALSE); ++ return(FFALSE); + } + i--; + nn = list[n+i]; +@@ -1055,7 +1055,7 @@ + break; + if(i > n) { + report(lp, CRITICAL, "SOS_can_activate: Internal index error at SOS %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + + /* SOS accepts an additional variable; confirm neighbourness of candidate */ +@@ -1068,7 +1068,7 @@ + return(TRUE); + + /* It is not the right neighbour; return false */ +- return(FALSE); ++ return(FFALSE); + } + } + return(TRUE); +@@ -1083,12 +1083,12 @@ + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(lp, IMPORTANT, "SOS_set_marked: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + + if(!(lp->var_type[column] & (ISSOS | ISGUB))) +- return(FALSE); ++ return(FFALSE); + + if(sosindex == 0) { + +@@ -1125,10 +1125,10 @@ + if(asactive) { + for(i = 1; i <= nn; i++) { + if(list[n+i] == column) +- return(FALSE); ++ return(FFALSE); + else if(list[n+i] == 0) { + list[n+i] = column; +- return(FALSE); ++ return(FFALSE); + } + } + } +@@ -1146,12 +1146,12 @@ + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(lp, IMPORTANT, "SOS_unmark: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + + if(!(lp->var_type[column] & (ISSOS | ISGUB))) +- return(FALSE); ++ return(FFALSE); + + + if(sosindex == 0) { +@@ -1159,7 +1159,7 @@ + /* Undefine a SOS3 member variable that has temporarily been set as integer */ + if(lp->var_type[column] & ISSOSTEMPINT) { + lp->var_type[column] &= !ISSOSTEMPINT; +- set_int(lp, column, FALSE); ++ set_int(lp, column, FFALSE); + } + + nn = 0; +@@ -1197,7 +1197,7 @@ + list[n+nn] = 0; + return(TRUE); + } +- return(FALSE); ++ return(FFALSE); + } + else + return(TRUE); +@@ -1214,7 +1214,7 @@ + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(lp, IMPORTANT, "SOS_fix_unmarked: Invalid SOS index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + +@@ -1365,7 +1365,7 @@ + #ifdef Paranoia + if((sosindex < 0) || (sosindex > group->sos_count)) { + report(lp, IMPORTANT, "SOS_fix_list: Invalid index %d\n", sosindex); +- return(FALSE); ++ return(FFALSE); + } + #endif + +diff -ru lp_solve_5.5.orig/lp_utils.c lp_solve_5.5/lp_utils.c +--- lp_solve_5.5.orig/lp_utils.c 2019-02-19 10:42:21.376737063 -0600 ++++ lp_solve_5.5/lp_utils.c 2019-02-19 12:05:12.316874613 -0600 +@@ -47,7 +47,7 @@ + if(((*ptr) == NULL) && (size > 0)) { + lp->report(lp, CRITICAL, "alloc of %d 'char' failed\n", size); + lp->spx_status = NOMEMORY; +- return( FALSE ); ++ return( FFALSE ); + } + else + return( TRUE ); +@@ -66,7 +66,7 @@ + if(((*ptr) == NULL) && (size > 0)) { + lp->report(lp, CRITICAL, "alloc of %d 'MYBOOL' failed\n", size); + lp->spx_status = NOMEMORY; +- return( FALSE ); ++ return( FFALSE ); + } + else + return( TRUE ); +@@ -85,7 +85,7 @@ + if(((*ptr) == NULL) && (size > 0)) { + lp->report(lp, CRITICAL, "alloc of %d 'INT' failed\n", size); + lp->spx_status = NOMEMORY; +- return( FALSE ); ++ return( FFALSE ); + } + else + return( TRUE ); +@@ -104,7 +104,7 @@ + if(((*ptr) == NULL) && (size > 0)) { + lp->report(lp, CRITICAL, "alloc of %d 'REAL' failed\n", size); + lp->spx_status = NOMEMORY; +- return( FALSE ); ++ return( FFALSE ); + } + else + return( TRUE ); +@@ -123,7 +123,7 @@ + if(((*ptr) == NULL) && (size > 0)) { + lp->report(lp, CRITICAL, "alloc of %d 'LREAL' failed\n", size); + lp->spx_status = NOMEMORY; +- return( FALSE ); ++ return( FFALSE ); + } + else + return( TRUE ); +@@ -138,7 +138,7 @@ + *ptr = NULL; + } + else { +- status = FALSE; ++ status = FFALSE; + lp->report(lp, CRITICAL, "free() failed on line %d of file %s\n", + __LINE__, __FILE__); + } +@@ -311,7 +311,7 @@ + break; + + if((i < 0) || (mempool->vectorsize[i] < 0)) +- return( FALSE ); ++ return( FFALSE ); + + if(forcefree) { + FREE(mempool->vectorarray[i]); +@@ -345,7 +345,7 @@ + REAL *newlist; + + size += 1; +- if(allocREAL(lp, &newlist, size, FALSE)) ++ if(allocREAL(lp, &newlist, size, FFALSE)) + MEMCOPY(newlist, origlist, size); + return(newlist); + } +@@ -354,7 +354,7 @@ + MYBOOL *newlist; + + size += 1; +- if(allocMYBOOL(lp, &newlist, size, FALSE)) ++ if(allocMYBOOL(lp, &newlist, size, FFALSE)) + MEMCOPY(newlist, origlist, size); + return(newlist); + } +@@ -363,7 +363,7 @@ + int *newlist; + + size += 1; +- if(allocINT(lp, &newlist, size, FALSE)) ++ if(allocINT(lp, &newlist, size, FFALSE)) + MEMCOPY(newlist, origlist, size); + return(newlist); + } +@@ -600,7 +600,7 @@ + /* ---------------------------------------------------------------------------------- */ + STATIC REAL rand_uniform(lprec *lp, REAL range) + { +- static MYBOOL randomized = FALSE; /* static ok here for reentrancy/multithreading */ ++ static MYBOOL randomized = FFALSE; /* static ok here for reentrancy/multithreading */ + + if(!randomized) { + randomized = TRUE; +@@ -659,7 +659,7 @@ + MYBOOL status = TRUE; + + if((linkmap == NULL) || (*linkmap == NULL)) +- status = FALSE; ++ status = FFALSE; + else { + if((*linkmap)->map != NULL) + free((*linkmap)->map); +@@ -681,7 +681,7 @@ + (linkmap->map[0] == itemnr)) + return( TRUE ); + else +- return( FALSE ); ++ return( FFALSE ); + } + + STATIC int countActiveLink(LLrec *linkmap) +@@ -710,7 +710,7 @@ + size = linkmap->size; + + if(linkmap->map[newitem] != 0) +- return( FALSE ); ++ return( FFALSE ); + + /* Link forward */ + k = linkmap->map[2*size+1]; +@@ -736,7 +736,7 @@ + size = linkmap->size; + + if(linkmap->map[newitem] != 0) +- return( FALSE ); ++ return( FFALSE ); + + if(afteritem == linkmap->map[2*size+1]) + appendLink(linkmap, newitem); +@@ -762,7 +762,7 @@ + STATIC MYBOOL setLink(LLrec *linkmap, int newitem) + { + if(isActiveLink(linkmap, newitem)) +- return( FALSE ); ++ return( FFALSE ); + else + return( insertLink(linkmap, prevActiveLink(linkmap, newitem), newitem) ); + } +@@ -774,7 +774,7 @@ + + k = firstActiveLink(linkmap); + if(k != 0) +- return( FALSE ); ++ return( FFALSE ); + for(k = 1; k <= size; k++) + appendLink(linkmap, k); + return( TRUE ); +@@ -936,7 +936,7 @@ + { + LLrec *testmap; + +- testmap = cloneLink(linkmap, -1, FALSE); ++ testmap = cloneLink(linkmap, -1, FFALSE); + if(doappend) { + appendLink(testmap, itemnr); + removeLink(testmap, itemnr); +@@ -1006,9 +1006,9 @@ + + /* Test for validity of the target and create it if necessary */ + if(target == NULL) +- return( FALSE ); ++ return( FFALSE ); + if(*target == NULL) +- allocREAL(NULL, target, PV->startpos[PV->count], FALSE); ++ allocREAL(NULL, target, PV->startpos[PV->count], FFALSE); + + /* Expand the packed vector into the target */ + i = PV->startpos[0]; +@@ -1025,7 +1025,7 @@ + + STATIC REAL getvaluePackedVector(PVrec *PV, int index) + { +- index = searchFor(index, PV->startpos, PV->count, 0, FALSE); ++ index = searchFor(index, PV->startpos, PV->count, 0, FFALSE); + index = abs(index)-1; + if(index >= 0) + return( PV->value[index] ); +@@ -1036,7 +1036,7 @@ + STATIC MYBOOL freePackedVector(PVrec **PV) + { + if((PV == NULL) || (*PV == NULL)) +- return( FALSE ); ++ return( FFALSE ); + + FREE((*PV)->value); + FREE((*PV)->startpos); +diff -ru lp_solve_5.5.orig/lp_wlp.c lp_solve_5.5/lp_wlp.c +--- lp_solve_5.5.orig/lp_wlp.c 2019-02-19 10:42:21.376737063 -0600 ++++ lp_solve_5.5/lp_wlp.c 2019-02-19 11:56:14.376859727 -0600 +@@ -59,7 +59,7 @@ + if(!first) + nchars += write_data(userhandle, write_modeldata, " "); + else +- first = FALSE; ++ first = FFALSE; + sprintf(buf, "%+.12g", (double)a); + if(strcmp(buf, "-1") == 0) + nchars += write_data(userhandle, write_modeldata, "-"); +@@ -95,14 +95,14 @@ + + if(!mat_validate(lp->matA)) { + report(lp, IMPORTANT, "LP_writefile: Could not validate the data matrix.\n"); +- return(FALSE); ++ return(FFALSE); + } + + /* Write name of model */ + ptr = get_lp_name(lp); + if(ptr != NULL) { + if(*ptr) +- write_lpcomment(userhandle, write_modeldata, ptr, FALSE); ++ write_lpcomment(userhandle, write_modeldata, ptr, FFALSE); + else + ptr = NULL; + } +@@ -183,7 +183,7 @@ + } + + /* Write bounds on variables */ +- ok = FALSE; ++ ok = FFALSE; + for(i = nrows + 1; i <= lp->sum; i++) + if(!is_splitvar(lp, i - nrows)) { + if(lp->orig_lowbo[i] == lp->orig_upbo[i]) { +diff -ru lp_solve_5.5.orig/shared/commonlib.c lp_solve_5.5/shared/commonlib.c +--- lp_solve_5.5.orig/shared/commonlib.c 2019-02-19 10:42:21.376737063 -0600 ++++ lp_solve_5.5/shared/commonlib.c 2019-02-19 12:11:34.268885181 -0600 +@@ -116,7 +116,7 @@ + char *ptr; + + if((descname == NULL) || (stdname == NULL) || (((int) strlen(descname)) >= buflen - 6)) +- return( FALSE ); ++ return( FFALSE ); + + strcpy(stdname, descname); + if((ptr = strrchr(descname, '/')) == NULL) +@@ -982,7 +982,7 @@ + + _searchenv( searchfile, envvar, pathbuffer ); + if(pathbuffer[0] == '\0') +- return( FALSE ); ++ return( FFALSE ); + else { + if(foundpath != NULL) + strcpy(foundpath, pathbuffer); +diff -ru lp_solve_5.5.orig/shared/commonlib.h lp_solve_5.5/shared/commonlib.h +--- lp_solve_5.5.orig/shared/commonlib.h 2019-02-19 10:42:21.376737063 -0600 ++++ lp_solve_5.5/shared/commonlib.h 2019-02-19 11:54:00.028856010 -0600 +@@ -84,8 +84,8 @@ + #define NULL 0 + #endif + +-#ifndef FALSE +- #define FALSE 0 ++#ifndef FFALSE ++ #define FFALSE 0 + #define TRUE 1 + #endif + +diff -ru lp_solve_5.5.orig/shared/myblas.c lp_solve_5.5/shared/myblas.c +--- lp_solve_5.5.orig/shared/myblas.c 2019-02-19 10:42:21.376737063 -0600 ++++ lp_solve_5.5/shared/myblas.c 2019-02-19 12:11:58.152885842 -0600 +@@ -42,7 +42,7 @@ + { + if(mustinitBLAS) { + load_BLAS(NULL); +- mustinitBLAS = FALSE; ++ mustinitBLAS = FFALSE; + } + } + +@@ -72,7 +72,7 @@ + + if(libname == NULL) { + if(!mustinitBLAS && is_nativeBLAS()) +- return( FALSE ); ++ return( FFALSE ); + BLAS_dscal = my_dscal; + BLAS_dcopy = my_dcopy; + BLAS_daxpy = my_daxpy; +@@ -82,7 +82,7 @@ + BLAS_dload = my_dload; + BLAS_dnormi = my_dnormi; + if(mustinitBLAS) +- mustinitBLAS = FALSE; ++ mustinitBLAS = FFALSE; + } + else { + #ifdef LoadableBlasLib +@@ -151,7 +151,7 @@ + (BLAS_dnormi == NULL)) + ) { + load_BLAS(NULL); +- result = FALSE; ++ result = FFALSE; + } + } + return( result ); From 509303558880bf9fca64d57d12d5b4fd9ea2e784 Mon Sep 17 00:00:00 2001 From: ebtest Date: Wed, 20 Feb 2019 14:14:08 +0000 Subject: [PATCH 0475/5331] adding easyconfigs: GlobalArrays-5.7-intel-2018b-ethernet.eb, OpenMolcas-18.09-intel-2018b-ethernet.eb --- .../GlobalArrays-5.7-intel-2018b-ethernet.eb | 33 +++++++++++++ .../OpenMolcas-18.09-intel-2018b-ethernet.eb | 47 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b-ethernet.eb create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b-ethernet.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b-ethernet.eb new file mode 100644 index 00000000000..32de4001b0f --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b-ethernet.eb @@ -0,0 +1,33 @@ + +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.7' +versionsuffix = '-ethernet' + +homepage = 'http://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['3ed1ab47adfda7bceb7beca12fc05a2e1631732f0e55bbaf9036dad4e3da4774'] + + +configopts = ' --with-mpi --enable-i8' +configopts += ' --with-blas8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_scalapack_ilp64"' + +#select armci network as Ethernet TCP/IP +configopts += ' --with-sockets' + + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' + diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb new file mode 100644 index 00000000000..562173aacca --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb @@ -0,0 +1,47 @@ + +easyblock = 'CMakeMake' +name = 'OpenMolcas' +version = '18.09' +versionsuffix = '-ethernet' + +homepage = "https://gitlab.com/Molcas/OpenMolcas" +description = "OpenMolcas is a quantum chemistry software package" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] +sources = ["OpenMolcas-v%(version)s.tar.gz"] + +dependencies = [ + ('GlobalArrays', '5.7', versionsuffix), + ('Python', '3.6.6'), + ('HDF5', '1.10.2'), +] + + +builddependencies = [('CMake', '3.12.1')] + +separate_build_dir = True + +preconfigopts = "GAROOT=$EBROOTGLOBALARRAYS" +configopts = '-DLINALG=MKL -DMKLROOT=$EBROOTIMKL/mkl -DMPI=ON -DGA=ON -DTOOLS=ON' + +modextravars = {'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/sbin/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', +} + +sanity_check_paths = { + 'files': ['lib/libmolcas.a','bin/alaska.exe', 'bin/casvb.exe', 'bin/cht3.exe', 'bin/espf.exe', 'bin/gateway.exe', + 'bin/gugaci.exe', 'bin/last_energy.exe', 'bin/mbpt2.exe', 'bin/mcpdft.exe', 'bin/mrci.exe', + 'bin/qmstat.exe', 'bin/rassi.exe', 'bin/seward.exe', 'bin/vibrot.exe', 'bin/averd.exe', 'bin/ccsdt.exe', + 'bin/cpf.exe', 'bin/expbas.exe', 'bin/genano.exe', 'bin/gugadrt.exe', 'bin/localisation.exe', + 'bin/mckinley.exe', 'bin/motra.exe', 'bin/numerical_gradient.exe', 'bin/quater.exe', 'bin/rpa.exe', + 'bin/slapaf.exe', 'bin/caspt2.exe', 'bin/chcc.exe', 'bin/dynamix.exe', 'bin/ffpt.exe', 'bin/guessorb.exe', + 'bin/guga.exe', 'bin/loprop.exe', 'bin/mclr.exe', 'bin/mpprop.exe', 'bin/parnell.exe', 'bin/rasscf.exe', + 'bin/scf.exe', 'bin/surfacehop.exe', 'sbin/pymolcas', 'sbin/help_basis'], + 'dirs': ['data/', 'basis_library/'], +} + +moduleclass = 'chem' From ee872f4b21f1c8467a14841ed2ca046a9798b61a Mon Sep 17 00:00:00 2001 From: ebtest Date: Wed, 20 Feb 2019 14:34:05 +0000 Subject: [PATCH 0476/5331] add checksums for OpenMolcas source --- .../o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb index 562173aacca..cc779a7a939 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb @@ -12,6 +12,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] sources = ["OpenMolcas-v%(version)s.tar.gz"] +checksums = ['b4f310fb65205c865ccc6373ce9c3833a586f8ff63a71a624cf793559c9b39cf'] dependencies = [ ('GlobalArrays', '5.7', versionsuffix), From 4bbc3f09544ba0e96f10024a717c6934b507a1f2 Mon Sep 17 00:00:00 2001 From: ebtest Date: Wed, 20 Feb 2019 17:10:46 +0000 Subject: [PATCH 0477/5331] fix style errors --- .../GlobalArrays-5.7-intel-2018b-ethernet.eb | 7 +++---- .../OpenMolcas-18.09-intel-2018b-ethernet.eb | 19 ++++++++++--------- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b-ethernet.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b-ethernet.eb index 32de4001b0f..5eeb4d3e9c8 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b-ethernet.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b-ethernet.eb @@ -20,14 +20,13 @@ configopts = ' --with-mpi --enable-i8' configopts += ' --with-blas8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' configopts += ' --with-scalapack8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_scalapack_ilp64"' -#select armci network as Ethernet TCP/IP -configopts += ' --with-sockets' +# select armci network as Ethernet TCP/IP +configopts += ' --with-sockets' -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libga.a'], 'dirs': ['include'], } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb index cc779a7a939..3786a853feb 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb @@ -14,7 +14,7 @@ source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] sources = ["OpenMolcas-v%(version)s.tar.gz"] checksums = ['b4f310fb65205c865ccc6373ce9c3833a586f8ff63a71a624cf793559c9b39cf'] -dependencies = [ +dependencies = [ ('GlobalArrays', '5.7', versionsuffix), ('Python', '3.6.6'), ('HDF5', '1.10.2'), @@ -28,19 +28,20 @@ separate_build_dir = True preconfigopts = "GAROOT=$EBROOTGLOBALARRAYS" configopts = '-DLINALG=MKL -DMKLROOT=$EBROOTIMKL/mkl -DMPI=ON -DGA=ON -DTOOLS=ON' -modextravars = {'MOLCAS': '%(installdir)s', - 'MOLCAS_DRIVER': '%(installdir)s/sbin/pymolcas', - 'MOLCAS_SOURCE': '%(installdir)s', +modextravars = { + 'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/sbin/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', } sanity_check_paths = { - 'files': ['lib/libmolcas.a','bin/alaska.exe', 'bin/casvb.exe', 'bin/cht3.exe', 'bin/espf.exe', 'bin/gateway.exe', + 'files': ['lib/libmolcas.a', 'bin/alaska.exe', 'bin/casvb.exe', 'bin/cht3.exe', 'bin/espf.exe', 'bin/gateway.exe', 'bin/gugaci.exe', 'bin/last_energy.exe', 'bin/mbpt2.exe', 'bin/mcpdft.exe', 'bin/mrci.exe', - 'bin/qmstat.exe', 'bin/rassi.exe', 'bin/seward.exe', 'bin/vibrot.exe', 'bin/averd.exe', 'bin/ccsdt.exe', - 'bin/cpf.exe', 'bin/expbas.exe', 'bin/genano.exe', 'bin/gugadrt.exe', 'bin/localisation.exe', + 'bin/qmstat.exe', 'bin/rassi.exe', 'bin/seward.exe', 'bin/vibrot.exe', 'bin/averd.exe', 'bin/ccsdt.exe', + 'bin/cpf.exe', 'bin/expbas.exe', 'bin/genano.exe', 'bin/gugadrt.exe', 'bin/localisation.exe', 'bin/mckinley.exe', 'bin/motra.exe', 'bin/numerical_gradient.exe', 'bin/quater.exe', 'bin/rpa.exe', - 'bin/slapaf.exe', 'bin/caspt2.exe', 'bin/chcc.exe', 'bin/dynamix.exe', 'bin/ffpt.exe', 'bin/guessorb.exe', - 'bin/guga.exe', 'bin/loprop.exe', 'bin/mclr.exe', 'bin/mpprop.exe', 'bin/parnell.exe', 'bin/rasscf.exe', + 'bin/slapaf.exe', 'bin/caspt2.exe', 'bin/chcc.exe', 'bin/dynamix.exe', 'bin/ffpt.exe', 'bin/guessorb.exe', + 'bin/guga.exe', 'bin/loprop.exe', 'bin/mclr.exe', 'bin/mpprop.exe', 'bin/parnell.exe', 'bin/rasscf.exe', 'bin/scf.exe', 'bin/surfacehop.exe', 'sbin/pymolcas', 'sbin/help_basis'], 'dirs': ['data/', 'basis_library/'], } From 3fa74b39c543c1b539aafcb5a0b4aec2bd736343 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 20 Feb 2019 13:06:45 -0600 Subject: [PATCH 0478/5331] adding easyconfigs: Exonerate-2.4.0-GCC-6.4.0-2.28.eb, Exonerate-2.4.0-iccifort-2017.4.196-GCC-6.4.0-2.28.eb --- .../Exonerate-2.4.0-GCC-6.4.0-2.28.eb | 35 +++++++++++++++++++ ....4.0-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-iccifort-2017.4.196-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..742ea84ce7d --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-6.4.0-2.28.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = ['http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +dependencies = [('GLib', '2.54.3')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..378b6608943 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +source_urls = ['http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +dependencies = [('GLib', '2.54.3')] + +# parallel build fails +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' From 6400b48da8fc05ca635dbac6671ea8cf36733cde Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 20 Feb 2019 13:28:30 -0600 Subject: [PATCH 0479/5331] adding easyconfigs: DBG2OLC-20180221-GCC-6.4.0-2.28.eb, DBG2OLC-20180221-iccifort-2017.4.196-GCC-6.4.0-2.28.eb --- .../DBG2OLC-20180221-GCC-6.4.0-2.28.eb | 26 +++++++++++++++++++ ...0221-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20180221-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20180221-iccifort-2017.4.196-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20180221-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20180221-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..241982bca14 --- /dev/null +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20180221-GCC-6.4.0-2.28.eb @@ -0,0 +1,26 @@ +easyblock = 'CmdCp' + +name = 'DBG2OLC' +version = '20180221' +commit = '0246e46' + +homepage = 'https://github.com/yechengxi/DBG2OLC' +description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation + Sequencing Technologies""" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] +sources = ['%s.tar.gz' % commit] +checksums = ['809e6af9936d1b1edfb988e4233911199f4e60849acd2fe911d4893f9e7c08ca'] + +cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20180221-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20180221-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..f1afe809413 --- /dev/null +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20180221-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,26 @@ +easyblock = 'CmdCp' + +name = 'DBG2OLC' +version = '20180221' +commit = '0246e46' + +homepage = 'https://github.com/yechengxi/DBG2OLC' +description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation + Sequencing Technologies""" + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] +sources = ['%s.tar.gz' % commit] +checksums = ['809e6af9936d1b1edfb988e4233911199f4e60849acd2fe911d4893f9e7c08ca'] + +cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +moduleclass = 'bio' From 815eca58b3ebd458c1b572895e222e00ca336e2e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 21 Feb 2019 09:09:29 +0100 Subject: [PATCH 0480/5331] adding easyconfigs: RNAclust-1.3-foss-2018b-Perl-5.28.0.eb, LocARNA-1.9.2.2-foss-2018b.eb --- .../l/LocARNA/LocARNA-1.9.2.2-foss-2018b.eb | 34 +++++++++++++++++++ .../RNAclust-1.3-foss-2018b-Perl-5.28.0.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b.eb create mode 100644 easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Perl-5.28.0.eb diff --git a/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b.eb b/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b.eb new file mode 100644 index 00000000000..2a49755b1ea --- /dev/null +++ b/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'LocARNA' +version = '1.9.2.2' + +homepage = 'http://www.bioinf.uni-freiburg.de/Software/%(name)s/' +description = """LocARNA is a collection of alignment tools for the structural analysis of RNA. + Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for + your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for + analyzing sets of related RNAs without known common structure.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/s-will/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['76024e6d12a52e36a2d1aaffb09a7e7c1148ade05e7584530e21ce584c26e45b'] + +dependencies = [ + ('ViennaRNA', '2.4.11', '-Python-3.6.6'), +] + +configopts = '--with-vrna=$EBROOTVIENNARNA' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [('%(namelower)s -h')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..0b4853223ae --- /dev/null +++ b/easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'RNAclust' +version = '1.3' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bioinf.uni-leipzig.de/~kristin/Software/%(name)s/' +description = """RNAclust is a perl script summarizing all the single steps required for clustering + of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure + motif. It requires as input a multiple FASTA file.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.bioinf.uni-leipzig.de/~kristin/Software/%(name)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['c86becf9aafd2d78350bc50ea597b5c6c6bf1b0e5fc74919d0a5d9ba91c22817'] + +dependencies = [ + ('Perl', '5.28.0'), + ('LocARNA', '1.9.2.2'), + ('ViennaRNA', '2.4.11', '-Python-3.6.6'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pgma', '%(namelower)sDecodeTable', '%(name)s.pl', 'RNAsoup']], + 'dirs': [], +} + +sanity_check_commands = [('%(name)s.pl --man')] + +moduleclass = 'bio' From bc255657bbb3f68b49a81ad2e6d3206154f1de0f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 21 Feb 2019 10:14:42 +0200 Subject: [PATCH 0481/5331] Rewrite PyQt as a bundle we can give it a private copy of the SIP module. --- ...yQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb | 55 +++++++++++++------ 1 file changed, 39 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb index c7a51dc2379..78c3bb1472b 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb @@ -1,7 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Bart Verleye -# Center for eResearch, Auckland -easyblock = 'ConfigureMakePythonPackage' +easyblock = 'Bundle' name = 'PyQt' version = '4.12.3' @@ -12,27 +9,53 @@ description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt appli toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] -sources = ['PyQt4_gpl_x11-%(version)s.tar.gz'] -checksums = ['a00f5abef240a7b5852b7924fa5fdf5174569525dc076cd368a566619e56d472'] - dependencies = [ ('Python', '2.7.15'), - ('SIP', '4.19.13', versionsuffix), ('Qt', '4.8.7'), ] -configopts = "configure-ng.py --confirm-license" -configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages " -configopts += " --sipdir=%(installdir)s/share/sip/PyQt%(version_major)s" +default_easyblock = 'ConfigureMakePythonPackage' + +common_cfgopts = '--bindir=%(installdir)s/bin ' +common_cfgopts += '--destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +common_cfgopts += '--sipdir=%(installdir)s/share/sip ' + +sipcfgopts = 'configure.py ' + common_cfgopts + '--incdir=%(installdir)s/include ' +sipcfgopts += '--sip-module=PyQt%(version_major)s.sip ' + +pyqtcfgopts = 'configure-ng.py --confirm-license --verbose --no-python-dbus ' +pyqtcfgopts += common_cfgopts + ' --sip=%(installdir)s/bin/sip ' +pyqtcfgopts += '--designer-plugindir=%(installdir)s/plugins/designer ' + +# PyQt needs a private copy of the sip module so we need to do this as a Bundle. +components = [ + ('SIP', '4.19.13', { + 'source_urls': ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'], + 'sources': ['sip-%(version)s.tar.gz'], + 'start_dir': 'sip-%(version)s', + 'configopts': sipcfgopts, + }), + (name, version, { + 'source_urls': ['http://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/%(name)s-%(version)s'], + 'sources': ['%(name)s%(version_major)s_gpl_x11-%(version)s.tar.gz'], + 'start_dir': '%(name)s%(version_major)s_gpl_x11-%(version)s', + 'configopts': pyqtcfgopts, + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_PLUGIN_PATH': 'plugins/designer' +} -options = {'modulename': '%(name)s%(version_major)s'} +sanity_check_commands = ["python -c 'import PyQt%(version_major)s.QtHelp'"] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} +libpath = 'lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s' sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s'], + 'files': ['bin/%s' % x for x in ['pyuic4', 'pyrcc4', 'pylupdate4']] + + [libpath + '/%s.%s' % (x, SHLIB_EXT) for x in ['sip', 'QtCore', 'Qt']], + 'dirs': ['include', 'plugins/designer', 'share/sip'], } moduleclass = 'vis' From cb3bf47d40975febe437afafda7078c4d69a2f2b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 21 Feb 2019 11:22:37 +0200 Subject: [PATCH 0482/5331] Make PyQt4 a bit more like PyQt5 easyconfig. --- ...yQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb | 23 ++++++++++--------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb index 78c3bb1472b..037f11f90e8 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb @@ -16,11 +16,14 @@ dependencies = [ default_easyblock = 'ConfigureMakePythonPackage' +pylibdir = 'lib/python%(pyshortver)s/site-packages' + common_cfgopts = '--bindir=%(installdir)s/bin ' -common_cfgopts += '--destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +common_cfgopts += '--destdir=%%(installdir)s/%s ' % pylibdir common_cfgopts += '--sipdir=%(installdir)s/share/sip ' -sipcfgopts = 'configure.py ' + common_cfgopts + '--incdir=%(installdir)s/include ' +sipcfgopts = 'configure.py ' + common_cfgopts +sipcfgopts += '--incdir=%(installdir)s/include ' sipcfgopts += '--sip-module=PyQt%(version_major)s.sip ' pyqtcfgopts = 'configure-ng.py --confirm-license --verbose --no-python-dbus ' @@ -31,31 +34,29 @@ pyqtcfgopts += '--designer-plugindir=%(installdir)s/plugins/designer ' components = [ ('SIP', '4.19.13', { 'source_urls': ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'], - 'sources': ['sip-%(version)s.tar.gz'], + 'sources': [SOURCELOWER_TAR_GZ], 'start_dir': 'sip-%(version)s', 'configopts': sipcfgopts, + 'options': {'modulename': 'PyQt4.sip'}, }), (name, version, { 'source_urls': ['http://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/%(name)s-%(version)s'], 'sources': ['%(name)s%(version_major)s_gpl_x11-%(version)s.tar.gz'], 'start_dir': '%(name)s%(version_major)s_gpl_x11-%(version)s', 'configopts': pyqtcfgopts, + 'options': {'modulename': 'PyQt4.QtCore'}, }), ] modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'QT_PLUGIN_PATH': 'plugins/designer' + 'PYTHONPATH': pylibdir, + 'QT_PLUGIN_PATH': 'plugins' } -sanity_check_commands = ["python -c 'import PyQt%(version_major)s.QtHelp'"] - -libpath = 'lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s' - sanity_check_paths = { 'files': ['bin/%s' % x for x in ['pyuic4', 'pyrcc4', 'pylupdate4']] + - [libpath + '/%s.%s' % (x, SHLIB_EXT) for x in ['sip', 'QtCore', 'Qt']], - 'dirs': ['include', 'plugins/designer', 'share/sip'], + [pylibdir + '/%%(name)s%%(version_major)s/%s.%s' % (x, SHLIB_EXT) for x in ['sip', 'QtCore', 'Qt']], + 'dirs': ['include', 'plugins', 'share/sip'], } moduleclass = 'vis' From 3156df36464b57c3e133c7fe589ce6ebc1b575d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Feb 2019 10:53:04 +0100 Subject: [PATCH 0483/5331] add -mno-fma to for Libint 2.0.3 with foss/2018b --- easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb index 4ae37c37d5e..9a8217520b3 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -12,4 +12,7 @@ source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc' sources = ['libint-%(version)s-stable.tgz'] checksums = ['5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02'] +# need to prevent GCC from emiting FMA instructions due to bugs in include/vector_x86.h for Libint 2.0.x +preconfigopts = 'export CXXFLAGS="$CXXFLAGS -mno-fma" && ' + moduleclass = 'chem' From 3404068af03f0fad49cc18893a20654fad6822fd Mon Sep 17 00:00:00 2001 From: sassmaj Date: Thu, 21 Feb 2019 13:56:16 +0100 Subject: [PATCH 0484/5331] Done the requested changes --- .../n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb | 27 +++++++++---------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb index dd1cf272297..d217437ed40 100644 --- a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb @@ -1,37 +1,36 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + easyblock = 'CmdCp' name = 'NGSadmix' version = '32' +CXX = 'g++' +CXXFLAGS = '-O3' homepage = 'http://www.popgen.dk/software/index.php/NgsAdmix' -description = """This page contains information about the program called -NGSadmix, which is a tool for finding admixture proportions +description = """NGSadmix is a tool for finding admixture proportions from NGS data, based on genotype likelihoods.""" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} -# This is a bit of a hack as there is no easyblock to simply download a cpp file and compile it. -# So we download the file from the source and copy it to the build directory. +# We download the file from the source and copy it to the build directory. +source_urls = ['http://popgen.dk/software/download/NGSadmix/'] sources = [{ - 'source_urls': ['http://popgen.dk/software/download/NGSadmix/'], - 'filename': 'ngsadmix32.cpp', - 'download_filename': 'ngsadmix32.cpp', + 'filename': 'ngsadmix%(version)s.cpp', 'extract_cmd': 'cp %s %(builddir)s', }] checksums = ['a5623b71d20114708cfd7ccc5f8c6ce38ff871d1b79af85bc89d38775f2d477e'] -build_str = "g++ ngsadmix32.cpp -O3 -lpthread -lz -o NGSadmix" -cmds_map = [('', build_str)] +cmds_map = [('', "${CXX} ngsadmix%(version)s.cpp ${CXXFLAGS} -lpthread -lz -o NGSadmix")] -files_to_copy = ['NGSadmix'] +files_to_copy = [(['NGSadmix'], 'bin')] sanity_check_paths = { - 'files': ['NGSadmix'], - 'dirs': [''], + 'files': ['bin/NGSadmix'], + 'dirs': [], } -modextrapaths = {'PATH': ''} - moduleclass = 'bio' From 31ddaa26035492c72bcf7e1f5e6ab325ff2fadf8 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 21 Feb 2019 09:19:58 -0400 Subject: [PATCH 0485/5331] adding easyconfigs: Hello-2.10-GCCcore-8.2.0.eb --- .../h/Hello/Hello-2.10-GCCcore-8.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hello/Hello-2.10-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/h/Hello/Hello-2.10-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/Hello/Hello-2.10-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..7cf260f10c2 --- /dev/null +++ b/easybuild/easyconfigs/h/Hello/Hello-2.10-GCCcore-8.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Hello' +version = '2.10' + +homepage = 'https://www.gnu.org/software/hello/' + +description = """ +The GNU Hello program produces a familiar, friendly greeting. Yes, this is another +implementation of the classic program that prints "Hello, world!" when you run it. + +However, unlike the minimal version often seen, GNU Hello processes its argument +list to modify its behavior, supports greetings in many languages, and so on. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['31e066137a962676e89f69d1b65382de95a7ef7d914b8cb956f41ea72e0f516b'] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [ + ('binutils', '2.31.1'), +] + +sanity_check_paths = { + 'files': ['bin/hello'], + 'dirs': ['share/man/man1'], +} +sanity_check_commands = ['hello'] + +moduleclass = 'system' From 9a42742d16164fc5d555237eecd96cf14838851d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Feb 2019 16:17:18 +0100 Subject: [PATCH 0486/5331] adding easyconfigs: OCaml-4.07.1-foss-2018b.eb --- .../o/OCaml/OCaml-4.07.1-foss-2018b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.07.1-foss-2018b.eb diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.07.1-foss-2018b.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.07.1-foss-2018b.eb new file mode 100644 index 00000000000..8505fd6b61d --- /dev/null +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.07.1-foss-2018b.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## +name = 'OCaml' +version = '4.07.1' + +homepage = 'http://ocaml.org/' +description = """OCaml is a general purpose industrial-strength programming language + with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria + it benefits from one of the most advanced type systems and supports functional, + imperative and object-oriented styles of programming.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +opam_ver = '2.0.3' +source_urls = [ + 'http://caml.inria.fr/pub/distrib/ocaml-%s' % '.'.join(version.split('.')[:2]), + 'https://github.com/ocaml/opam/releases/download/%s' % opam_ver, +] +sources = [ + SOURCELOWER_TAR_GZ, + 'opam-full-%s.tar.gz' % opam_ver, +] +checksums = [ + '2ad43be17ed5c74ea27887ae0cc4793b835408180c0b9175bc9ad53082a59af4', # ocaml-4.07.1.tar.gz + '0589da4da184584a5445d59385009536534f60bc0e27772245b2f49e5fa8f0e2', # opam-full-2.0.3.tar.gz +] + +builddependencies = [('Autotools', '20180311')] +dependencies = [ + ('ncurses', '6.1'), + ('libreadline', '7.0'), + ('GSL', '2.5'), +] + +# parallel build tends to break +parallel = 1 + +# handled by OPAM, order matters! +# see https://opam.ocaml.org/packages +exts_list = [ + ('ocamlfind', '1.8.0',), + ('batteries', '2.9.0',), + ('ocaml-twt', '0.94.0',), + ('gsl', '1.24.0',), +] + +moduleclass = 'lang' From a817e5cc04263d8cfef7f2e35a2d000f3f7240ba Mon Sep 17 00:00:00 2001 From: sassmaj Date: Thu, 21 Feb 2019 16:22:47 +0100 Subject: [PATCH 0487/5331] adding easyconfigs: STAR-2.7.0d-foss-2018b.eb --- .../s/STAR/STAR-2.7.0d-foss-2018b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.0d-foss-2018b.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.0d-foss-2018b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.0d-foss-2018b.eb new file mode 100644 index 00000000000..e615d73267d --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.0d-foss-2018b.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.0d' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b3152b476161c7da324cf2cc1b55c35d3898b4ba0a57ec4cc699f48399b95799'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/STAR', 'bin/STARlong'], + 'dirs': [], +} + +moduleclass = 'bio' From f131ef1e15c2a27a35fd07ab891f21f82a249bfe Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 21 Feb 2019 12:24:33 -0600 Subject: [PATCH 0488/5331] adding easyconfigs: Pysam-0.14-foss-2017b-Python-2.7.14.eb --- .../Pysam-0.14-foss-2017b-Python-2.7.14.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..d72ea651d83 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.14' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c9c8ea82b4deee7607d5885fc7cc92311f06e765ff30e0b2b2d3d85b28cf5687'] + +dependencies = [ + ('XZ', '5.2.3'), + ('Python', '2.7.14'), + ('ncurses', '6.0'), + ('cURL', '7.56.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 6c5975cc340037f19ac240825627a306abddfa14 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 21 Feb 2019 13:11:05 -0600 Subject: [PATCH 0489/5331] change the file name of the patch --- ...> lpsolve-5.5.2.5_Fix_expected_identifier_error_for_gcc.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/l/lpsolve/{lpsolve-5.5.2.5_Fix_expected_identifier_error.patch => lpsolve-5.5.2.5_Fix_expected_identifier_error_for_gcc.patch} (100%) diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5_Fix_expected_identifier_error.patch b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5_Fix_expected_identifier_error_for_gcc.patch similarity index 100% rename from easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5_Fix_expected_identifier_error.patch rename to easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5_Fix_expected_identifier_error_for_gcc.patch From 9af1ffd2ef05090cbf3c3eaf6d8967a4611278c5 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 21 Feb 2019 13:11:58 -0600 Subject: [PATCH 0490/5331] remove the path in intel eb file --- .../lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 2895e0056b0..6a3a0faa427 100644 --- a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -10,11 +10,8 @@ toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} source_urls = [SOURCEFORGE_SOURCE] sources = ['lp_solve_%(version)s_source.tar.gz'] -patches = ['lpsolve-5.5.2.5_Fix_expected_identifier_error.patch'] checksums = [ '201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a', # lp_solve_5.5.2.5_source.tar.gz - # lpsolve-5.5.2.5_Fix_expected_identifier_error.patch - 'be46d06035797b455ff616c74f83c4e36c9cad6c41b0c8680b29cb6b3208f49c', ] lpsolve_ver = '%(version_major)s%(version_minor)s' From c47b067423be93db8b0ca31231a7910cfbea92b8 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 21 Feb 2019 13:14:50 -0600 Subject: [PATCH 0491/5331] update the patch file name in the eb file --- .../easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb index fa899fc0053..47edd80537e 100644 --- a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = [SOURCEFORGE_SOURCE] sources = ['lp_solve_%(version)s_source.tar.gz'] -patches = ['lpsolve-5.5.2.5_Fix_expected_identifier_error.patch'] +patches = ['lpsolve-5.5.2.5_Fix_expected_identifier_error_for_gcc.patch'] checksums = [ '201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a', # lp_solve_5.5.2.5_source.tar.gz # lpsolve-5.5.2.5_Fix_expected_identifier_error.patch From df90d3189b3ee34b6a67081f691e367dd5b01905 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 21 Feb 2019 13:18:29 -0600 Subject: [PATCH 0492/5331] update the writting of the version for patch file name in eb file --- .../easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb index 47edd80537e..3a7cce6c5cc 100644 --- a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-GCC-6.4.0-2.28.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = [SOURCEFORGE_SOURCE] sources = ['lp_solve_%(version)s_source.tar.gz'] -patches = ['lpsolve-5.5.2.5_Fix_expected_identifier_error_for_gcc.patch'] +patches = ['lpsolve-%(version)s_Fix_expected_identifier_error_for_gcc.patch'] checksums = [ '201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a', # lp_solve_5.5.2.5_source.tar.gz # lpsolve-5.5.2.5_Fix_expected_identifier_error.patch From d168b1699a04609a8e2eb215b12bed2f3ce8d616 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 22 Feb 2019 09:56:22 +0100 Subject: [PATCH 0493/5331] add Python versionsuffix, follow up for pr #7702 --- ...s-2018b.eb => LocARNA-1.9.2.2-foss-2018b-Python-3.6.6.eb} | 5 ++--- ...erl-5.28.0.eb => RNAclust-1.3-foss-2018b-Python-3.6.6.eb} | 4 ++-- 2 files changed, 4 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/l/LocARNA/{LocARNA-1.9.2.2-foss-2018b.eb => LocARNA-1.9.2.2-foss-2018b-Python-3.6.6.eb} (92%) rename easybuild/easyconfigs/r/RNAclust/{RNAclust-1.3-foss-2018b-Perl-5.28.0.eb => RNAclust-1.3-foss-2018b-Python-3.6.6.eb} (93%) diff --git a/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b.eb b/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b-Python-3.6.6.eb similarity index 92% rename from easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b.eb rename to easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b-Python-3.6.6.eb index 2a49755b1ea..a38d94075af 100644 --- a/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b.eb +++ b/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b-Python-3.6.6.eb @@ -4,6 +4,7 @@ easyblock = 'ConfigureMake' name = 'LocARNA' version = '1.9.2.2' +versionsuffix = '-Python-3.6.6' homepage = 'http://www.bioinf.uni-freiburg.de/Software/%(name)s/' description = """LocARNA is a collection of alignment tools for the structural analysis of RNA. @@ -18,9 +19,7 @@ source_urls = ['https://github.com/s-will/%(name)s/releases/download/v%(version) sources = [SOURCELOWER_TAR_GZ] checksums = ['76024e6d12a52e36a2d1aaffb09a7e7c1148ade05e7584530e21ce584c26e45b'] -dependencies = [ - ('ViennaRNA', '2.4.11', '-Python-3.6.6'), -] +dependencies = [('ViennaRNA', '2.4.11', '-Python-3.6.6')] configopts = '--with-vrna=$EBROOTVIENNARNA' diff --git a/easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Python-3.6.6.eb similarity index 93% rename from easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Perl-5.28.0.eb rename to easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Python-3.6.6.eb index 0b4853223ae..4c66769f7df 100644 --- a/easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ easyblock = 'ConfigureMake' name = 'RNAclust' version = '1.3' -versionsuffix = '-Perl-%(perlver)s' +versionsuffix = '-Python-3.6.6' homepage = 'http://www.bioinf.uni-leipzig.de/~kristin/Software/%(name)s/' description = """RNAclust is a perl script summarizing all the single steps required for clustering @@ -20,7 +20,7 @@ checksums = ['c86becf9aafd2d78350bc50ea597b5c6c6bf1b0e5fc74919d0a5d9ba91c22817'] dependencies = [ ('Perl', '5.28.0'), - ('LocARNA', '1.9.2.2'), + ('LocARNA', '1.9.2.2', '-Python-3.6.6'), ('ViennaRNA', '2.4.11', '-Python-3.6.6'), ] From 0812834da5140570e235ca418c85de77196dca2d Mon Sep 17 00:00:00 2001 From: sassmaj Date: Fri, 22 Feb 2019 10:30:21 +0100 Subject: [PATCH 0494/5331] Some more tidying up --- .../easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb index d217437ed40..f47112e6b61 100644 --- a/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/n/NGSadmix/NGSadmix-32-GCC-7.3.0-2.30.eb @@ -5,8 +5,6 @@ easyblock = 'CmdCp' name = 'NGSadmix' version = '32' -CXX = 'g++' -CXXFLAGS = '-O3' homepage = 'http://www.popgen.dk/software/index.php/NgsAdmix' description = """NGSadmix is a tool for finding admixture proportions @@ -24,6 +22,8 @@ sources = [{ checksums = ['a5623b71d20114708cfd7ccc5f8c6ce38ff871d1b79af85bc89d38775f2d477e'] +dependencies = [('zlib', '1.2.11')] + cmds_map = [('', "${CXX} ngsadmix%(version)s.cpp ${CXXFLAGS} -lpthread -lz -o NGSadmix")] files_to_copy = [(['NGSadmix'], 'bin')] From 1702667b468038cb5e6359f6510090c41ceabda6 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Fri, 22 Feb 2019 11:05:40 +0100 Subject: [PATCH 0495/5331] Patch for FMA issues in Libint --- .../l/Libint/Libint-2.0.3-foss-2018b.eb | 12 ++- .../l/Libint/Libint-2.0.3-stable-fma.patch | 95 +++++++++++++++++++ 2 files changed, 103 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb index 9a8217520b3..769fd172792 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -10,9 +10,13 @@ toolchainopts = {'pic': True} source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] sources = ['libint-%(version)s-stable.tgz'] -checksums = ['5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02'] - -# need to prevent GCC from emiting FMA instructions due to bugs in include/vector_x86.h for Libint 2.0.x -preconfigopts = 'export CXXFLAGS="$CXXFLAGS -mno-fma" && ' +# Remove some problematic (and not very useful) FMA header code that does not compile with GCC. +# This is done with a patch, because it also affects anything that links against Libint. +# This way, FMA compilert optimization can remain enabled. +patches = ['Libint-2.0.3-stable-fma.patch'] +checksums = [ + '5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02', # libint-2.0.3-stable.tgz + '4db3795818bc37340a45453e8cc9d1d8ab7e08c0c2e9e5b64df2dfc7f0322390', # Libint-2.0.3-stable-fma.patch +] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch new file mode 100644 index 00000000000..bd670511e7c --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch @@ -0,0 +1,95 @@ +--- libint-2.0.3-stable.orig/include/vector_x86.h 2019-02-22 09:16:11.718287697 +0100 ++++ libint-2.0.3-stable/include/vector_x86.h 2019-02-22 09:17:37.628678533 +0100 +@@ -141,30 +141,6 @@ + return c; + } + +-#if defined(__FMA__) +- inline VectorSSEDouble fma_plus(VectorSSEDouble a, VectorSSEDouble b, VectorSSEDouble c) { +- VectorSSEDouble d; +- d.d = _mm_fmadd_pd(a.d, b.d, c.d); +- return d; +- } +- inline VectorSSEDouble fma_minus(VectorSSEDouble a, VectorSSEDouble b, VectorSSEDouble c) { +- VectorSSEDouble d; +- d.d = _mm_fmsub_pd(a.d, b.d, c.d); +- return d; +- } +-#elif defined(__FMA4__) +- inline VectorSSEDouble fma_plus(VectorSSEDouble a, VectorSSEDouble b, VectorSSEDouble c) { +- VectorSSEDouble d; +- d.d = _mm_macc_pd(a.d, b.d, c.d); +- return d; +- } +- inline VectorSSEDouble fma_minus(VectorSSEDouble a, VectorSSEDouble b, VectorSSEDouble c) { +- VectorSSEDouble d; +- d.d = _mm_msub_pd(a.d, b.d, c.d); +- return d; +- } +-#endif +- + //@} + + //@{ standard functions +@@ -365,30 +341,6 @@ + return c; + } + +-#if defined(__FMA__) +- inline VectorSSEFloat fma_plus(VectorSSEFloat a, VectorSSEFloat b, VectorSSEFloat c) { +- VectorSSEFloat d; +- d.d = _mm_fmadd_ps(a.d, b.d, c.d); +- return d; +- } +- inline VectorSSEFloat fma_minus(VectorSSEFloat a, VectorSSEFloat b, VectorSSEFloat c) { +- VectorSSEFloat d; +- d.d = _mm_fmsub_ps(a.d, b.d, c.d); +- return d; +- } +-#elif defined(__FMA4__) +- inline VectorSSEFloat fma_plus(VectorSSEFloat a, VectorSSEFloat b, VectorSSEFloat c) { +- VectorSSEFloat d; +- d.d = _mm_macc_ps(a.d, b.d, c.d); +- return d; +- } +- inline VectorSSEFloat fma_minus(VectorSSEFloat a, VectorSSEFloat b, VectorSSEFloat c) { +- VectorSSEFloat d; +- d.d = _mm_msub_ps(a.d, b.d, c.d); +- return d; +- } +-#endif +- + //@} + + //@{ standard functions +@@ -591,30 +543,6 @@ + return c; + } + +-#if defined(__FMA__) +- inline VectorAVXDouble fma_plus(VectorAVXDouble a, VectorAVXDouble b, VectorAVXDouble c) { +- VectorAVXDouble d; +- d.d = _mm256_fmadd_pd(a.d, b.d, c.d); +- return d; +- } +- inline VectorAVXDouble fma_minus(VectorAVXDouble a, VectorAVXDouble b, VectorAVXDouble c) { +- VectorAVXDouble d; +- d.d = _mm256_fmsub_pd(a.d, b.d, c.d); +- return d; +- } +-#elif defined(__FMA4__) +- inline VectorAVXDouble fma_plus(VectorAVXDouble a, VectorAVXDouble b, VectorAVXDouble c) { +- VectorAVXDouble d; +- d.d = _mm256_facc_pd(a.d, b.d, c.d); +- return d; +- } +- inline VectorAVXDouble fma_minus(VectorAVXDouble a, VectorAVXDouble b, VectorAVXDouble c) { +- VectorAVXDouble d; +- d.d = _mm256_fsub_pd(a.d, b.d, c.d); +- return d; +- } +-#endif +- + //@} + + //@{ standard functions From 70017c70f780914f6008fcd8b2f066a701ad95f6 Mon Sep 17 00:00:00 2001 From: "Carl von Ossietzky University Oldenburg (Germany)" <43003344+HPC-UniOldenburg@users.noreply.github.com> Date: Fri, 22 Feb 2019 11:58:58 +0100 Subject: [PATCH 0496/5331] Delete Salmon-0.11.2-intel-2018a-Python-2.7.14.eb replaced with non-python version --- ...Salmon-0.11.2-intel-2018a-Python-2.7.14.eb | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a-Python-2.7.14.eb deleted file mode 100644 index 8460f531e29..00000000000 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.11.2-intel-2018a-Python-2.7.14.eb +++ /dev/null @@ -1,40 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'CMakeMake' - -name = 'Salmon' -version = '0.11.2' -versionsuffix = '-Python-2.7.14' - -toolchainopts = {'cstd': 'c++14'} - -homepage = 'https://github.com/COMBINE-lab/%(namelower)s' -description = """Salmon is a wicked-fast program to produce a highly-accurate, - transcript-level quantification estimates from RNA-seq data.""" - -toolchain = {'name': 'intel', 'version': '2018a'} -toolchainopts = {'optarch': True, 'pic': True, 'openmp': True} - -source_urls = ['https://github.com/COMBINE-lab/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['Salmon-%(version)s_Intel-compilers.patch'] -checksums = [ - 'bbdb70173be3c54d1bff8ab370efab74a7b6c45c509b83d28ae24f85da15b5ab', # v0.11.2.tar.gz - '420c248e0e494fa75ded42aae6218adf84fb6682d9a0a29a3dfb2ecf8b9113a9', # Salmon-0.11.2_Intel-compilers.patch -] - -builddependencies = [('CMake', '3.9.5', '', ('GCCcore', '6.4.0'))] - -dependencies = [ - ('Boost', '1.66.0', '', ('intel', '2018a')), - ('tbb', '2018_U3'), - ('Jellyfish', '2.2.10'), - ('bzip2', '1.0.6', '', ('GCCcore', '6.4.0')) -] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [] -} - -moduleclass = 'bio' From 4cdfe62af93c9968a2dc0c411a7ccc865f41710b Mon Sep 17 00:00:00 2001 From: Andreas Henkel Date: Fri, 22 Feb 2019 12:32:12 +0100 Subject: [PATCH 0497/5331] Update Theano-1.0.4-foss-2018a-Python-3.6.4.eb --- .../t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb index 611578980a5..cefdcc58151 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018a-Python-3.6.4.eb @@ -15,6 +15,9 @@ sources = [SOURCE_TAR_GZ] checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] dependencies = [('Python', '3.6.4')] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': ['bin/theano-cache', 'bin/theano-nose'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From aaa6883ea526e900f7254ddcb3a87fa68a2ae973 Mon Sep 17 00:00:00 2001 From: Andreas Henkel Date: Fri, 22 Feb 2019 12:33:34 +0100 Subject: [PATCH 0498/5331] Update Meson-0.48.1-foss-2018a-Python-3.6.4.eb --- .../m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb index d4a975ad33a..eec0fddf9fd 100644 --- a/easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/Meson/Meson-0.48.1-foss-2018a-Python-3.6.4.eb @@ -17,6 +17,9 @@ dependencies = [ ('Ninja', '1.8.2'), ] +download_dep_fail = True +use_pip = True + options = {'modulename': 'mesonbuild'} sanity_check_paths = { From 9c8015b289489591daf777b64cda0dc7dcb6248b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Feb 2019 13:03:06 +0100 Subject: [PATCH 0499/5331] fix location of 'bin' in install prefix in runCA script for MaSuRCA 3.3.0 --- .../m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb index c122a16fb5a..9693f0d6499 100644 --- a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb @@ -39,11 +39,17 @@ dependencies = [ buildopts = "install-special" start_dir = "global-1" +# escaping single quotes within single quotes is tricky, so we use $'...' to use ANSI C-like escaping +postinstallcmds = ["sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA"] + sanity_check_paths = { 'files': ['bin/masurca'], 'dirs': ['include', 'lib'], } -sanity_check_commands = ["masurca --help"] +sanity_check_commands = [ + "masurca --help", + "runCA --help", +] moduleclass = 'bio' From f7cc207a7550f16ad50fca8e047a785965182749 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 22 Feb 2019 14:54:58 +0200 Subject: [PATCH 0500/5331] Add missing dependency for jsonschema. --- .../i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb index d66086e0a89..70688c36bcc 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb @@ -140,6 +140,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], + }), ('jsonschema', '2.6.0', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], From c328eaa21d0e20050b5884b8b10c4f1df6bd723b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 22 Feb 2019 14:56:04 +0200 Subject: [PATCH 0501/5331] adding easyconfigs: IPython-7.2.0-fosscuda-2018b-Python-3.6.6.eb --- ...ython-7.2.0-fosscuda-2018b-Python-3.6.6.eb | 190 ++++++++++++++++++ 1 file changed, 190 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-7.2.0-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.2.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/IPython/IPython-7.2.0-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..33dfb20ba39 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-7.2.0-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,190 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '7.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('ZeroMQ', '4.2.5'), + ('matplotlib', '3.0.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('Pygments', '2.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'checksums': ['82666aac15622bd7bb685a4ee7f6625dd716da3ef7473620c192c0168aae64fc'], + }), + ('ipython_genutils', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'checksums': ['6a9496209b76463f1dec126ab928919aaf1f55b38beb9219af3fe202f6bbdd12'], + }), + ('pexpect', '4.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], + }), + ('pickleshare', '0.7.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('wcwidth', '0.1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + }), + ('prompt_toolkit', '2.0.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], + 'checksums': ['fd17048d8335c1e6d5ee403c3569953ba3eb8555d710bfc548faf0712666ea39'], + }), + ('ptyprocess', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('traitlets', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], + }), + ('parso', '0.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], + 'checksums': ['35704a43a3c113cce4de228ddb39aab374b8004f4f2407d070b6a2ca784ce8a2'], + }), + ('jedi', '0.13.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], + 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], + }), + ('testpath', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], + 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('Send2Trash', '1.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], + 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], + }), + ('webencodings', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], + 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], + }), + ('bleach', '3.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], + 'checksums': ['48d39675b80a75f6d1c3bdbffec791cf0bbbab665cf01e20da701c77de278718'], + }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], + }), + ('pandocfilters', '1.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], + }), + ('pyzmq', '17.1.2', { + 'modulename': 'zmq', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], + 'checksums': ['a72b82ac1910f2cf61a49139f4974f994984475f771b0faa730839607eeedddf'], + }), + ('entrypoints', '0.2.3', { + 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], + 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], + }), + ('jupyter_core', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], + }), + ('nbformat', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], + }), + ('mistune', '0.8.4', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('defusedxml', '0.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], + 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], + }), + ('nbconvert', '5.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'checksums': ['a8a2749f972592aa9250db975304af6b7337f32337e523a2c995cc9e12c07807'], + }), + ('terminado', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], + }), + ('tornado', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], + }), + ('jupyter_client', '5.2.3', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], + }), + ('backcall', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], + 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], + }), + ('ipykernel', '5.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + 'checksums': ['0fc0bf97920d454102168ec2008620066878848fcfca06c22b669696212e292f'], + }), + ('prometheus_client', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], + 'checksums': ['046cb4fffe75e55ff0e6dfd18e2ea16e54d86cc330f369bebcc683475c8b68a9'], + }), + ('notebook', '5.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + 'checksums': ['91705b109fc785198faed892489cddb233265564d5e2dad5e4f7974af05ee8dd'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "iptest", +] + +moduleclass = 'tools' From 9afb7ac438fd8d9c5217ec05919cf5349c10ab3c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Feb 2019 14:44:35 +0100 Subject: [PATCH 0502/5331] adding easyconfigs: wget-1.20.1-GCCcore-7.3.0.eb, libidn-1.35-GCCcore-7.3.0.eb --- .../l/libidn/libidn-1.35-GCCcore-7.3.0.eb | 22 +++++++++ .../w/wget/wget-1.20.1-GCCcore-7.3.0.eb | 47 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.35-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.35-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.35-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..5873950934d --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.35-GCCcore-7.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.35' + +homepage = 'http://www.gnu.org/software/libidn' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f11af1005b46b7b15d057d7f107315a1ad46935c7fcdf243c16e46ec14f0fe1e'] + +builddependencies = [('binutils', '2.30')] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..a87bbb39caf --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.20.1' + +homepage = 'https://www.gnu.org/software/wget/' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b783b390cb571c837b392857945f5a1f00ec6b043177cc42abb8ee1b542ee1b3'] + +builddependencies = [ + ('binutils', '2.30'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('PCRE', '8.41'), + ('libidn', '1.35'), + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1s'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.4.11'), +] + +# make sure pkg-config picks up system packages (OpenSSL & co) +preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +configopts = '--with-ssl=openssl ' + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['bin/wget'], + 'dirs': [] +} + +moduleclass = 'devel' From 6abd3a52b86f31575fb9713ad28ce5b6889c373d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Feb 2019 14:53:39 +0100 Subject: [PATCH 0503/5331] adding easyconfigs: CheckM-1.0.13-foss-2018b-Python-2.7.15.eb, prodigal-2.6.3-GCCcore-7.3.0.eb, pplacer-1.1.alpha19.eb --- .../CheckM-1.0.13-foss-2018b-Python-2.7.15.eb | 39 +++++++++++++++++ .../p/pplacer/pplacer-1.1.alpha19.eb | 33 +++++++++++++++ .../prodigal/prodigal-2.6.3-GCCcore-7.3.0.eb | 42 +++++++++++++++++++ 3 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb create mode 100644 easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..d9a79187f12 --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'CheckM' +version = '1.0.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Ecogenomics/CheckM' +description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, + single cells, or metagenomes.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), + ('pplacer', '1.1.alpha19', '', True), + ('prodigal', '2.6.3'), + ('HMMER', '3.2.1'), +] + +use_pip = True + +exts_list = [ + ('DendroPy', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/D/DendroPy'], + 'checksums': ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'], + }), + ('checkm-genome', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/checkm-genome'], + 'checksums': ['ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e'], + 'modulename': 'checkm', + }), +] + +sanity_check_paths = { + 'files': ['bin/checkm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb new file mode 100644 index 00000000000..28d3bf694be --- /dev/null +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'pplacer' +version = '1.1.alpha19' + +homepage = 'http://matsen.fhcrc.org/pplacer/' +description = """Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic + likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give + useful information about uncertainty, and to offer advanced visualization and downstream analysis.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# compiler pplacer from source requires an ancient OCaml version, +# which is a huge PITA with recent compilers +# cfr. http://matsen.github.io/pplacer/compiling.html +# so we use the recommended pre-built binaries instead... +source_urls = ['https://github.com/matsen/pplacer/releases/download/v%(version)s/'] +sources = ['pplacer-linux-v%(version)s.zip'] +checksums = ['9131b45c35ddb927f866385f149cf64af5dffe724234cd4548c22303a992347d'] + +sanity_check_paths = { + 'files': ['guppy', 'pplacer', 'rppr'], + 'dirs': ['scripts'], +} + +sanity_check_commands = [ + "pplacer --version | grep %(version)s", + "pplacer --help", +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..7f0a13751e2 --- /dev/null +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-7.3.0.eb @@ -0,0 +1,42 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'prodigal' +version = '2.6.3' + +homepage = 'http://prodigal.ornl.gov/' + +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f'] + +builddependencies = [('binutils', '2.30')] + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +moduleclass = 'bio' From da8556988ab91e356a1485b431a03b953a6a67c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Feb 2019 15:04:24 +0100 Subject: [PATCH 0504/5331] adding easyconfigs: QUAST-5.0.2-foss-2018b-Python-2.7.15.eb --- .../QUAST-5.0.2-foss-2018b-Python-2.7.15.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..c37e4091704 --- /dev/null +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'QUAST' +version = '5.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ablab/%(namelower)s' +description = """QUAST evaluates genome assemblies by computing various metrics. + It works both with and without reference genomes. The tool accepts multiple + assemblies, thus is suitable for comparison.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '2.7.15'), + ('Perl', '5.28.0'), + ('matplotlib', '2.2.3', versionsuffix), + ('Java', '1.8', '', True), + ('Boost', '1.67.0'), +] + +exts_list = [ + ('simplejson', '3.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson'], + 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], + }), + (name, version, { + 'source_tmpl': 'quast_%(version)s.tar.gz', + 'source_urls': ['https://github.com/ablab/quast/archive/'], + 'checksums': ['9f30c03e0bfd261492fe6b72fb07645bdee5b29d741f75fc75857b6fa095d91d'], + 'install_target': 'install_full', + 'modulename': 'quast_libs', + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "wget quast.sf.net/test_data.tar.gz && " + "tar xzf test_data.tar.gz && " + "%(namelower)s.py --test && " + "rm ./test_data.tar.gz ./test_data -rf" +] + +moduleclass = 'bio' From c6c5d593a3348728304fa04b679ada7f53b5b179 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Feb 2019 15:25:19 +0100 Subject: [PATCH 0505/5331] adding easyconfigs: Seaborn-0.9.0-foss-2018b-Python-2.7.15.eb --- .../Seaborn-0.9.0-foss-2018b-Python-2.7.15.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..f7dbb662709 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] + +dependencies = [ + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From f1d61572e156572b83bb07f788d1c40458772185 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 22 Feb 2019 17:12:07 +0100 Subject: [PATCH 0506/5331] added Canvas and .Net-core dependency --- .../c/Canvas/Canvas-1.39.0.1598.eb | 33 +++++++++++++++++++ .../easyconfigs/n/Net-core/Net-core-2.1.8.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/c/Canvas/Canvas-1.39.0.1598.eb create mode 100644 easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb diff --git a/easybuild/easyconfigs/c/Canvas/Canvas-1.39.0.1598.eb b/easybuild/easyconfigs/c/Canvas/Canvas-1.39.0.1598.eb new file mode 100644 index 00000000000..d5ba0a34d90 --- /dev/null +++ b/easybuild/easyconfigs/c/Canvas/Canvas-1.39.0.1598.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'Canvas' +version = '1.39.0.1598' + +homepage = 'https://github.com/Illumina/canvas' +description = "Copy number variant (CNV) calling from DNA sequencing data" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/Illumina/canvas/releases/download/%(version)s%2Bmaster/'] +sources = ['Canvas-%(version)s.master_x64.tar.gz'] +checksums = ['fc326cc7476cd1a6d0379745b7bde68a5938a21a94e882e51b81b35b20a6b952'] + +unpack_options = '--strip-components=1' + +dependencies = [ + ('Net-core', '2.1.8') +] + +sanity_check_paths = { + 'files': ['Canvas.dll', 'Canvas'], + 'dirs': [], +} + +modloadmsg = """To execute run: dotnet $EBROOTCANVAS/Canvas.dll""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb b/easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb new file mode 100644 index 00000000000..8253f2426fc --- /dev/null +++ b/easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'Net-core' +version = '2.1.8' + +homepage = 'https://dotnet.microsoft.com/' +description = """.NET Core is a free and open-source managed computer software framework for the Windows, + Linux, and macOS operating systems .NET Core fully supports C# and F# and partially supports Visual Basic""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'https://download.visualstudio.microsoft.com/download/pr/927cbf41-157f-488b-ac7d-32034defebc3/41b011418f795d5a76bf930ad57a055b/' +] +sources = ['aspnetcore-runtime-%(version)s-linux-x64.tar.gz'] +checksums = ['88831762a54fec8f8d1408a31a1a6dd226ffaf72eac6373ac93ccac21ec4fa56'] + +sanity_check_paths = { + 'files': ['dotnet'], + 'dirs': [], +} + +# add install dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'lang' From b0431bd93e70c3ecdeb4cbcde5ee9a68f95c262e Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 22 Feb 2019 15:17:45 -0600 Subject: [PATCH 0507/5331] adding easyconfigs: PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb, PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb --- ...orch-0.3.1-fosscuda-2017b-Python-2.7.14.eb | 98 +++++++++++++++++++ ...Torch-0.3.1-fosscuda-2017b-Python-3.6.3.eb | 98 +++++++++++++++++++ 2 files changed, 196 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..785063baaba --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,98 @@ +easyblock = 'PythonPackage' + +name = 'PyTorch' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +pytorchdir = 'pytorch-%(version)s' +extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' + +source_urls = [ + 'https://github.com/pytorch/pytorch/archive', + "https://github.com/facebookincubator/gloo/archive", + "https://github.com/google/googletest/archive", + "https://github.com/nanopb/nanopb/archive", + "https://github.com/pybind/pybind11/archive", + "https://github.com/wjakob/clang-cindex-python3/archive", +] +# PyTorch pulls in a bunch of submodules which don't have releases. +# We download the submodule revisions from their repos. +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'download_filename': 'cb002e4eb8d167c2c60fc3bdaae4e1844e0f9353.tar.gz', + 'filename': 'gloo-20180105.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo'), + }, + { + 'download_filename': 'ec44c6c1675c25b9827aacd08c02433cccde7780.tar.gz', + 'filename': 'googletest-20160714.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo/third-party/googletest'), + }, + { + 'download_filename': '14efb1a47a496652ab08b1ebcefb0ea24ae4a5e4.tar.gz', + 'filename': 'nanopb-20170723.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/nanopb'), + }, + { + 'download_filename': '9f6a636e547fc70a02fa48436449aad67080698f.tar.gz', + 'filename': 'pybind11-20170821.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11'), + }, + { + 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', + 'filename': 'clang-cindex-python3-20170330.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11/tools/clang'), + }, +] +patches = [ + '%(name)s-%(version)s-cmake.patch', + '%(name)s-%(version)s_skip_MPI_tests.patch', +] +checksums = [ + 'ee7e5633382bcf9866852e6eaa7bae9000ffb92d6f35605b0031b8d836c4cd94', # v0.3.1.tar.gz + 'c470bccdef90b300e8b50d27e7850cc5789ecd1045a85bd8625088c7c7e47a36', # gloo-20180105.tar.gz + '175a22300b3450e27e5f2e6f95cc9abca74617cbc21a1e0ed19bdfbd22ea0305', # googletest-20160714.tar.gz + '7d18b9bdc10de382da1643c2b1b0227131db47eef89998050b5e0a829d3bd0af', # nanopb-20170723.tar.gz + '3a53dac15e87056a9724b9b6403343b47bb71fec26c090979562f71d7ec9ee98', # pybind11-20170821.tar.gz + '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz + '710bbd38973a94c5c20695d25b819c4b41565bd4723ee4e07542d9537fa2bf18', # PyTorch-0.3.1-cmake.patch + '72c8d6804bff568c2a49b1b7019171c93309a1853a90d5e3abe778f8aa80ca4f', # PyTorch-0.3.1_skip_MPI_tests.patch +] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('Python', '2.7.14'), + ('PyYAML', '3.12', versionsuffix), + ('magma', '2.3.0'), + ('cuDNN', '7.0.5.15'), +] + +use_pip = True +download_dep_fail = True + +# This environment is needed to prevent setup.py from invoking git to determine version. +prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1' + +# you can choice here: either give a list of CUDA cc version or tell it All +# by default it does autodetect of the GPU on the local machine +prebuildopts += ' TORCH_CUDA_ARCH_LIST="3.0 3.2 3.5 3.7 5.0 5.2 5.3 6.0 6.1 7.0"' + +runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' +runtest += '&& cd test && bash run_test.sh' + +options = {'modulename': 'torch'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..38a3799bd06 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,98 @@ +easyblock = 'PythonPackage' + +name = 'PyTorch' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +pytorchdir = 'pytorch-%(version)s' +extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' + +source_urls = [ + 'https://github.com/pytorch/pytorch/archive', + "https://github.com/facebookincubator/gloo/archive", + "https://github.com/google/googletest/archive", + "https://github.com/nanopb/nanopb/archive", + "https://github.com/pybind/pybind11/archive", + "https://github.com/wjakob/clang-cindex-python3/archive", +] +# PyTorch pulls in a bunch of submodules which don't have releases. +# We download the submodule revisions from their repos. +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'download_filename': 'cb002e4eb8d167c2c60fc3bdaae4e1844e0f9353.tar.gz', + 'filename': 'gloo-20180105.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo'), + }, + { + 'download_filename': 'ec44c6c1675c25b9827aacd08c02433cccde7780.tar.gz', + 'filename': 'googletest-20160714.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo/third-party/googletest'), + }, + { + 'download_filename': '14efb1a47a496652ab08b1ebcefb0ea24ae4a5e4.tar.gz', + 'filename': 'nanopb-20170723.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/nanopb'), + }, + { + 'download_filename': '9f6a636e547fc70a02fa48436449aad67080698f.tar.gz', + 'filename': 'pybind11-20170821.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11'), + }, + { + 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', + 'filename': 'clang-cindex-python3-20170330.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11/tools/clang'), + }, +] +patches = [ + '%(name)s-%(version)s-cmake.patch', + '%(name)s-%(version)s_skip_MPI_tests.patch', +] +checksums = [ + 'ee7e5633382bcf9866852e6eaa7bae9000ffb92d6f35605b0031b8d836c4cd94', # v0.3.1.tar.gz + 'c470bccdef90b300e8b50d27e7850cc5789ecd1045a85bd8625088c7c7e47a36', # gloo-20180105.tar.gz + '175a22300b3450e27e5f2e6f95cc9abca74617cbc21a1e0ed19bdfbd22ea0305', # googletest-20160714.tar.gz + '7d18b9bdc10de382da1643c2b1b0227131db47eef89998050b5e0a829d3bd0af', # nanopb-20170723.tar.gz + '3a53dac15e87056a9724b9b6403343b47bb71fec26c090979562f71d7ec9ee98', # pybind11-20170821.tar.gz + '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz + '710bbd38973a94c5c20695d25b819c4b41565bd4723ee4e07542d9537fa2bf18', # PyTorch-0.3.1-cmake.patch + '72c8d6804bff568c2a49b1b7019171c93309a1853a90d5e3abe778f8aa80ca4f', # PyTorch-0.3.1_skip_MPI_tests.patch +] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('Python', '3.6.3'), + ('PyYAML', '3.12', versionsuffix), + ('magma', '2.3.0'), + ('cuDNN', '7.0.5.15'), +] + +use_pip = True +download_dep_fail = True + +# This environment is needed to prevent setup.py from invoking git to determine version. +prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1' + +# you can choice here: either give a list of CUDA cc version or tell it All +# by default it does autodetect of the GPU on the local machine +prebuildopts += ' TORCH_CUDA_ARCH_LIST="3.0 3.2 3.5 3.7 5.0 5.2 5.3 6.0 6.1 7.0"' + +runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' +runtest += '&& cd test && bash run_test.sh' + +options = {'modulename': 'torch'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' From 935d3cc2cd81c5b577d005e97faed53589cfb68b Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 22 Feb 2019 15:18:57 -0600 Subject: [PATCH 0508/5331] Add dependencies --- ...yYAML-3.12-fosscuda-2017b-Python-2.7.14.eb | 31 +++++++++++++++++++ ...PyYAML-3.12-fosscuda-2017b-Python-3.6.3.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..0413cca4381 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] + +dependencies = [ + ('Python', '2.7.14'), + ('libyaml', '0.1.7'), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..0aaa6640869 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['592766c6303207a20efc445587778322d7f73b161bd994f227adaa341ba212ab'] + +dependencies = [ + ('Python', '3.6.3'), + ('libyaml', '0.1.7'), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 23c2d88d498d4a0d3874b1b71f4043b2915845d6 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 22 Feb 2019 15:46:50 -0600 Subject: [PATCH 0509/5331] adding easyconfigs: Theano-1.0.2-fosscuda-2017b-Python-2.7.14.eb, Theano-1.0.2-fosscuda-2017b-Python-3.6.3.eb --- ...eano-1.0.2-fosscuda-2017b-Python-2.7.14.eb | 31 +++++++++++++++++++ ...heano-1.0.2-fosscuda-2017b-Python-3.6.3.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..f1bd26f1a67 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde'] + +dependencies = [ + ('Python', '2.7.14'), + ('libgpuarray', '0.7.5', '-Python-%(pyver)s'), + ('cuDNN', '7.0.5.15'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..f424f5723ad --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde'] + +dependencies = [ + ('Python', '3.6.3'), + ('libgpuarray', '0.7.5', '-Python-%(pyver)s'), + ('cuDNN', '7.0.5.15'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From b1e1144f4fd904560f6893db88e0b003b260aa2c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 22 Feb 2019 15:47:46 -0600 Subject: [PATCH 0510/5331] Add dependencies --- ...rray-0.7.5-fosscuda-2017b-Python-2.7.14.eb | 38 +++++++++++++++++++ ...array-0.7.5-fosscuda-2017b-Python-3.6.3.eb | 38 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..284524975d2 --- /dev/null +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'libgpuarray' +version = '0.7.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/libgpuarray/' +description = "Library to manipulate tensors on the GPU." + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [('Python', '2.7.14')] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + (name, version, { + 'buildcmd': 'build_ext', + 'modulename': 'pygpu', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], + 'checksums': ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgpuarray.%s' % SHLIB_EXT, 'lib/libgpuarray-static.a'], + 'dirs': ['include/gpuarray', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..276518b694c --- /dev/null +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'libgpuarray' +version = '0.7.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/libgpuarray/' +description = "Library to manipulate tensors on the GPU." + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [('Python', '3.6.3')] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + (name, version, { + 'buildcmd': 'build_ext', + 'modulename': 'pygpu', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], + 'checksums': ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgpuarray.%s' % SHLIB_EXT, 'lib/libgpuarray-static.a'], + 'dirs': ['include/gpuarray', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From d407255186d3588049a861490c9dccb5a789db5d Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 22 Feb 2019 16:26:26 -0600 Subject: [PATCH 0511/5331] adding easyconfigs: Theano-1.0.2-intelcuda-2017b-Python-2.7.14.eb, Theano-1.0.2-intelcuda-2017b-Python-3.6.3.eb --- ...ano-1.0.2-intelcuda-2017b-Python-2.7.14.eb | 31 +++++++++++++++++++ ...eano-1.0.2-intelcuda-2017b-Python-3.6.3.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..2188089c17a --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-2.7.14.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde'] + +dependencies = [ + ('Python', '2.7.14'), + ('libgpuarray', '0.7.5', '-Python-%(pyver)s'), + ('cuDNN', '7.0.5.15'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..71d31c573e7 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.2-intelcuda-2017b-Python-3.6.3.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6768e003d328a17011e6fca9126fbb8a6ffd3bb13cb21c450f3e724cca29abde'] + +dependencies = [ + ('Python', '3.6.3'), + ('libgpuarray', '0.7.5', '-Python-%(pyver)s'), + ('cuDNN', '7.0.5.15'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From 26d528346efe755376f637df4e00c3fef1340faf Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 22 Feb 2019 16:27:48 -0600 Subject: [PATCH 0512/5331] Add dependencies --- ...ray-0.7.5-intelcuda-2017b-Python-2.7.14.eb | 38 +++++++++++++++++++ ...rray-0.7.5-intelcuda-2017b-Python-3.6.3.eb | 38 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..6d45e16e3b4 --- /dev/null +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-2.7.14.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'libgpuarray' +version = '0.7.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/libgpuarray/' +description = "Library to manipulate tensors on the GPU." + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +source_urls = ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [('Python', '2.7.14')] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + (name, version, { + 'buildcmd': 'build_ext', + 'modulename': 'pygpu', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], + 'checksums': ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgpuarray.%s' % SHLIB_EXT, 'lib/libgpuarray-static.a'], + 'dirs': ['include/gpuarray', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..6be15556e91 --- /dev/null +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.5-intelcuda-2017b-Python-3.6.3.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'libgpuarray' +version = '0.7.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/libgpuarray/' +description = "Library to manipulate tensors on the GPU." + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +source_urls = ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [('Python', '3.6.3')] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + (name, version, { + 'buildcmd': 'build_ext', + 'modulename': 'pygpu', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], + 'checksums': ['d802299cd97bc1831416e64e23a7711cff4895348f45acba345840c4de461bb8'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgpuarray.%s' % SHLIB_EXT, 'lib/libgpuarray-static.a'], + 'dirs': ['include/gpuarray', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 720a862cde5669576978cbbb2071fc95f7345769 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 22 Feb 2019 17:47:10 -0600 Subject: [PATCH 0513/5331] adding easyconfigs: Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb, Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb --- ...eras-2.2.0-fosscuda-2017b-Python-2.7.14.eb | 46 +++++++++++++++++++ ...Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb | 46 +++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..b0df131178e --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'Keras' +version = '2.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://keras.io/' +description = """Keras is a minimalist, highly modular neural networks library, written in Python and +capable of running on top of either TensorFlow or Theano.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +dependencies = [ + ('Python', '2.7.14'), + ('TensorFlow', '1.8.0', versionsuffix), + ('Theano', '1.0.2', versionsuffix), + ('h5py', '2.7.1', versionsuffix), + ('PyYAML', '3.12', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +exts_list = [ + ('Keras-Applications', '1.0.4', { + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], + 'checksums': ['8c95300328630ae74fb0828b6fa38269a25c0228a02f1e5181753bfd48961f49'], + }), + ('Keras-Preprocessing', '1.0.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], + 'checksums': ['f5306554d2b454d825b36f35e327744f5477bd2ae21017f1a93b2097bed6757e'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras'], + 'checksums': ['5b8499d157af217f1a5ee33589e774127ebc3e266c833c22cb5afbb0ed1734bf'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..598e8518591 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'Keras' +version = '2.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://keras.io/' +description = """Keras is a minimalist, highly modular neural networks library, written in Python and +capable of running on top of either TensorFlow or Theano.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +dependencies = [ + ('Python', '3.6.3'), + ('TensorFlow', '1.8.0', versionsuffix), + ('Theano', '1.0.2', versionsuffix), + ('h5py', '2.7.1', versionsuffix), + ('PyYAML', '3.12', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +exts_list = [ + ('Keras-Applications', '1.0.4', { + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], + 'checksums': ['8c95300328630ae74fb0828b6fa38269a25c0228a02f1e5181753bfd48961f49'], + }), + ('Keras-Preprocessing', '1.0.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], + 'checksums': ['f5306554d2b454d825b36f35e327744f5477bd2ae21017f1a93b2097bed6757e'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras'], + 'checksums': ['5b8499d157af217f1a5ee33589e774127ebc3e266c833c22cb5afbb0ed1734bf'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From 87143b851d5835ab01c6e210f7c6bf5b1ad3f111 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 22 Feb 2019 17:48:13 -0600 Subject: [PATCH 0514/5331] Add dependencies --- .../h/HDF5/HDF5-1.10.1-fosscuda-2017b.eb | 21 +++++++++++ ...h5py-2.7.1-fosscuda-2017b-Python-2.7.14.eb | 36 +++++++++++++++++++ .../h5py-2.7.1-fosscuda-2017b-Python-3.6.3.eb | 36 +++++++++++++++++++ ...nfig-1.2.2-fosscuda-2017b-Python-2.7.14.eb | 30 ++++++++++++++++ ...onfig-1.2.2-fosscuda-2017b-Python-3.6.3.eb | 30 ++++++++++++++++ 5 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-fosscuda-2017b.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-fosscuda-2017b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-fosscuda-2017b.eb new file mode 100644 index 00000000000..4681e2d24fb --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-fosscuda-2017b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.1' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..c254f513aec --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.14'), + ('HDF5', '1.10.1'), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..99997f9907c --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.6.3'), + ('HDF5', '1.10.1'), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..6e9c3b9162f --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] + +dependencies = [ + ('Python', '2.7.14'), + ('pkg-config', '0.29.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..8190e84270a --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] + +dependencies = [ + ('Python', '3.6.3'), + ('pkg-config', '0.29.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'devel' From 842373418c2c80249a881ebcb07f483b6dae8026 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Sat, 23 Feb 2019 09:37:52 +0100 Subject: [PATCH 0515/5331] update dependencies to use the java/1.8 wrapper --- easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb index f0ac6a6085f..23597dae65c 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb @@ -22,7 +22,7 @@ source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(versi sources = ['%(namelower)s-%(version)s.zip'] checksums = ['d667c08ec44f4dc2029d00ca16cfcfe7850ae9bfdcdd6e35f3048b8e7e83647b'] -dependencies = [('Java', '1.8.0_92')] +dependencies = [('Java', '1.8')] # add install dir to PATH modextrapaths = {'PATH': ''} From 092000a07a5dbbc62f862b6629481aeef3f80878 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Sat, 23 Feb 2019 09:39:19 +0100 Subject: [PATCH 0516/5331] rename file to Java-1.8.eb (no hardcoded java version) --- .../{GATK-4.0.1.2-Java-1.8.0_92.eb => GATK-4.0.1.2-Java-1.8.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/GATK/{GATK-4.0.1.2-Java-1.8.0_92.eb => GATK-4.0.1.2-Java-1.8.eb} (100%) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb similarity index 100% rename from easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.0_92.eb rename to easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb From ce99303c3a05c745e31461b60297f5bb4c224acf Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Sat, 23 Feb 2019 09:43:22 +0100 Subject: [PATCH 0517/5331] update modloadmsg --- easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb index 23597dae65c..dcefba10398 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb @@ -27,8 +27,10 @@ dependencies = [('Java', '1.8')] # add install dir to PATH modextrapaths = {'PATH': ''} -modloadmsg = "To execute GATK run 'gatk'\n" -modloadmsg += "\rTo enable bash completion run 'source $EBROOTGATK/gatk-completion.sh'\n\r" +modloadmsg = """ +To execute GATK run 'gatk' +To enable bash completion run 'source $EBROOTGATK/gatk-completion.sh' +""" sanity_check_paths = { 'files': ["gatk", "gatk-package-%(version)s-spark.jar", "gatk-package-%(version)s-local.jar"], From aebd9cb0d37ff3728b6b417de240245de416fe68 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Sat, 23 Feb 2019 09:45:58 +0100 Subject: [PATCH 0518/5331] fixed modloadmsg format --- easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb index 7d4dfca9f06..230106f2e30 100644 --- a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb @@ -27,7 +27,9 @@ sanity_check_paths = { postinstallcmds = ['cd %(installdir)s && ln -s %(namelower)s-%(version)s.jar pilon.jar'] -modloadmsg = "To execute Pilon run: java -Xmx8G -jar $EBROOTPILON/pilon.jar\n" -modloadmsg += "\rAdjust the memory value according to the size of your input files\n\r" +modloadmsg = """ +To execute Pilon run: java -Xmx8G -jar $EBROOTPILON/pilon.jar +Adjust the memory value according to the size of your input files +""" moduleclass = 'bio' From 572c6716a76c70ed7d02daf316b8437805f0b3cb Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Sat, 23 Feb 2019 09:46:35 +0100 Subject: [PATCH 0519/5331] fixed deps to use generic java/1.8 module --- .../{Pilon-1.22-Java-1.8.0_92.eb => Pilon-1.22-Java-1.8.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/Pilon/{Pilon-1.22-Java-1.8.0_92.eb => Pilon-1.22-Java-1.8.eb} (96%) diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.eb similarity index 96% rename from easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb rename to easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.eb index 230106f2e30..5469cd44e5b 100644 --- a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.eb @@ -18,7 +18,7 @@ source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(ver sources = ['%(namelower)s-%(version)s.jar'] checksums = ['ff738f3bbb964237f6b2cf69243ebf9a21cb7f4edf10bbdcc66fa4ebaad5d13d'] -dependencies = [('Java', '1.8.0_92')] +dependencies = [('Java', '1.8')] sanity_check_paths = { 'files': ["%(namelower)s-%(version)s.jar"], From 271ac25abc26b0e78847e4951d135fe970330605 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 23 Feb 2019 11:40:13 +0100 Subject: [PATCH 0520/5331] Clean up Libint-2.0.3 config and patch --- easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb | 7 ++----- .../easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch | 3 +++ 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb index 769fd172792..249cb59796f 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -10,13 +10,10 @@ toolchainopts = {'pic': True} source_urls = ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'] sources = ['libint-%(version)s-stable.tgz'] -# Remove some problematic (and not very useful) FMA header code that does not compile with GCC. -# This is done with a patch, because it also affects anything that links against Libint. -# This way, FMA compilert optimization can remain enabled. -patches = ['Libint-2.0.3-stable-fma.patch'] +patches = ['Libint-%(version)s-stable-fma.patch'] checksums = [ '5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02', # libint-2.0.3-stable.tgz - '4db3795818bc37340a45453e8cc9d1d8ab7e08c0c2e9e5b64df2dfc7f0322390', # Libint-2.0.3-stable-fma.patch + '948388d66e898fb8fdb4964b7852fd7d13999bcfb97339bf8e69ef471ca982b1', # Libint-2.0.3-stable-fma.patch ] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch index bd670511e7c..7ec9c500202 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch @@ -1,3 +1,6 @@ +Remove some problematic (and not very useful) FMA header code that does not compile with GCC. +This is done with a patch, because this problem also affects anything that links against Libint. +This way, FMA compiler optimization can remain enabled. --- libint-2.0.3-stable.orig/include/vector_x86.h 2019-02-22 09:16:11.718287697 +0100 +++ libint-2.0.3-stable/include/vector_x86.h 2019-02-22 09:17:37.628678533 +0100 @@ -141,30 +141,6 @@ From 6bfbcc79e1154d125ed108408734c2a6470512c2 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Sat, 23 Feb 2019 12:01:05 +0100 Subject: [PATCH 0521/5331] added checksums --- easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb index 595317b6944..818052dcf9d 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/soedinglab/MMseqs2/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['e756a0e5cb3aa8e1e5a5b834a58ae955d9594be1806f0f32800427c55f3a45d5'] separate_build_dir = True From 7618d5bc617ffc2e2368bac141d845990ca714b1 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Sat, 23 Feb 2019 21:44:37 +0100 Subject: [PATCH 0522/5331] added sanity_check_commands --- easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb index dcefba10398..b9d6b8121d2 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb @@ -37,4 +37,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["gatk --help"] + moduleclass = 'bio' From 4695e51a8f6dbd3f1542e161f5b51a67990a3364 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Sat, 23 Feb 2019 21:48:46 +0100 Subject: [PATCH 0523/5331] updated pilon-1.23 with symlink and load message --- .../p/Pilon/Pilon-1.23-Java-1.8.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb new file mode 100644 index 00000000000..30ce452926f --- /dev/null +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb @@ -0,0 +1,30 @@ +easyblock = 'JAR' + +name = 'Pilon' +version = '1.23' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/broadinstitute/pilon' +description = " Pilon is an automated genome assembly improvement and variant detection tool" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.jar'] +checksums = ['bde1d3c8da5537abbc80627f0b2a4165c2b68551690e5733a6adf62413b87185'] + +dependencies = [('Java', '1.8')] + +sanity_check_paths = { + 'files': ['pilon-%(version)s.jar'], + 'dirs': [], +} + +postinstallcmds = ['cd %(installdir)s && ln -s %(namelower)s-%(version)s.jar pilon.jar'] + +modloadmsg = """ +To execute Pilon run: java -Xmx8G -jar $EBROOTPILON/pilon.jar +Adjust the memory value according to the size of your input files +""" + +moduleclass = 'bio' From 399e1ebbdb6475fde6ce19738ad38e220df6cf88 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 24 Feb 2019 10:06:59 +0100 Subject: [PATCH 0524/5331] adding easyconfigs: KronaTools-2.7-GCCcore-7.3.0.eb --- .../KronaTools-2.7-GCCcore-7.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/k/KronaTools/KronaTools-2.7-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.7-GCCcore-7.3.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.7-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..9be493e76f0 --- /dev/null +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.7-GCCcore-7.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'Binary' + +name = 'KronaTools' +version = '2.7' + +homepage = 'https://github.com/marbl/Krona/wiki/KronaTools' +description = """Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools + as well as from text and XML files.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] +sources = [SOURCE_TAR] +checksums = ['388270ac299da7e38b96bb144e72bd6844d42176c327c03a594e338d19a56f73'] + +builddependencies = [('binutils', '2.30')] + +dependencies = [('Perl', '5.28.0')] + +extract_sources = True + +install_cmd = "./install.pl --prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/ktClassifyBLAST', 'bin/ktImportBLAST', 'bin/ktImportTaxonomy'], + 'dirs': [], +} + +moduleclass = 'bio' From 8ed1a68c699d91a55b93d051ccc88b9abc645e74 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 24 Feb 2019 10:28:37 +0100 Subject: [PATCH 0525/5331] {compiler}[dummy] GCC(core) 8.3.0 + binutils 2.32 --- .../b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb | 28 +++++++++++ easybuild/easyconfigs/b/Bison/Bison-3.3.2.eb | 29 +++++++++++ .../b/binutils/binutils-2.32-GCCcore-8.3.0.eb | 22 +++++++++ .../easyconfigs/b/binutils/binutils-2.32.eb | 21 ++++++++ .../f/flex/flex-2.6.4-GCCcore-8.3.0.eb | 34 +++++++++++++ easybuild/easyconfigs/g/GCC/GCC-8.3.0-2.32.eb | 25 ++++++++++ .../easyconfigs/g/GCCcore/GCCcore-8.3.0.eb | 49 +++++++++++++++++++ .../help2man/help2man-1.47.8-GCCcore-8.3.0.eb | 25 ++++++++++ .../m/M4/M4-1.4.18-GCCcore-8.3.0.eb | 34 +++++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb | 26 ++++++++++ 10 files changed, 293 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.3.2.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.32.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-8.3.0-2.32.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..d6c005dfb35 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.3.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.32', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2.eb new file mode 100644 index 00000000000..5f3d4865db8 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.3.2' + +homepage = 'http://www.gnu.org/software/bison' + +description = """ + Bison is a general-purpose parser generator that converts an annotated + context-free grammar into a deterministic LR or generalized LR (GLR) parser + employing LALR(1) parser tables. +""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] + +builddependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..282f81deb1e --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb @@ -0,0 +1,22 @@ +name = 'binutils' +version = '2.32' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.3.2'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb new file mode 100644 index 00000000000..aeeea2b58ea --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.32' + +homepage = 'http://directory.fsf.org/project/binutils/' + +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.3.2'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..f5fc0ba9248 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.3.2'), + ('help2man', '1.47.8'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.32', '', True), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/g/GCC/GCC-8.3.0-2.32.eb new file mode 100644 index 00000000000..5111e6b2eb5 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-8.3.0-2.32.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '8.3.0' + +binutilsver = '2.32' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb new file mode 100644 index 00000000000..23e2b9335ac --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '8.3.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '4.0.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.1.2.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.1.0.tar.gz', + 'isl-0.20.tar.bz2', +] +patches = ['GCCcore-6.2.0-fix-find-isl.patch'] +checksums = [ + 'ea71adc1c3d86330874b8df19611424b143308f0d6612d542472600532c96d2d', # gcc-8.3.0.tar.gz + '5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2', # gmp-6.1.2.tar.bz2 + 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc', # mpfr-4.0.2.tar.bz2 + '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz + 'b587e083eb65a8b394e833dea1744f21af3f0e413a448c17536b5549ae42a4c2', # isl-0.20.tar.bz2 + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.32'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..21de8022b13 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.8' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['528f6a81ad34cbc76aa7dce5a82f8b3d2078ef065271ab81fda033842018a8dc'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.32', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..0d5a496fbf0 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['M4-1.4.18_glibc_2.28.patch'] +checksums = [ + 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz + 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.32', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..b1c7a447036 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.32', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From f0dbbe23b3971c3addad87699faade0528888317 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sun, 24 Feb 2019 13:03:09 +0100 Subject: [PATCH 0526/5331] Add author to patch for Libint --- easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch index 7ec9c500202..9c0ef2eba11 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-stable-fma.patch @@ -1,6 +1,7 @@ Remove some problematic (and not very useful) FMA header code that does not compile with GCC. This is done with a patch, because this problem also affects anything that links against Libint. This way, FMA compiler optimization can remain enabled. +Author: Toon Verstraelen (UGent, toon.verstraelen@ugent.be) --- libint-2.0.3-stable.orig/include/vector_x86.h 2019-02-22 09:16:11.718287697 +0100 +++ libint-2.0.3-stable/include/vector_x86.h 2019-02-22 09:17:37.628678533 +0100 @@ -141,30 +141,6 @@ From c6dc946d8ba5d40c138c73d83aad9af5202be0f3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 25 Feb 2019 08:51:01 +0100 Subject: [PATCH 0527/5331] use versionsuffix --- .../l/LocARNA/LocARNA-1.9.2.2-foss-2018b-Python-3.6.6.eb | 2 +- .../r/RNAclust/RNAclust-1.3-foss-2018b-Python-3.6.6.eb | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b-Python-3.6.6.eb index a38d94075af..9ab15b2891b 100644 --- a/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.2-foss-2018b-Python-3.6.6.eb @@ -19,7 +19,7 @@ source_urls = ['https://github.com/s-will/%(name)s/releases/download/v%(version) sources = [SOURCELOWER_TAR_GZ] checksums = ['76024e6d12a52e36a2d1aaffb09a7e7c1148ade05e7584530e21ce584c26e45b'] -dependencies = [('ViennaRNA', '2.4.11', '-Python-3.6.6')] +dependencies = [('ViennaRNA', '2.4.11', versionsuffix)] configopts = '--with-vrna=$EBROOTVIENNARNA' diff --git a/easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Python-3.6.6.eb index 4c66769f7df..427457d4714 100644 --- a/easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RNAclust/RNAclust-1.3-foss-2018b-Python-3.6.6.eb @@ -20,8 +20,8 @@ checksums = ['c86becf9aafd2d78350bc50ea597b5c6c6bf1b0e5fc74919d0a5d9ba91c22817'] dependencies = [ ('Perl', '5.28.0'), - ('LocARNA', '1.9.2.2', '-Python-3.6.6'), - ('ViennaRNA', '2.4.11', '-Python-3.6.6'), + ('LocARNA', '1.9.2.2', versionsuffix), + ('ViennaRNA', '2.4.11', versionsuffix), ] sanity_check_paths = { From 7b25a12dd9912a00bd111c8f68cdc366cffad8ad Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 25 Feb 2019 10:48:42 +0200 Subject: [PATCH 0528/5331] Change to use PythonBundle. Add missing dependency for backports.shutil_get_terminal_size. --- ...ython-5.8.0-fosscuda-2018b-Python-2.7.15.eb | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb index 70688c36bcc..f72df2c79b5 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'IPython' version = '5.8.0' @@ -20,11 +20,7 @@ dependencies = [ ('matplotlib', '2.2.3', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') - -# let sanity check fail when auto-downloaded dependencies are detected when installing extensions -exts_download_dep_fail = True +use_pip = True exts_list = [ ('Pygments', '2.2.0', { @@ -95,7 +91,6 @@ exts_list = [ }), ('configparser', '3.5.0', { 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], - 'use_pip': True, 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), ('defusedxml', '0.5.0', { @@ -104,12 +99,10 @@ exts_list = [ }), ('nbconvert', '5.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - 'use_pip': True, 'checksums': ['a8a2749f972592aa9250db975304af6b7337f32337e523a2c995cc9e12c07807'], }), ('nbformat', '4.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - 'use_pip': True, 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('MarkupSafe', '1.0', { @@ -163,12 +156,10 @@ exts_list = [ }), ('jupyter_core', '4.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], - 'use_pip': True, 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), ('jupyter_client', '5.2.3', { 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], - 'use_pip': True, 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], }), ('mistune', '0.8.4', { @@ -192,6 +183,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], + }), ('tornado', '5.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], @@ -210,7 +205,6 @@ exts_list = [ }), ('notebook', '5.7.0', { 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], - 'use_pip': True, 'checksums': ['b85e4de3d54cf4f14fe1d0515a980ccb49ddd4cdd21250cc0d4fb6374d50b1a7'], }), ] From 3115fc1f8892eaba76ec56e83ffc8cc3411ef557 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Mon, 25 Feb 2019 10:27:37 +0100 Subject: [PATCH 0529/5331] Fix checksum in Libint eb --- easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb index 249cb59796f..ff6129c1666 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.0.3-foss-2018b.eb @@ -13,7 +13,7 @@ sources = ['libint-%(version)s-stable.tgz'] patches = ['Libint-%(version)s-stable-fma.patch'] checksums = [ '5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02', # libint-2.0.3-stable.tgz - '948388d66e898fb8fdb4964b7852fd7d13999bcfb97339bf8e69ef471ca982b1', # Libint-2.0.3-stable-fma.patch + 'e8dad3b3da0df26dc64677f56af25923158a2414a4d85b72a8068470d28ced4c', # Libint-2.0.3-stable-fma.patch ] moduleclass = 'chem' From 6ba0397544e21fc73e4c826da6625b1ec80e650d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 25 Feb 2019 11:09:46 +0100 Subject: [PATCH 0530/5331] adding easyconfigs: pizzly-0.37.3-foss-2018b.eb and patches: pizzly-0.37.3_add-install-target.patch --- .../p/pizzly/pizzly-0.37.3-foss-2018b.eb | 37 +++++++++++++++++++ .../pizzly-0.37.3_add-install-target.patch | 10 +++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/pizzly/pizzly-0.37.3-foss-2018b.eb create mode 100644 easybuild/easyconfigs/p/pizzly/pizzly-0.37.3_add-install-target.patch diff --git a/easybuild/easyconfigs/p/pizzly/pizzly-0.37.3-foss-2018b.eb b/easybuild/easyconfigs/p/pizzly/pizzly-0.37.3-foss-2018b.eb new file mode 100644 index 00000000000..80427327483 --- /dev/null +++ b/easybuild/easyconfigs/p/pizzly/pizzly-0.37.3-foss-2018b.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'pizzly' +version = '0.37.3' + +github_account = 'pmelsted' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = "Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_add-install-target.patch'] +checksums = [ + 'adfb221ed079aa60760e44af6baa300ad0fbdc92b407f7576cc7eab72ec6b310', # v0.37.3.tar.gz + 'afd238b88005cb04afd34492812684ebc207fc96c31d58cfe14f2739fff539cc', # pizzly-0.37.3_add-install-target.patch +] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [('zlib', '1.2.11')] + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pizzly/pizzly-0.37.3_add-install-target.patch b/easybuild/easyconfigs/p/pizzly/pizzly-0.37.3_add-install-target.patch new file mode 100644 index 00000000000..cc03a614f8c --- /dev/null +++ b/easybuild/easyconfigs/p/pizzly/pizzly-0.37.3_add-install-target.patch @@ -0,0 +1,10 @@ +add install target +author: Paul Jähne +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -30,3 +30,5 @@ set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}" ) + # Add executable and link against SeqAn dependencies. + add_executable (pizzly main.cpp) + target_link_libraries (pizzly pthread ${ZLIB_LIBRARIES} ) ++ ++install(TARGETS pizzly DESTINATION bin) From f95d083be4ab36be4c662ce881db904254cc3f82 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 25 Feb 2019 11:21:55 +0100 Subject: [PATCH 0531/5331] use BLAST+ 2.7.1 --- .../k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb index 91f1f9ee61f..7b7a45eb639 100644 --- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb @@ -28,7 +28,7 @@ checksums = [ dependencies = [ ('Perl', '5.28.0'), - ('BLAST+', '2.8.1'), + ('BLAST+', '2.7.1'), ('wget', '1.20.1', '-GCCcore-7.3.0', True), ] From 3e7fff73b19f1219bb3646f2e1c0b7bb19dcbb17 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 25 Feb 2019 13:14:11 +0100 Subject: [PATCH 0532/5331] remove suffix --- .../easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb | 2 +- .../k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb index 39ecfad1069..681800b893d 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb @@ -29,7 +29,7 @@ checksums = [ dependencies = [ ('Perl', '5.28.0'), ('Jellyfish', '1.1.12'), - ('wget', '1.20.1', '-GCCcore-7.3.0', True), + ('wget', '1.20.1'), ] install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb index 7b7a45eb639..1221f886210 100644 --- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.7-beta-foss-2018b-Perl-5.28.0.eb @@ -29,7 +29,7 @@ checksums = [ dependencies = [ ('Perl', '5.28.0'), ('BLAST+', '2.7.1'), - ('wget', '1.20.1', '-GCCcore-7.3.0', True), + ('wget', '1.20.1'), ] install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' From 2f79d627aa14d4ee44c1b37862d825aeccbda4dd Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 25 Feb 2019 14:28:51 +0100 Subject: [PATCH 0533/5331] adding easyconfigs: numba-0.37.0-foss-2018a-Python-2.7.14.eb, numba-0.37.0-foss-2018a-Python-3.6.4.eb --- .../numba-0.37.0-foss-2018a-Python-2.7.14.eb | 52 +++++++++++++++++++ .../numba-0.37.0-foss-2018a-Python-3.6.4.eb | 52 +++++++++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb diff --git a/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..3aff3d0bfdc --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb @@ -0,0 +1,52 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.37.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'pic': True} + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +dependencies = [ + ('Python', '2.7.14'), + ('LLVM', '5.0.1'), +] + +exts_list = [ + ('llvmlite', '0.22.0', { + 'patches': ['llvmlite-0.22.0_fix-ffi-Makefile.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'checksums': [ + 'a0a875f3d502f41f4a24444aa98fbf076a6bf36e2a0b3b4481b22e1c4a3acdc2', # llvmlite-0.22.0.tar.gz + # llvmlite-0.22.0_fix-ffi-Makefile.patch + '72f3972d554a8b8f91b009fc7277db6cc47e468d73039ac2e7624845e876d154', + ], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + 'checksums': ['c62121b2d384d8b4d244ef26c1cf8bb5cb819278a80b893bf41918ad6d391258'], + }), +] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..db5ffad5fc6 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb @@ -0,0 +1,52 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.37.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'pic': True} + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +dependencies = [ + ('Python', '3.6.4'), + ('LLVM', '5.0.1'), +] + +exts_list = [ + ('llvmlite', '0.22.0', { + 'patches': ['llvmlite-0.22.0_fix-ffi-Makefile.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'checksums': [ + 'a0a875f3d502f41f4a24444aa98fbf076a6bf36e2a0b3b4481b22e1c4a3acdc2', # llvmlite-0.22.0.tar.gz + # llvmlite-0.22.0_fix-ffi-Makefile.patch + '72f3972d554a8b8f91b009fc7277db6cc47e468d73039ac2e7624845e876d154', + ], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + 'checksums': ['c62121b2d384d8b4d244ef26c1cf8bb5cb819278a80b893bf41918ad6d391258'], + }), +] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' From 9b30ea865dbaf83ce3e6206c8337be91c0bf6176 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 25 Feb 2019 14:34:24 +0100 Subject: [PATCH 0534/5331] adding easyconfigs: PCAngsd-0.97-foss-2018a-Python-2.7.14.eb and patches: PCAngsd-python-hashbang.patch --- .../PCAngsd-0.97-foss-2018a-Python-2.7.14.eb | 52 +++++++++++++++++++ .../p/PCAngsd/PCAngsd-python-hashbang.patch | 8 +++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/PCAngsd/PCAngsd-python-hashbang.patch diff --git a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..292db083a40 --- /dev/null +++ b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb @@ -0,0 +1,52 @@ +easyblock = 'Tarball' + +name = 'PCAngsd' +version = '0.97' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.popgen.dk/software/index.php/PCAngsd' +description = """PCAngsd, which estimates the covariance matrix for low depth +NGS data in an iterative procedure based on genotype likelihoods and is able +to perform multiple population genetic analyses in heterogeneous populations.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://github.com/Rosemeis/pcangsd/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'PCAngsd-python-hashbang.patch', +] +checksums = [ + '05507ccf70b6464656ad9a63bb4d43d771d72d633055a08e056b9feb91f5c60a', + '8729dbda52a94aa61cbd48bc73cd15155831ce22aebc30d9b4e96ff12c12a482', # PCAngsd-python-hashbang.patch +] + +dependencies = [ + ('Python', '2.7.14'), + ('numba', '0.37.0', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +#exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('pysnptools', '0.3.13', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pysnptools'], + 'checksums': ['158f05cb72687772c61bd306c166a7bfc40f158beb1d473e04711daa7bd1d152'], + 'use_pip': True, + }), +] + +postinstallcmds = ["chmod +x %(installdir)s/pcangsd.py"] + +sanity_check_paths = { + 'files': ['pcangsd.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = { + 'PATH': [''], + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-python-hashbang.patch b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-python-hashbang.patch new file mode 100644 index 00000000000..778ec3c5f5a --- /dev/null +++ b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-python-hashbang.patch @@ -0,0 +1,8 @@ +diff -ru pcangsd-0.97/pcangsd.py pcangsd-0.97.patched/pcangsd.py +--- pcangsd-0.97/pcangsd.py 2018-12-09 10:37:34.000000000 +0100 ++++ pcangsd-0.97.patched/pcangsd.py 2019-02-25 12:55:47.000000000 +0100 +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python + """ + PCAngsd Framework: Population genetic analyses for NGS data using PCA. Main caller. + """ From 05a6d0d904381512834334f35a9f1465cfa988d3 Mon Sep 17 00:00:00 2001 From: ebtest Date: Mon, 25 Feb 2019 13:46:14 +0000 Subject: [PATCH 0535/5331] add flag to build comex library for GA --- ...18b-ethernet.eb => GlobalArrays-5.7-intel-2018b.eb} | 9 +++------ ...18b-ethernet.eb => OpenMolcas-18.09-intel-2018b.eb} | 10 ++++------ 2 files changed, 7 insertions(+), 12 deletions(-) rename easybuild/easyconfigs/g/GlobalArrays/{GlobalArrays-5.7-intel-2018b-ethernet.eb => GlobalArrays-5.7-intel-2018b.eb} (85%) rename easybuild/easyconfigs/o/OpenMolcas/{OpenMolcas-18.09-intel-2018b-ethernet.eb => OpenMolcas-18.09-intel-2018b.eb} (86%) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b-ethernet.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb similarity index 85% rename from easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b-ethernet.eb rename to easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb index 5eeb4d3e9c8..8c2bc3aa316 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b-ethernet.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb @@ -3,7 +3,6 @@ easyblock = 'ConfigureMake' name = 'GlobalArrays' version = '5.7' -versionsuffix = '-ethernet' homepage = 'http://hpc.pnl.gov/globalarrays' description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" @@ -15,17 +14,15 @@ source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] sources = ['v%(version)s/ga-%(version)s.tar.gz'] checksums = ['3ed1ab47adfda7bceb7beca12fc05a2e1631732f0e55bbaf9036dad4e3da4774'] - configopts = ' --with-mpi --enable-i8' configopts += ' --with-blas8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' configopts += ' --with-scalapack8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_scalapack_ilp64"' -# select armci network as Ethernet TCP/IP -configopts += ' --with-sockets' - +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' sanity_check_paths = { - 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libga.a'], + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libcomex.a', 'lib/libga.a'], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b.eb similarity index 86% rename from easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb rename to easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b.eb index 3786a853feb..422c4da5c4f 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-ethernet.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b.eb @@ -2,7 +2,6 @@ easyblock = 'CMakeMake' name = 'OpenMolcas' version = '18.09' -versionsuffix = '-ethernet' homepage = "https://gitlab.com/Molcas/OpenMolcas" description = "OpenMolcas is a quantum chemistry software package" @@ -15,18 +14,17 @@ sources = ["OpenMolcas-v%(version)s.tar.gz"] checksums = ['b4f310fb65205c865ccc6373ce9c3833a586f8ff63a71a624cf793559c9b39cf'] dependencies = [ - ('GlobalArrays', '5.7', versionsuffix), + ('GlobalArrays', '5.7'), ('Python', '3.6.6'), ('HDF5', '1.10.2'), ] - builddependencies = [('CMake', '3.12.1')] separate_build_dir = True -preconfigopts = "GAROOT=$EBROOTGLOBALARRAYS" -configopts = '-DLINALG=MKL -DMKLROOT=$EBROOTIMKL/mkl -DMPI=ON -DGA=ON -DTOOLS=ON' +preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' +configopts = '-DLINALG=MKL -DMKLROOT=$EBROOTIMKL/mkl -DMPI=ON -DGA=ON -DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON' modextravars = { 'MOLCAS': '%(installdir)s', @@ -35,7 +33,7 @@ modextravars = { } sanity_check_paths = { - 'files': ['lib/libmolcas.a', 'bin/alaska.exe', 'bin/casvb.exe', 'bin/cht3.exe', 'bin/espf.exe', 'bin/gateway.exe', + 'files': ['lib/libmolcas.so', 'bin/alaska.exe', 'bin/casvb.exe', 'bin/cht3.exe', 'bin/espf.exe', 'bin/gateway.exe', 'bin/gugaci.exe', 'bin/last_energy.exe', 'bin/mbpt2.exe', 'bin/mcpdft.exe', 'bin/mrci.exe', 'bin/qmstat.exe', 'bin/rassi.exe', 'bin/seward.exe', 'bin/vibrot.exe', 'bin/averd.exe', 'bin/ccsdt.exe', 'bin/cpf.exe', 'bin/expbas.exe', 'bin/genano.exe', 'bin/gugadrt.exe', 'bin/localisation.exe', From b7b1c29713cea458e0c3442a1592c6187cf8b57c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 25 Feb 2019 15:43:57 +0100 Subject: [PATCH 0536/5331] adding easyconfigs: aiohttp-3.5.4-foss-2018b-Python-3.6.6.eb --- .../aiohttp-3.5.4-foss-2018b-Python-3.6.6.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/a/aiohttp/aiohttp-3.5.4-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.5.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.5.4-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..21287eb13dd --- /dev/null +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.5.4-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'aiohttp' +version = '3.5.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/aio-libs/aiohttp' +description = """" Async http client/server framework """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), +] + +use_pip = True + +exts_list = [ + ('attrs', '18.2.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], + }), + ('multidict', '4.5.2', { + 'source_urls': ['https://pypi.python.org/packages/source/m/multidict/'], + 'checksums': ['024b8129695a952ebd93373e45b5d341dbb87c17ce49637b34000093f243dd4f'], + }), + ('yarl', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/y/yarl/'], + 'checksums': ['024ecdc12bc02b321bc66b41327f930d1c2c543fa9a561b39861da9388ba7aa9'], + }), + ('async-timeout', '3.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/async-timeout/'], + 'checksums': ['0c3c816a028d47f659d6ff5c745cb2acf1f966da1fe5c19c77a70282b25f4c5f'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('idna-ssl', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/idna-ssl/'], + 'checksums': ['a933e3bb13da54383f9e8f35dc4f9cb9eb9b3b78c6b36f311254d6d0d92c6c7c'], + }), + ('typing_extensions', '3.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typing_extensions/'], + 'checksums': ['fb2cd053238d33a8ec939190f30cfd736c00653a85a2919415cecf7dc3d9da71'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/a/aiohttp/'], + 'checksums': ['9c4c83f4fa1938377da32bc2d59379025ceeee8e24b89f72fcbccd8ca22dc9bf'], + }), + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('aiohttp-jinja2', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/aiohttp-jinja2/'], + 'checksums': ['aef9b6595f962182ad00c990095fb51d731c280e1d183e2b28cf0bdb5a942d0c'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 12140e16ec56c2ee231af9f8286d46c07bf057ca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 25 Feb 2019 15:50:31 +0100 Subject: [PATCH 0537/5331] adding easyconfigs: BLAST+-2.7.1-foss-2018b.eb --- .../b/BLAST+/BLAST+-2.7.1-foss-2018b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1-foss-2018b.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1-foss-2018b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1-foss-2018b.eb new file mode 100644 index 00000000000..2471e2d8fda --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.7.1-foss-2018b.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.7.1' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = ['%(name)s-%(version)s_boost_backport.patch'] +checksums = [ + '10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca', # ncbi-blast-2.7.1+-src.tar.gz + 'e3f9c80ea242dd58759f18919467d9af0e1bec5c01142d130ee479c18cecc654', # BLAST+-2.7.1_boost_backport.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('PCRE', '8.41'), + ('Boost', '1.67.0'), + ('GMP', '6.1.2'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '2.0.0'), + ('LMDB', '0.9.22'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 --with-pcre=$EBROOTPCRE " +configopts += "--with-boost=$EBROOTBOOST --with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' From ae8b2a382afabf90c2056291f51f1c6ce4591a44 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 25 Feb 2019 12:17:33 -0600 Subject: [PATCH 0538/5331] adding easyconfigs: RSEM-1.3.1-foss-2017b.eb, RSEM-1.3.1-intel-2017b.eb --- .../r/RSEM/RSEM-1.3.1-foss-2017b.eb | 36 +++++++++++++++++++ .../r/RSEM/RSEM-1.3.1-intel-2017b.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.3.1-foss-2017b.eb create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.3.1-intel-2017b.eb diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.1-foss-2017b.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.1-foss-2017b.eb new file mode 100644 index 00000000000..f426171f532 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.1-foss-2017b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'RSEM' +version = '1.3.1' + +homepage = 'http://deweylab.github.io/RSEM/' +description = """RNA-Seq by Expectation-Maximization""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['RSEM-1.3.0_makefiles.patch'] +checksums = [ + '93c749a03ac16e94b1aab94d032d4fd5687d3261316ce943ecb89d3ae3ec2e11', # v1.3.1.tar.gz + '2d244659206c78655b92f1bd519ee65f28a6b5f9418dfad04e887b64eca6641b', # RSEM-1.3.0_makefiles.patch +] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), + ('Perl', '5.26.0'), + ('R', '3.4.3', '-X11-20171023'), +] + +sanity_check_paths = { + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'dirs': ['bin/samtools-1.3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.1-intel-2017b.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.1-intel-2017b.eb new file mode 100644 index 00000000000..6cc5620fb57 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.1-intel-2017b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'RSEM' +version = '1.3.1' + +homepage = 'http://deweylab.github.io/RSEM/' +description = """RNA-Seq by Expectation-Maximization""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['RSEM-1.3.0_makefiles.patch'] +checksums = [ + '93c749a03ac16e94b1aab94d032d4fd5687d3261316ce943ecb89d3ae3ec2e11', # v1.3.1.tar.gz + '2d244659206c78655b92f1bd519ee65f28a6b5f9418dfad04e887b64eca6641b', # RSEM-1.3.0_makefiles.patch +] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), + ('Perl', '5.26.0'), + ('R', '3.4.3', '-X11-20171023'), +] + +sanity_check_paths = { + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'dirs': ['bin/samtools-1.3'], +} + +moduleclass = 'bio' From d99c3fd5a3f6d20a9e370cab4694679a520f2d92 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 25 Feb 2019 22:36:20 +0100 Subject: [PATCH 0539/5331] adding easyconfigs: Flask-1.0.2-foss-2018b-Python-3.6.6.eb --- .../Flask-1.0.2-foss-2018b-Python-3.6.6.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flask/Flask-1.0.2-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/f/Flask/Flask-1.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/Flask/Flask-1.0.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..deed4c6a7db --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-1.0.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '1.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.palletsprojects.com/p/flask/' +description = """" Flask is a lightweight WSGI web application framework. + It is designed to make getting started quick and easy, with the ability to scale up to complex applications. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), +] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('Click', '7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('itsdangerous', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Werkzeug', '0.14.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/Werkzeug'], + 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/f/flask/'], + 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], + }), + ('Flask-Cors', '3.0.7', { + 'source_urls': ['https://pypi.python.org/packages/source/f/flask-cors/'], + 'checksums': ['7e90bf225fdf163d11b84b59fb17594d0580a16b97ab4e1146b1fb2737c1cfec'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 7361717dd2bedddc367ea5f753296ddfe9ca25f4 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 25 Feb 2019 16:08:59 -0600 Subject: [PATCH 0540/5331] Added fix find AVX patch --- .../p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb | 3 +++ .../p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb index 785063baaba..19509f99788 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb @@ -21,6 +21,7 @@ source_urls = [ "https://github.com/pybind/pybind11/archive", "https://github.com/wjakob/clang-cindex-python3/archive", ] + # PyTorch pulls in a bunch of submodules which don't have releases. # We download the submodule revisions from their repos. sources = [ @@ -54,6 +55,7 @@ sources = [ patches = [ '%(name)s-%(version)s-cmake.patch', '%(name)s-%(version)s_skip_MPI_tests.patch', + '%(name)s-%(version)s_fix_findAVX.patch', ] checksums = [ 'ee7e5633382bcf9866852e6eaa7bae9000ffb92d6f35605b0031b8d836c4cd94', # v0.3.1.tar.gz @@ -64,6 +66,7 @@ checksums = [ '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz '710bbd38973a94c5c20695d25b819c4b41565bd4723ee4e07542d9537fa2bf18', # PyTorch-0.3.1-cmake.patch '72c8d6804bff568c2a49b1b7019171c93309a1853a90d5e3abe778f8aa80ca4f', # PyTorch-0.3.1_skip_MPI_tests.patch + '951d5fde89df3be98c1bc6750546259c1b3d0c77574fa3f9e67d9e8fe5b08161', # PyTorch-0.3.1_fix_findAVX.patch ] builddependencies = [('CMake', '3.9.5')] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb index 38a3799bd06..b632224fc9a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb @@ -21,6 +21,7 @@ source_urls = [ "https://github.com/pybind/pybind11/archive", "https://github.com/wjakob/clang-cindex-python3/archive", ] + # PyTorch pulls in a bunch of submodules which don't have releases. # We download the submodule revisions from their repos. sources = [ @@ -54,6 +55,7 @@ sources = [ patches = [ '%(name)s-%(version)s-cmake.patch', '%(name)s-%(version)s_skip_MPI_tests.patch', + '%(name)s-%(version)s_fix_findAVX.patch', ] checksums = [ 'ee7e5633382bcf9866852e6eaa7bae9000ffb92d6f35605b0031b8d836c4cd94', # v0.3.1.tar.gz @@ -64,6 +66,7 @@ checksums = [ '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz '710bbd38973a94c5c20695d25b819c4b41565bd4723ee4e07542d9537fa2bf18', # PyTorch-0.3.1-cmake.patch '72c8d6804bff568c2a49b1b7019171c93309a1853a90d5e3abe778f8aa80ca4f', # PyTorch-0.3.1_skip_MPI_tests.patch + '951d5fde89df3be98c1bc6750546259c1b3d0c77574fa3f9e67d9e8fe5b08161', # PyTorch-0.3.1_fix_findAVX.patch ] builddependencies = [('CMake', '3.9.5')] From 86f0cac1fb569b3f30cb28b16a76b7b0929a73b6 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 25 Feb 2019 16:16:12 -0600 Subject: [PATCH 0541/5331] Removed use_pip --- .../p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb | 1 - .../p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb index 19509f99788..002c195faa7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb @@ -78,7 +78,6 @@ dependencies = [ ('cuDNN', '7.0.5.15'), ] -use_pip = True download_dep_fail = True # This environment is needed to prevent setup.py from invoking git to determine version. diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb index b632224fc9a..4bc5422fdcd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb @@ -78,7 +78,6 @@ dependencies = [ ('cuDNN', '7.0.5.15'), ] -use_pip = True download_dep_fail = True # This environment is needed to prevent setup.py from invoking git to determine version. From 64b32c04e2687ebcbfa377fb3155d75d9806a504 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 26 Feb 2019 09:15:39 +0000 Subject: [PATCH 0542/5331] Update hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb --- .../h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb index b601f23494d..0d98b76f18a 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb @@ -17,6 +17,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True exts_list = [ ('attrs', '18.2.0', { From b3de19ce8ba15d352fde8d7d573c8b41b974719e Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 26 Feb 2019 09:16:12 +0000 Subject: [PATCH 0543/5331] Update hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb --- .../h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb index 7bde035e223..aa39f3f7e5c 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb @@ -17,6 +17,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True exts_list = [ ('attrs', '18.2.0', { From 0bd796a6345632a20811fb9da68f678b80915484 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 26 Feb 2019 09:16:54 +0000 Subject: [PATCH 0544/5331] Update PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb --- .../p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb index ea1c91595c5..eef7b12c8e0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb @@ -206,7 +206,6 @@ dependencies = [ ('Ninja', '1.8.2'), ] -use_pip = True download_dep_fail = True # This environment is needed to prevent setup.py from invoking git to determine version. From 672c646596e9590a733112a6d83cb979f2809a9d Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 26 Feb 2019 09:17:20 +0000 Subject: [PATCH 0545/5331] Update PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb --- .../p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb index 670609ca9ca..b5ee18ef8cc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -206,7 +206,6 @@ dependencies = [ ('Ninja', '1.8.2'), ] -use_pip = True download_dep_fail = True # This environment is needed to prevent setup.py from invoking git to determine version. From 4d95e4403f5cb73a87d212b8ebc1e991f8301ae2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 10:19:18 +0100 Subject: [PATCH 0546/5331] adding easyconfigs: MitoZ-2.3-foss-2018b-Python-3.6.6.eb, ETE-3.1.1-foss-2018b-Python-3.6.6.eb, tbl2asn-20190117-linux64.eb --- .../ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb | 32 ++++++++++++++ .../MitoZ-2.3-foss-2018b-Python-3.6.6.eb | 43 +++++++++++++++++++ .../t/tbl2asn/tbl2asn-20190117-linux64.eb | 35 +++++++++++++++ 3 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..8d2e3a53a51 --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +checksums = ['870a3d4b496a36fbda4b13c7c6b9dfa7638384539ae93551ec7acb377fb9c385'] + +dependencies = [ + ('Python', '3.6.6'), + ('lxml', '4.2.5', versionsuffix), + ('PyQt5', '5.11.3', versionsuffix), +] + +download_dep_fail = True +#use_pip = True + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..1c4cf8f66a4 --- /dev/null +++ b/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,43 @@ +easyblock = 'Tarball' + +name = 'MitoZ' +version = '2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/linzhi2013/MitoZ' +description = """MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), + assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome + (genbank file as result), and mitogenome visualization.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/linzhi2013/MitoZ/raw/master/version_%(version)s/'] +sources = ['release_MitoZ_v%(version)s.tar.bz2'] +checksums = ['13fc5d3c6f41a6eb17498dfb1e69735a2b3f4e62ac7393d3ed71ea9502038841'] + +dependencies = [ + ('Python', '3.6.6'), + ('Perl', '5.28.0'), + ('Java', '1.8', '', True), + ('libgd', '2.2.5'), + ('Biopython', '1.72', versionsuffix), + ('BioPerl', '1.7.2', '-Perl-%(perlver)s'), + ('BLAST+', '2.7.1'), + ('HMMER', '3.2.1'), + ('BWA', '0.7.17'), + ('SAMtools', '1.9'), + ('Infernal', '1.1.2'), + ('ETE', '3.1.1', versionsuffix), + ('tbl2asn', '20190117', '-linux64', True), +] + +sanity_check_paths = { + 'files': ['MitoZ.py'], + 'dirs': [], +} + +sanity_check_commands = ["MitoZ.py --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb new file mode 100644 index 00000000000..461aa3042e9 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20190117-linux64.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CmdCp' + +name = 'tbl2asn' +version = '20190117' +versionsuffix = '-linux64' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/'] +sources = [{'download_filename': 'linux64.tbl2asn.gz', 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}] +checksums = ['1f41acb9eacd6e0fa78657b17727b8f94d97490617563686d28b3f6c24d39117'] + +cmds_map = [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")] + +files_to_copy = [ + (['tbl2asn'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn'], + 'dirs': [], +} + +postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] + +moduleclass = 'bio' From 3f32da575645f7b590035b130d95f50408c69aa7 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 26 Feb 2019 09:20:46 +0000 Subject: [PATCH 0547/5331] Delete PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb --- ...PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb deleted file mode 100644 index f134c1e17ad..00000000000 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-fosscuda-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyYAML' -version = '3.13' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://pypi.python.org/pypi/PyYAML/" -description = """PyYAML is a YAML parser and emitter for the Python programming language.""" - -toolchain = {'name': 'fosscuda', 'version': '2018b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'] - -dependencies = [ - ('Python', '3.6.6'), - ('libyaml', '0.2.1'), -] - -use_pip = True -download_dep_fail = True - -options = {'modulename': 'yaml'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'lib' From 45b5f0ed91a817771e3df13e41edf6da7996c09d Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 26 Feb 2019 09:21:42 +0000 Subject: [PATCH 0548/5331] Delete Python-3.6.6-fosscuda-2018b.eb --- .../p/Python/Python-3.6.6-fosscuda-2018b.eb | 238 ------------------ 1 file changed, 238 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb deleted file mode 100644 index 4163f294a45..00000000000 --- a/easybuild/easyconfigs/p/Python/Python-3.6.6-fosscuda-2018b.eb +++ /dev/null @@ -1,238 +0,0 @@ -name = 'Python' -version = '3.6.6' - -homepage = 'http://python.org/' -description = """Python is a programming language that lets you work more quickly and integrate your systems - more effectively.""" - -toolchain = {'name': 'fosscuda', 'version': '2018b'} -toolchainopts = {'pic': True} - -source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] -checksums = ['7d56dadf6c7d92a238702389e80cfe66fbfae73e584189ed6f89c75bbf3eda58'] - -# python needs bzip2 to build the bz2 package -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.11'), - ('libreadline', '7.0'), - ('ncurses', '6.1'), - ('SQLite', '3.24.0'), - ('XZ', '5.2.4'), - ('GMP', '6.1.2'), # required for pycrypto - ('libffi', '3.2.1'), # required for cryptography - # OS dependency should be preferred if the OS version is more recent then this version, - # it's nice to have an up to date OpenSSL for security reasons; - # ('OpenSSL', '1.1.0h'), -] - -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] - -# Try to make sure stack limit is set to unlimited, to avoid compilation errors for hashlib with Intel compilers -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/6484 -ulimit_unlimited = True -exts_download_dep_fail = True - -# workaround for "undefined symbol: __stack_chk_guard" -# see also https://software.intel.com/en-us/forums/intel-c-compiler/topic/610514 -buildopts = 'LDFLAGS="$LDFLAGS -lssp"' - -# order is important! -# package versions updated August 15th 2018 -exts_list = [ - ('setuptools', '40.0.0', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - 'checksums': ['012adb8e25fbfd64c652e99e7bab58799a3aaf05d39ab38561f69190a909015f'], - }), - ('pip', '18.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], - 'checksums': ['a0e11645ee37c90b40c46d607070c4fd583e2cd46231b1c06e389c5e814eed76'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], - }), - ('numpy', '1.15.0', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], - 'checksums': ['f28e73cf18d37a413f7d5de35d024e6b98f14566a10d82100f9dc491a7d449f9'], - }), - ('scipy', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], - 'checksums': ['878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1'], - }), - ('blist', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], - 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], - }), - ('mpi4py', '3.0.0', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - 'checksums': ['b457b02d85bdd9a4775a097fac5234a20397b43e073f14d9e29b6cd78c68efd7'], - }), - ('paycheck', '1.0.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], - 'patches': ['paycheck-1.0.2_setup-open-README-utf8.patch'], - 'checksums': [ - '6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34', # paycheck-1.0.2.tar.gz - # paycheck-1.0.2_setup-open-README-utf8.patch - 'ceb7f08aebf016cdcd94ae41c1c76c8c120907f85cbfce240d3a112afb264d79', - ], - }), - ('pbr', '4.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], - 'checksums': ['1b8be50d938c9bb75d0eaf7eda111eec1bf6dc88a62a6412e33bf077457e0f45'], - }), - ('Cython', '0.28.5', { - 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], - 'checksums': ['b64575241f64f6ec005a4d4137339fb0ba5e156e826db2fdb5f458060d9979e0'], - }), - ('six', '1.11.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], - 'checksums': ['70e8a77beed4562e7f14fe23a786b54f6296e34344c23bc42f07b15018ff98e9'], - }), - ('python-dateutil', '2.7.3', { - 'modulename': 'dateutil', - 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], - 'checksums': ['e27001de32f627c22380a688bcc43ce83504a7bc5da472209b4c70f02829f0b8'], - }), - ('deap', '1.2.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], - 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], - }), - ('decorator', '4.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], - 'checksums': ['c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c'], - }), - ('liac-arff', '2.3', { - 'modulename': 'arff', - 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], - 'checksums': ['21b1b17c082cacd7b554bf9a42f6de61d2bf02feef6eb31ec36b5486c31b2ae9'], - }), - ('pycrypto', '2.6.1', { - 'modulename': 'Crypto', - 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], - 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], - }), - ('ecdsa', '0.13', { - 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], - 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], - }), - ('pycparser', '2.18', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], - 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], - }), - ('cffi', '1.11.5', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], - 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], - }), - ('asn1crypto', '0.24.0', { - 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], - 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], - }), - ('idna', '2.7', { - 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], - 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], - }), - ('cryptography', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], - 'checksums': ['8d10113ca826a4c29d5b85b2c4e045ffa8bad74fb525ee0eceb1d38d4c70dfd6'], - }), - ('pyasn1', '0.4.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], - 'checksums': ['f58f2a3d12fd754aa123e9fa74fb7345333000a035f3921dbdaa08597aa53137'], - }), - ('PyNaCl', '1.2.1', { - 'modulename': 'nacl', - 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], - 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], - }), - ('bcrypt', '3.1.4', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], - 'checksums': ['67ed1a374c9155ec0840214ce804616de49c3df9c5bc66740687c1c9b1cd9e8d'], - }), - ('paramiko', '2.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], - 'checksums': ['33e36775a6c71790ba7692a73f948b329cf9295a72b0102144b031114bd2a4f3'], - }), - ('pyparsing', '2.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], - 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], - }), - ('netifaces', '0.10.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], - 'checksums': ['bd590fcb75421537d4149825e1e63cca225fd47dad861710c46bd1cb329d8cbd'], - }), - ('netaddr', '0.7.19', { - 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], - 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], - }), - ('mock', '2.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], - 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], - }), - ('pytz', '2018.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], - 'checksums': ['ffb9ef1de172603304d9d2819af6f5ece76f2e85ec10692a524dd876e72bf277'], - }), - ('pandas', '0.23.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], - 'checksums': ['5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4'], - }), - ('bitstring', '3.1.5', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], - 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], - }), - ('virtualenv', '16.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], - 'checksums': ['ca07b4c0b54e14a91af9f34d0919790b016923d157afda5efdde55c96718f752'], - }), - ('docopt', '0.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], - 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], - }), - ('joblib', '0.12.2', { - 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], - 'checksums': ['e9f04885cf11704669f3a731ea6ac00bbc7dea16137aa4394ef7c272cdb9d008'], - }), - ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], - 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], - }), - ('certifi', '2018.8.13', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - 'checksums': ['4c1d68a1408dd090d2f3a869aa94c3947cc1d967821d1ed303208c9f41f0f2f4'], - }), - ('urllib3', '1.23', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], - 'checksums': ['a68ac5e15e76e7e5dd2b8f94007233e01effe3e50e8daddf69acfd81cb686baf'], - }), - ('requests', '2.19.1', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - 'checksums': ['ec22d826a36ed72a7358ff3fe56cbd4ba69dd7a6718ffd450ff0e9df7a47ce6a'], - }), - ('xlrd', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], - 'checksums': ['8a21885513e6d915fe33a8ee5fdfa675433b61405ba13e2a69e62ee36828d7e2'], - }), - ('py_expression_eval', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], - 'checksums': ['b9662c58f8835f6fa3380990f870429fe1176008718a47ce054a7867c4091ad8'], - }), - ('mpmath', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath'], - 'checksums': ['04d14803b6875fe6d69e6dccea87d5ae5599802e4b1df7997bddd2024001050c'], - }), - ('tabulate', '0.8.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], - 'checksums': ['e4ca13f26d0a6be2a2915428dc21e732f1e44dad7f76d7030b2ef1ec251cf7f2'], - }), - ('ujson', '1.35', { - 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], - 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], - }), -] - -moduleclass = 'lang' From 3d0a95b516a098aed9425da3c69460676a8e9a4e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 10:24:56 +0100 Subject: [PATCH 0549/5331] enable download_dep_fail and use_pip in BamM easyconfig --- .../b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb index 043995344a0..52d1b7c6822 100644 --- a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb @@ -36,7 +36,10 @@ dependencies = [ ('BWA', '0.7.17'), ] -prebuildopts = "cd c && ./autogen.sh && cd .. &&" +download_dep_fail = True +use_pip = True + +preinstallopts = "cd c && ./autogen.sh && cd .. &&" sanity_check_paths = { 'files': ['bin/bamm'], From 353d050d64d3de34c286ffa90a7468d214f29b14 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 26 Feb 2019 11:22:22 +0100 Subject: [PATCH 0550/5331] Changed to PythonBundle --- .../n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb | 12 +++--------- .../n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb | 12 +++--------- 2 files changed, 6 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb index 3aff3d0bfdc..4a0b29f8e1b 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'numba' version = '0.37.0' @@ -11,17 +11,13 @@ description = """Numba is an Open Source NumPy-aware optimizing compiler for Pyt toolchain = {'name': 'foss', 'version': '2018a'} toolchainopts = {'pic': True} -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} - dependencies = [ ('Python', '2.7.14'), ('LLVM', '5.0.1'), ] +use_pip = True + exts_list = [ ('llvmlite', '0.22.0', { 'patches': ['llvmlite-0.22.0_fix-ffi-Makefile.patch'], @@ -47,6 +43,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb index db5ffad5fc6..1aa6703b4f3 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.37.0-foss-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'numba' version = '0.37.0' @@ -11,17 +11,13 @@ description = """Numba is an Open Source NumPy-aware optimizing compiler for Pyt toolchain = {'name': 'foss', 'version': '2018a'} toolchainopts = {'pic': True} -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} - dependencies = [ ('Python', '3.6.4'), ('LLVM', '5.0.1'), ] +use_pip = True + exts_list = [ ('llvmlite', '0.22.0', { 'patches': ['llvmlite-0.22.0_fix-ffi-Makefile.patch'], @@ -47,6 +43,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'lang' From 1788876b04d5ab91cf13a4cbd6e886b3b3c61ec2 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 26 Feb 2019 12:04:47 +0100 Subject: [PATCH 0551/5331] Style changes --- .../PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb | 8 +++----- .../p/PCAngsd/PCAngsd-0.97_python-hashbang.patch | 11 +++++++++++ 2 files changed, 14 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97_python-hashbang.patch diff --git a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb index 292db083a40..65c59c08c84 100644 --- a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb @@ -13,12 +13,11 @@ toolchain = {'name': 'foss', 'version': '2018a'} source_urls = ['https://github.com/Rosemeis/pcangsd/archive/v%(version)s/'] sources = [SOURCE_TAR_GZ] -patches = [ - 'PCAngsd-python-hashbang.patch', -] +patches = [ 'PCAngsd-%(version)s_python-hashbang.patch' ] + checksums = [ '05507ccf70b6464656ad9a63bb4d43d771d72d633055a08e056b9feb91f5c60a', - '8729dbda52a94aa61cbd48bc73cd15155831ce22aebc30d9b4e96ff12c12a482', # PCAngsd-python-hashbang.patch + 'f90018eec41ae47a41bfbd09c54a773f61d4c4d67279ee4c69c2a7ed6afa2e23', # PCAngsd-%(version)s-python-hashbang.patch ] dependencies = [ @@ -27,7 +26,6 @@ dependencies = [ ] exts_defaultclass = 'PythonPackage' -#exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('pysnptools', '0.3.13', { diff --git a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97_python-hashbang.patch b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97_python-hashbang.patch new file mode 100644 index 00000000000..70992d3d141 --- /dev/null +++ b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97_python-hashbang.patch @@ -0,0 +1,11 @@ +# Add hashbang for python to allow the main script to be executed directly +# Author: Fokke Dijkstra +# University of Groningen, NL +diff -ru pcangsd-0.97/pcangsd.py pcangsd-0.97.patched/pcangsd.py +--- pcangsd-0.97/pcangsd.py 2018-12-09 10:37:34.000000000 +0100 ++++ pcangsd-0.97.patched/pcangsd.py 2019-02-25 12:55:47.000000000 +0100 +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python + """ + PCAngsd Framework: Population genetic analyses for NGS data using PCA. Main caller. + """ From 7d73f0f2ade0c1318bd4bec0fbf2aefc4db3d539 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 13:00:19 +0100 Subject: [PATCH 0552/5331] adding easyconfigs: barrnap-0.9-foss-2018b.eb --- .../b/barrnap/barrnap-0.9-foss-2018b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/barrnap/barrnap-0.9-foss-2018b.eb diff --git a/easybuild/easyconfigs/b/barrnap/barrnap-0.9-foss-2018b.eb b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-foss-2018b.eb new file mode 100644 index 00000000000..682705b6218 --- /dev/null +++ b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-foss-2018b.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'barrnap' +version = '0.9' + +homepage = 'https://github.com/tseemann/barrnap' +description = "Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/tseemann/barrnap/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['36c27cd4350531d98b3b2fb7d294a2d35c15b7365771476456d7873ba33cce15'] + +dependencies = [ + ('Perl', '5.28.0'), + ('HMMER', '3.2.1'), + ('BEDTools', '2.27.1'), +] + +sanity_check_paths = { + 'files': ['bin/barrnap'], + 'dirs': [], +} + +sanity_check_commands = ["barrnap --help"] + +moduleclass = 'bio' From 4fb840496f7b5faa56b48bf36467a385ffdfc295 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 13:02:28 +0100 Subject: [PATCH 0553/5331] adding easyconfigs: Ruby-2.6.1-GCCcore-7.3.0.eb --- .../r/Ruby/Ruby-2.6.1-GCCcore-7.3.0.eb | 133 ++++++++++++++++++ 1 file changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.6.1-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.6.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.6.1-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..a4569eecfc5 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.6.1-GCCcore-7.3.0.eb @@ -0,0 +1,133 @@ +name = 'Ruby' +version = '2.6.1' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['17024fb7bb203d9cf7a5a42c78ff6ce77140f9d083676044a7db67f1e5191cb8'] + +builddependencies = [('binutils', '2.30')] + +exts_default_options = { + 'source_urls': ['http://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_list = [ + ('ffi', '1.10.0', { + 'checksums': ['17001940b28a961c94251a39f0ae00b32c2d0850479b5978c971759591fc1749'], + }), + ('childprocess', '1.0.1', { + 'checksums': ['7fe65b8d220967e8b47d8027274db40667641829f12ce9c6145022949c564fb4'], + }), + ('json', '2.1.0', { + 'checksums': ['b76fd09b881088c6c64a12721a1528f2f747a1c2ee52fab4c1f60db8af946607'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.11.4', { + 'checksums': ['0ff9c1601e381e51f93fca3b9931b5e0de4ff0f359da536603fa40c1799750c3'], + }), + ('arr-pm', '0.0.10', { + 'checksums': ['0fa2d425a84eeeaf8f95268568e826723b41aeefa14511d1f0ed1368c30bdd1f'], + }), + ('clamp', '1.3.0', { + 'checksums': ['1c466e93c14ed78078a428990f113b30f256189ec76f682f759e5aa2a181acfb'], + }), + ('multipart-post', '2.0.0', { + 'checksums': ['3dc44e50d3df3d42da2b86272c568fd7b75c928d8af3cc5f9834e2e5d9586026'], + }), + ('faraday', '0.15.4', { + 'checksums': ['00e6ffd6f1bccd9dc9e3b993a0004e69680559422206ce4cbb81fd2d0ba8e268'], + }), + ('faraday_middleware', '0.13.1', { + 'checksums': ['b94e3e7845f78db0eacdfc7e0185f0310765ccd70a46b6ce6478aa858ace23a9'], + }), + ('highline', '2.0.1', { + 'checksums': ['ec0bab47f397b32d09b599629cf32f4fc922470a09bef602ef5e492127bb263f'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.2.2', { + 'checksums': ['c8cc9446bcc51034103c1259ad70b91dc9f5297d13460b2c0cce7e5a93e8d451'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.13.1', { + 'checksums': ['db8613c039b9501e6b2fb85efe4feabb02f55c3365bae52bba35381b89c780e6'], + }), + ('public_suffix', '3.0.3', { + 'checksums': ['d4f4addffbd1ad3e7b5bb2e258a761ccef5670c23c29b0476b2299bcca220623'], + }), + ('addressable', '2.4.0', { + 'checksums': ['7abfff765571b0a73549c9a9d2f7e143979cd0c252f7fa4c81e7102a973ef656'], + }), + ('gh', '0.15.1', { + 'checksums': ['ef733f81c17846f217f5ad9616105e9adc337775d41de1cc330133ad25708d3c'], + }), + ('launchy', '2.4.3', { + 'checksums': ['42f52ce12c6fe079bac8a804c66522a0eefe176b845a62df829defe0e37214a4'], + }), + ('ethon', '0.12.0', { + 'checksums': ['e99d3095e89f82c5a7e63d9261ddf4a21f28ae5d12a9d3abaa6920cce6cbef3d'], + }), + ('typhoeus', '1.3.1', { + 'checksums': ['257e7163d50bed15e52c3c25bde890ea3ad854f3bd2e3fd16ce0b216c342d132'], + }), + ('websocket', '1.2.8', { + 'checksums': ['1d8155c1cdaab8e8e72587a60e08423c9dd84ee44e4e827358ce3d4c2ccb2138'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.3', { + 'checksums': ['ea7bf591567e391ef262a7c29edaf87c6205204afb5bb39dfa8f08f2e51282a3'], + }), + ('rspec-support', '3.8.0', { + 'checksums': ['0918cc4165bb7626e518cef41046ddab90d0435868b0fb85dc90e61e733b755c'], + }), + ('rspec-mocks', '3.8.0', { + 'checksums': ['d73b926d641676025ba086b4854f70b8a70d6cb763d50e9d278b792c1902c51b'], + }), + ('rspec-expectations', '3.8.2', { + 'checksums': ['753620b7f9511454a98cd77c90dd85335025ec98272c2fd8bb82b51f3c0c82a2'], + }), + ('rspec-core', '3.8.0', { + 'checksums': ['97d0b30c5687075417ac6f837c44a95e4a825007d0017fccec7a5cbcec2a3adc'], + }), + ('rspec', '3.8.0', { + 'checksums': ['83f519611bb674d456e87397fea7c5b15b1af8bdc77ce929673ae3b4b656f796'], + }), + ('rack', '2.0.6', { + 'checksums': ['f5874ac9c2223ecc65fcad3120c884fc2a868c1c18f548ff676a6eb21bda8fdd'], + }), + ('rack-protection', '2.0.5', { + 'checksums': ['53cb7ad3f8119fac5a3d2be13e288f29fa15e29058421339beb1d75c043e2694'], + }), + ('tilt', '2.0.9', { + 'checksums': ['9fd77f52eb8dbeae741a7110c08fd9777679bb25dd8873fc9e19384e19984431'], + }), + ('mustermann', '1.0.3', { + 'checksums': ['219ecbefebccb10778273bbd64ae468e5da30ac55f346b93700b786feb7ccc53'], + }), + ('sinatra', '2.0.5', { + 'checksums': ['3e9f56189bc6d40eb8c3ef9ee1b5ec905d23c63521823011d8be96e08a7d5abd'], + }), + ('rack-test', '1.1.0', { + 'checksums': ['154161f40f162b1c009a655b7b0c5de3a3102cc6d7d2e94b64e1f46ace800866'], + }), + ('bundler', '2.0.1', { + 'checksums': ['c7e38039993c9c2edc27397aef4a3370a4b35c7fae3d93e434e501c4bd7656ea'], + }), +] + +moduleclass = 'lang' From 7703df5f28ceca32cca5d3f96502c48bcd9c6970 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 13:05:03 +0100 Subject: [PATCH 0554/5331] adding easyconfigs: pullseq-1.0.2-GCCcore-7.3.0.eb --- .../p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..bc6e3f50681 --- /dev/null +++ b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pullseq' +version = '1.0.2' + +homepage = 'https://github.com/bcthomas/pullseq' +description = "Utility program for extracting sequences from a fasta/fastq file" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://github.com/bcthomas/pullseq/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a295d7e0e2d64ed05d293d795d1716376707e465f2c42ede6454f27db586c85f'] + +builddependencies = [ + ('binutils', '2.30'), + ('Autotools', '20180311'), +] + +preconfigopts = "./bootstrap && " + +sanity_check_paths = { + 'files': ['bin/pullseq', 'bin/seqdiff'], + 'dirs': [], +} + +moduleclass = 'bio' From a9e6f0e87950a9e43042147a2a043204baab5225 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 13:23:36 +0100 Subject: [PATCH 0555/5331] {bio}[foss/2018b] DAS_Tool v1.1.1 w/ R 3.5.1 + Python 2.7.15 --- ...-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb new file mode 100644 index 00000000000..166fefe7cc4 --- /dev/null +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb @@ -0,0 +1,53 @@ +easyblock = 'Tarball' + +name = 'DAS_Tool' +version = '1.1.1' +versionsuffix = '-R-%(rver)s-Python-%(pyver)s' + +homepage = 'https://github.com/cmks/DAS_Tool' +description = """DAS Tool is an automated method that integrates the results of a flexible number of binning + algorithms to calculate an optimized, non-redundant set of bins from a single assembly.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a'] + +dependencies = [ + ('Python', '2.7.15'), + ('R', '3.5.1', '-Python-%(pyver)s'), + ('Ruby', '2.6.1'), + ('pullseq', '1.0.2'), + ('prodigal', '2.6.3'), + ('BLAST+', '2.7.1'), +] + +exts_defaultclass = 'RPackage' + +exts_list = [ + (name, version, { + 'source_tmpl': 'DASTool_%(version)s.tar.gz', + 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], + 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], + 'modulename': 'DASTool', + }), +] + +postinstallcmds = [ + "cd %(installdir)s; unzip db.zip", + "chmod a+x %(installdir)s/DAS_Tool", +] + +sanity_check_paths = { + 'files': ['DAS_Tool'], + 'dirs': ['DASTool/R'], +} + +modextrapaths = { + 'PATH': '', + 'R_LIBS': '', +} + + +moduleclass = 'bio' From fa24b3ec2c4b67e9ea3d7fa99accccffbaa7941e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 13:33:49 +0100 Subject: [PATCH 0556/5331] Delete PCAngsd-python-hashbang.patch delete PCAngsd-python-hashbang.patch, replaced by PCAngsd-0.97_python-hashbang.patch --- .../easyconfigs/p/PCAngsd/PCAngsd-python-hashbang.patch | 8 -------- 1 file changed, 8 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PCAngsd/PCAngsd-python-hashbang.patch diff --git a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-python-hashbang.patch b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-python-hashbang.patch deleted file mode 100644 index 778ec3c5f5a..00000000000 --- a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-python-hashbang.patch +++ /dev/null @@ -1,8 +0,0 @@ -diff -ru pcangsd-0.97/pcangsd.py pcangsd-0.97.patched/pcangsd.py ---- pcangsd-0.97/pcangsd.py 2018-12-09 10:37:34.000000000 +0100 -+++ pcangsd-0.97.patched/pcangsd.py 2019-02-25 12:55:47.000000000 +0100 -@@ -1,3 +1,4 @@ -+#!/usr/bin/env python - """ - PCAngsd Framework: Population genetic analyses for NGS data using PCA. Main caller. - """ From 684bda15b694bf4aadf51bc6c9bc9e925dc966cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 13:41:10 +0100 Subject: [PATCH 0557/5331] adding easyconfigs: CD-HIT-4.6.8-foss-2018b.eb --- .../c/CD-HIT/CD-HIT-4.6.8-foss-2018b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-foss-2018b.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-foss-2018b.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-foss-2018b.eb new file mode 100644 index 00000000000..63b2706742c --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-foss-2018b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.6.8' + +homepage = 'http://weizhong-lab.ucsd.edu/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/archive/'] +sources = ['V%(version)s.tar.gz'] +checksums = ['37d685e4aa849314401805fe4d4db707e1d06070368475e313d6f3cb8fb65949'] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +postinstallcmds = ["sed -i 's@#!/usr/bin/perl@/usr/bin/env perl@' %(installdir)s/bin/*.pl"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' From eb2318fa3b17cb920bff9666b61ba5a9761e67e0 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 26 Feb 2019 13:48:14 +0100 Subject: [PATCH 0558/5331] Improved references to Java version --- .../r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb index 763c2f99741..24380b2e17f 100644 --- a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb +++ b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb @@ -2,6 +2,7 @@ easyblock = 'Tarball' name = 'RDP-Classifier' version = '2.12' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/rdp-classifier' description = """The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic @@ -13,11 +14,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['rdp_classifier_%(version)s.zip'] checksums = ['977896248189a1ce2146dd3a61d203c3c6bc9aa3982c60332d463832922f7d0a'] -java = 'Java' -javaver = '1.8' -versionsuffix = '-%s-%s' % (java, javaver) - -dependencies = [(java, javaver)] +dependencies = [('Java', '1.8')] modextrapaths = { 'CLASSPATH': 'dist/classifier.jar', From 65705a3b788cb3386e4e15be53a4c484ed330cc4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 13:53:53 +0100 Subject: [PATCH 0559/5331] fix Jellyfish dependency in easyconfig for Kraken 1.0 (Jellyfish 1.x is required) --- .../Jellyfish/Jellyfish-1.1.12-intel-2018a.eb | 29 +++++++++++++++++++ .../Kraken-1.0-intel-2018a-Perl-5.26.1.eb | 3 +- 2 files changed, 31 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.12-intel-2018a.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.12-intel-2018a.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.12-intel-2018a.eb new file mode 100644 index 00000000000..e0612b36bc3 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-1.1.12-intel-2018a.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '1.1.12' + +homepage = 'http://www.cbcb.umd.edu/software/%(namelower)s/' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'intel', 'version': '2018a'} + +github_account = 'gmarcais' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['1ae32d3775e551272a757608671dc1d69d0659d253b174e393b6cb24f6a7e181'] + +builddependencies = [('Autotools', '20170619')] + +preconfigopts = "autoreconf -i && " + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-1.0-intel-2018a-Perl-5.26.1.eb b/easybuild/easyconfigs/k/Kraken/Kraken-1.0-intel-2018a-Perl-5.26.1.eb index fa286a0eb07..9429610372e 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-1.0-intel-2018a-Perl-5.26.1.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-1.0-intel-2018a-Perl-5.26.1.eb @@ -27,7 +27,8 @@ checksums = [ dependencies = [ ('Perl', '5.26.1'), - ('Jellyfish', '2.2.10'), + # Jellyfish 1.x is required, see https://github.com/DerrickWood/kraken/issues/69 + ('Jellyfish', '1.1.12'), ('wget', '1.19.4'), ] From 2531c5cfc733df17b843b8fa4040cbdf868b2025 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 14:49:00 +0100 Subject: [PATCH 0560/5331] add oddsratio/mltools/h2o extensions to R 3.5.1 easyconfigs --- .../easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 9 +++++++++ easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index ee8828958a2..414adfa2845 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -2069,6 +2069,15 @@ exts_list = [ ('liquidSVM', '1.2.2', { 'checksums': ['96f545e5878d2cce27f37185757945607b00fdeaa43258f0884a578be6c3688a'], }), + ('oddsratio', '1.0.3', { + 'checksums': ['b33861d8beae189c66e6b94d59cc698bf08aeafb47262b5f7a1d2e88a2b2b8cd'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.22.1.1', { + 'checksums': ['e4c9d50d2a6a42ffecb15aa1561495599b206a7edd77db95501c7d09253fc412'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 7d71a230890..9f1aa8ce8cd 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -2067,6 +2067,15 @@ exts_list = [ ('liquidSVM', '1.2.2', { 'checksums': ['96f545e5878d2cce27f37185757945607b00fdeaa43258f0884a578be6c3688a'], }), + ('oddsratio', '1.0.3', { + 'checksums': ['b33861d8beae189c66e6b94d59cc698bf08aeafb47262b5f7a1d2e88a2b2b8cd'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.22.1.1', { + 'checksums': ['e4c9d50d2a6a42ffecb15aa1561495599b206a7edd77db95501c7d09253fc412'], + }), ] moduleclass = 'lang' From 383b93b6d584eac339accdc128478230d2ca0c33 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 26 Feb 2019 15:16:29 +0100 Subject: [PATCH 0561/5331] update to include PLUMED version number in versionsuffix --- ...b-PLUMED.eb => GROMACS-2018.4-foss-2018b-PLUMED-2.5.0.eb} | 5 +++-- ...UMED.eb => GROMACS-2018.4-fosscuda-2018b-PLUMED-2.5.0.eb} | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/g/GROMACS/{GROMACS-2018.4-foss-2018b-PLUMED.eb => GROMACS-2018.4-foss-2018b-PLUMED-2.5.0.eb} (93%) rename easybuild/easyconfigs/g/GROMACS/{GROMACS-2018.4-fosscuda-2018b-PLUMED.eb => GROMACS-2018.4-fosscuda-2018b-PLUMED-2.5.0.eb} (93%) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED-2.5.0.eb similarity index 93% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED-2.5.0.eb index 6604dc0b50c..f16e20dffa3 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED-2.5.0.eb @@ -14,7 +14,8 @@ name = 'GROMACS' version = '2018.4' -versionsuffix = '-PLUMED' +plum_ver = '2.5.0' +versionsuffix = '-PLUMED-%s' % plum_ver homepage = 'http://www.gromacs.org' description = """ @@ -41,7 +42,7 @@ builddependencies = [ ] dependencies = [ - ('PLUMED', '2.5.0', '-Python-2.7.15'), + ('PLUMED', plum_ver, '-Python-2.7.15'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED-2.5.0.eb similarity index 93% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED-2.5.0.eb index 93d0e8a25a5..ba0826248ca 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED-2.5.0.eb @@ -14,7 +14,8 @@ name = 'GROMACS' version = '2018.4' -versionsuffix = '-PLUMED' +plum_ver = '2.5.0' +versionsuffix = '-PLUMED-%s' % plum_ver homepage = 'http://www.gromacs.org' description = """ @@ -45,7 +46,7 @@ builddependencies = [ ] dependencies = [ - ('PLUMED', '2.5.0', '-Python-2.7.15'), + ('PLUMED', plum_ver, '-Python-2.7.15'), ] moduleclass = 'bio' From 580c91b4dc2c77ae852898e8a0af9410570fba54 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 26 Feb 2019 16:31:12 +0200 Subject: [PATCH 0562/5331] Update Qt 4.8.7 for fosscuda/2018b to match the existing foss/2018b version. --- .../easyconfigs/q/Qt/Qt-4.8.7-fosscuda-2018b.eb | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-fosscuda-2018b.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-fosscuda-2018b.eb index 18048029ac1..4c865b396eb 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-fosscuda-2018b.eb @@ -12,14 +12,22 @@ source_urls = [ 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] -patches = ['Qt-%(version)s_phonon-export.patch'] +patches = [ + 'Qt-%(version)s_phonon-export.patch', + 'Qt-%(version)s_no-ssl3.patch', + 'Qt-%(version)s_openssl_1.1.patch', +] checksums = [ 'e2882295097e47fe089f8ac741a95fef47e0a73a3f3cdf21b56990638f626ea0', # qt-everywhere-opensource-src-4.8.7.tar.gz '3853c87c33695bfa57e207ffb0d94cb2565aa462eccdf44d2b2804fd44ecbad6', # Qt-4.8.7_phonon-export.patch + '744514a2c7d1fb8c127ea91da7655911c13f72499127e0cc1bceba0c2551a0e2', # Qt-4.8.7_no-ssl3.patch + '754eab951fa63abdb04c1530d386363a45471a2759a4253f5b014c1f0f7a8e47', # Qt-4.8.7_openssl_1.1.patch ] builddependencies = [ ('pkg-config', '0.29.2'), + ('Bison', '3.0.5'), + ('flex', '2.6.4'), ] dependencies = [ @@ -27,6 +35,11 @@ dependencies = [ ('libpng', '1.6.34'), ('X11', '20180604'), ('libGLU', '9.0.0'), + ('SQLite', '3.24.0'), + ('fontconfig', '2.13.0'), + ('libjpeg-turbo', '2.0.0'), ] +configopts = '-webkit -opensource ' + moduleclass = 'devel' From dc9ce438642b3bf3882c490a431a5975ed80ca7d Mon Sep 17 00:00:00 2001 From: jdemeul Date: Tue, 26 Feb 2019 15:34:53 +0000 Subject: [PATCH 0563/5331] {bio}[foss/2018b] STAR-Fusion v1.5.0 w/ Perl v5.28.0 --- ...TAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb | 41 +++++++++++++++---- 1 file changed, 34 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb index 03765f06118..249bc289140 100644 --- a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb @@ -2,6 +2,7 @@ # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics +# updated for v1.5.0 by Jonas Demulemeester easyblock = 'Tarball' @@ -15,14 +16,14 @@ description = """STAR-Fusion uses the STAR aligner to identify candidate fusion to map junction reads and spanning reads to a reference annotation set.""" toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = ['https://github.com/STAR-Fusion/STAR-Fusion/releases/download/%(name)s-v%(version)s/'] +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(name)s-v%(version)s/'] sources = ['%(name)s-v%(version)s.FULL.tar.gz'] checksums = ['229cbf7980496d72de0bfab5bde7148ff3111a99b72c6169d1a04120a52508b4'] dependencies = [ ('Perl', '5.28.0'), - ('STAR', '2.6.1c'), + ('DB', '18.1.25'), + ('STAR', '2.7.0d', '', ('foss', '2018b')), ] # these are the perl libraries dependencies @@ -30,18 +31,44 @@ exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") exts_list = [ - ('Set::IntervalTree', '0.10', { - 'source_tmpl': 'Set-IntervalTree-0.10.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BE/BENBOOTH/'], - 'checksums': ['e3bd9ccf0d074b5f879eef1ed88254983697bf83d02744fce62150ee46553ebc'], + ('ExtUtils::CppGuess', '0.12', { + 'source_tmpl': 'ExtUtils-CppGuess-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ/'], + 'checksums': ['31c47b5b15e3e9fd5ae7b35881a0fffd26a2983b241e7e3a1bc340d6d446186b'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD/'], + 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], }), ('DB_File', '1.843', { 'source_tmpl': 'DB_File-1.843.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], 'checksums': ['de24e3d1e56b1b56c1f143590fb8ab8b812ebd9697e9c01349b0ba11c36f346a'], }), + ('URI::Escape', '1.76', { + 'source_tmpl': 'URI-1.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS/'], + 'checksums': ['b2c98e1d50d6f572483ee538a6f4ccc8d9185f91f0073fd8af7390898254413e'], + }), + ('Carp::Assert', '0.21', { + 'source_tmpl': 'Carp-Assert-0.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], + 'checksums': ['924f8e2b4e3cb3d8b26246b5f9c07cdaa4b8800cef345fa0811d72930d73a54e'], + }), + ('JSON::XS', '4.01', { + 'source_tmpl': 'JSON-XS-4.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], + 'checksums': ['cc1062e39a1fd6ff8bd9df84a102e8572468cea29d43190672a10f9c39973e5c'], + }), + ('PerlIO::gzip', '0.20', { + 'source_tmpl': 'PerlIO-gzip-0.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], + 'checksums': ['4848679a3f201e3f3b0c5f6f9526e602af52923ffa471a2a3657db786bd3bdc5'], + }), ] + modextrapaths = { 'PATH': "", # add installation dir to PATH 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' From 504f61b8f357dbe7b4a99c9be4f0ed899509e9a2 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 26 Feb 2019 17:08:27 +0100 Subject: [PATCH 0564/5331] Style changes --- .../p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb index 65c59c08c84..67c60ea6119 100644 --- a/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PCAngsd/PCAngsd-0.97-foss-2018a-Python-2.7.14.eb @@ -13,11 +13,11 @@ toolchain = {'name': 'foss', 'version': '2018a'} source_urls = ['https://github.com/Rosemeis/pcangsd/archive/v%(version)s/'] sources = [SOURCE_TAR_GZ] -patches = [ 'PCAngsd-%(version)s_python-hashbang.patch' ] +patches = ['PCAngsd-%(version)s_python-hashbang.patch'] checksums = [ - '05507ccf70b6464656ad9a63bb4d43d771d72d633055a08e056b9feb91f5c60a', - 'f90018eec41ae47a41bfbd09c54a773f61d4c4d67279ee4c69c2a7ed6afa2e23', # PCAngsd-%(version)s-python-hashbang.patch + '05507ccf70b6464656ad9a63bb4d43d771d72d633055a08e056b9feb91f5c60a', + 'f90018eec41ae47a41bfbd09c54a773f61d4c4d67279ee4c69c2a7ed6afa2e23', # PCAngsd-%(version)s-python-hashbang.patch ] dependencies = [ From 15a43a297bc427d9455a0521171162a80c2e2036 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 26 Feb 2019 17:20:13 +0100 Subject: [PATCH 0565/5331] adding easyconfigs: Miniconda3-4.5.12.eb --- .../m/Miniconda3/Miniconda3-4.5.12.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.5.12.eb diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.5.12.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.5.12.eb new file mode 100644 index 00000000000..0565a5cfa43 --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.5.12.eb @@ -0,0 +1,18 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda3' +version = '4.5.12' + +homepage = 'https://www.continuum.io/anaconda-overview' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://repo.continuum.io/miniconda/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['e5e5b4cd2a918e0e96b395534222773f7241dc59d776db1b9f7fedfcb489157a'] + +moduleclass = 'lang' From 5bc599547e06dc34d4542d3b7cca51b97c881bf3 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 26 Feb 2019 16:25:52 +0000 Subject: [PATCH 0566/5331] added patch and recipe for AUGUSTUS-3.3.2 --- ...UGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb | 45 ++++++++++ .../AUGUSTUS-3.3.2_fix-hardcoding.patch | 86 +++++++++++++++++++ 2 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_fix-hardcoding.patch diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb new file mode 100644 index 00000000000..7f1484baf58 --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.2.3' +versionsuffix = '-Python-2.7.13' + +homepage = 'http://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [ + 'http://bioinf.uni-greifswald.de/augustus/binaries/', + 'http://bioinf.uni-greifswald.de/augustus/binaries/old/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.63.0', versionsuffix), + ('SQLite', '3.17.0'), + ('GSL', '2.3'), + ('SuiteSparse', '4.5.5', '-ParMETIS-4.0.3'), + ('lpsolve', '5.5.2.5'), + ('BamTools', '2.4.1'), +] + +skipsteps = ['configure'] + +prebuildopts = "unset LDFLAGS && unset LIBS && " +buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX"' +installopts = 'INSTALLDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/aln2wig', 'bin/augustus', 'bin/bam2hints', 'bin/bam2wig', 'bin/espoca', 'bin/etraining', + 'bin/fastBlockSearch', 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} + +modextrapaths = {'PATH': 'scripts'} +modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_fix-hardcoding.patch b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_fix-hardcoding.patch new file mode 100644 index 00000000000..0173fae980b --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_fix-hardcoding.patch @@ -0,0 +1,86 @@ +diff -ru augustus-3.3.2.orig/auxprogs/bam2wig/Makefile augustus-3.3.2/auxprogs/bam2wig/Makefile +--- augustus-3.3.2.orig/auxprogs/bam2wig/Makefile 2019-02-26 14:52:06.899673626 +0000 ++++ augustus-3.3.2/auxprogs/bam2wig/Makefile 2019-02-26 15:20:39.258854823 +0000 +@@ -15,15 +15,15 @@ + PROGRAM = bam2wig + SOURCES = $(PROGRAM) + OBJECTS = $(SOURCES:.c=.o) +-SAMTOOLS=$(TOOLDIR)/samtools/ +-HTSLIB=$(TOOLDIR)/htslib/ +-BCFTOOLS=$(TOOLDIR)/bcftools/ +-TABIX=$(TOOLDIR)/tabix/ +-INCLUDES=-I$(SAMTOOLS) -I. -I$(HTSLIB) -I$(BCFTOOLS) -I$(TABIX) ++SAMTOOLS=$(EBROOTSAMTOOLS) ++HTSLIB=$(EBROOTHTSLIB) ++#BCFTOOLS=$(TOOLDIR)/bcftools/ ++#TABIX=$(TOOLDIR)/tabix/ ++INCLUDES=-I$(SAMTOOLS)/include/bam -I. -I$(HTSLIB)/include + VPATH=$(SAMTOOLS) +-LIBS=$(SAMTOOLS)/libbam.a $(HTSLIB)/libhts.a -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto +-CFLAGS=-Wall -O2 $(INCLUDES) +-CC=gcc ++LIBS=$(SAMTOOLS)/lib/libbam.a $(HTSLIB)/lib/libhts.a -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto ++CFLAGS:=-Wall -O2 $(CFLAGS) $(INCLUDES) ++CC:=$(CC) + + $(PROGRAM) : bam2wig.o + $(CC) $(CFLAGS) $^ -o $@ $(LIBS) -lbz2 -llzma +diff -ru augustus-3.3.2.orig/auxprogs/compileSpliceCands/Makefile augustus-3.3.2/auxprogs/compileSpliceCands/Makefile +--- augustus-3.3.2.orig/auxprogs/compileSpliceCands/Makefile 2019-02-26 14:52:07.122673914 +0000 ++++ augustus-3.3.2/auxprogs/compileSpliceCands/Makefile 2019-02-26 14:55:08.623907877 +0000 +@@ -1,8 +1,8 @@ + compileSpliceCands : compileSpliceCands.o list.h list.o +- gcc $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o; ++ $(CC) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o; + # cp compileSpliceCands ../../bin + compileSpliceCands.o : compileSpliceCands.c +- gcc -Wall -pedantic -ansi $(CPPFLAGS) -c compileSpliceCands.c ++ $(CC) -Wall -pedantic -ansi $(CPPFLAGS) -c compileSpliceCands.c + + all : compileSpliceCands + +diff -ru augustus-3.3.2.orig/auxprogs/homGeneMapping/src/Makefile augustus-3.3.2/auxprogs/homGeneMapping/src/Makefile +--- augustus-3.3.2.orig/auxprogs/homGeneMapping/src/Makefile 2019-02-26 14:52:07.074673852 +0000 ++++ augustus-3.3.2/auxprogs/homGeneMapping/src/Makefile 2019-02-26 14:55:08.623907877 +0000 +@@ -7,7 +7,7 @@ + # database access for retrieval of hints + # SQLITE = true + +-CC = g++ ++CC = $(CXX) + + # Notes: - "-Wno-sign-compare" eliminates a high number of warnings (see footnote below). Please adopt + # a strict signed-only usage strategy to avoid mistakes since we are not warned about this. +diff -ru augustus-3.3.2.orig/auxprogs/joingenes/Makefile augustus-3.3.2/auxprogs/joingenes/Makefile +--- augustus-3.3.2.orig/auxprogs/joingenes/Makefile 2019-02-26 14:52:06.893673619 +0000 ++++ augustus-3.3.2/auxprogs/joingenes/Makefile 2019-02-26 14:55:08.624907879 +0000 +@@ -1,4 +1,4 @@ +-CC=g++ ++CC=$(CXX) + CFLAGS=-Wall -std=gnu++0x + + all: joingenes +diff -ru augustus-3.3.2.orig/Makefile augustus-3.3.2/Makefile +--- augustus-3.3.2.orig/Makefile 2019-02-26 14:52:07.123673915 +0000 ++++ augustus-3.3.2/Makefile 2019-02-26 14:55:08.624907879 +0000 +@@ -17,13 +17,13 @@ + install: + install -d $(INSTALLDIR) + cp -a config bin scripts $(INSTALLDIR) +- ln -sf $(INSTALLDIR)/bin/augustus /usr/local/bin/augustus +- ln -sf $(INSTALLDIR)/bin/etraining /usr/local/bin/etraining +- ln -sf $(INSTALLDIR)/bin/prepareAlign /usr/local/bin/prepareAlign +- ln -sf $(INSTALLDIR)/bin/fastBlockSearch /usr/local/bin/fastBlockSearch +- ln -sf $(INSTALLDIR)/bin/load2db /usr/local/bin/load2db +- ln -sf $(INSTALLDIR)/bin/getSeq /usr/local/bin/getSeq +- ln -sf $(INSTALLDIR)/bin/espoca /usr/local/bin/espoca ++ #ln -sf $(INSTALLDIR)/bin/augustus /usr/local/bin/augustus ++ #ln -sf $(INSTALLDIR)/bin/etraining /usr/local/bin/etraining ++ #ln -sf $(INSTALLDIR)/bin/prepareAlign /usr/local/bin/prepareAlign ++ #ln -sf $(INSTALLDIR)/bin/fastBlockSearch /usr/local/bin/fastBlockSearch ++ #ln -sf $(INSTALLDIR)/bin/load2db /usr/local/bin/load2db ++ #ln -sf $(INSTALLDIR)/bin/getSeq /usr/local/bin/getSeq ++ #ln -sf $(INSTALLDIR)/bin/espoca /usr/local/bin/espoca + + # for internal purposes: + release: From 3c77fc05426cef140b2cd5fcd9399033f15d1348 Mon Sep 17 00:00:00 2001 From: jdemeul Date: Tue, 26 Feb 2019 17:08:23 +0000 Subject: [PATCH 0567/5331] made requested changes --- .../s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb index 249bc289140..c33f9318fa8 100644 --- a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb @@ -16,6 +16,7 @@ description = """STAR-Fusion uses the STAR aligner to identify candidate fusion to map junction reads and spanning reads to a reference annotation set.""" toolchain = {'name': 'foss', 'version': '2018b'} + source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(name)s-v%(version)s/'] sources = ['%(name)s-v%(version)s.FULL.tar.gz'] checksums = ['229cbf7980496d72de0bfab5bde7148ff3111a99b72c6169d1a04120a52508b4'] @@ -23,7 +24,7 @@ checksums = ['229cbf7980496d72de0bfab5bde7148ff3111a99b72c6169d1a04120a52508b4'] dependencies = [ ('Perl', '5.28.0'), ('DB', '18.1.25'), - ('STAR', '2.7.0d', '', ('foss', '2018b')), + ('STAR', '2.6.1c', '', ('foss', '2018b')), ] # these are the perl libraries dependencies @@ -68,7 +69,6 @@ exts_list = [ }), ] - modextrapaths = { 'PATH': "", # add installation dir to PATH 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' From b071a0856e3fdc0584a6c917ec69c641d631fc08 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 26 Feb 2019 11:33:16 -0600 Subject: [PATCH 0568/5331] adding easyconfigs: Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb, Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb --- ...ss-2017b-AmberTools-17-patchlevel-10-15.eb | 91 +++++++++++++++++++ ...el-2017b-AmberTools-17-patchlevel-10-15.eb | 85 +++++++++++++++++ 2 files changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb new file mode 100644 index 00000000000..aff2b7082b3 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb @@ -0,0 +1,91 @@ +name = 'Amber' +version = '16' +ambertools_ver = '17' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (10, 15) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] +patches = [ + 'Amber-%%(version)s-AT-%s_fix-hardcoding.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_intel_mpi_compiler_version_detection.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_mkl_include_path.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_fftw_from_mkl_or_external.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_FFTW_FFT_instead_of_PUBFFT.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_sander_link_with_external_fftw.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix-cpptraj-dont-use-static.patch' % ambertools_ver, + # Must come after fix-cpptraj-dont-use-static.patch + 'Amber-%%(version)s-AT-%s_cpptraj_use_mkl_fft.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_incorrect_omp_directive_rism.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_openmp_at_link.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_CUSTOMBUILDFLAGS_for_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_do_parallel_in_checkrismunsupported.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_fixed_size_cmd_in_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch' % ambertools_ver, + 'Amber-%(version)s-fix_missing_build_target.patch', + 'Amber-%(version)s-dont_use_ipo.patch', + 'Amber-%%(version)s-AT-%s_use_FFTW_FFT_instead_of_PUBFFT_part2.patch' % ambertools_ver, +] +checksums = [ + '3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d', # Amber16.tar.bz2 + '4fbb2cf57d27422949909cc6f7e434c9855333366196a1d539264617c8bc5dec', # AmberTools17.tar.bz2 + '5bf43acaa720815640e54f0872e119dd33bb223e7e1c2f01b459b86efc71ae6e', # Amber-16-AT-17_fix-hardcoding.patch + # Amber-16-AT-17-fix_intel_mpi_compiler_version_detection.patch + '43e79b40388caa2bc14f80acbe72e520b245459dde519d528c07928909dd3c08', + '35fc82573ede194d11090f1df8fdef36d681bf78d2107a495e57a7f1d5ca0b69', # Amber-16-AT-17-fix_mkl_include_path.patch + # Amber-16-AT-17-use_fftw_from_mkl_or_external.patch + 'dc42817ae02ba605a9a74044a0775e9be43fe9d5c8160977da01d68c533b9464', + # Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch + '8a377c87f95756bb072664a77d417eec66912872c4c02e354f4068104ee2a51c', + # Amber-16-AT-17-fix_sander_link_with_external_fftw.patch + '092d70bec83b4383fd2722095026e069acac0f6bf57a9ac8ae030fe537bc64f9', + # Amber-16-AT-17-fix-cpptraj-dont-use-static.patch + '9ae4d6ac172d30a9b3a48992ad4217e8e21336c94107ae2435850c0f77dc0993', + '17bb30c77e204c57cfb6e78f0a7a70994df206d6309f425d83ca0a026323b955', # Amber-16-AT-17_cpptraj_use_mkl_fft.patch + # Amber-16-AT-17-fix_incorrect_omp_directive_rism.patch + '46455dd23f93bdb657f27edc9f92fad503f12048184b926711ee41a6f28b916c', + # Amber-16-AT-17-fix_missing_openmp_at_link.patch + '2116f52b5051eb07cfe74fe5bd751e237d1792c248dc0e5a204a19aea25ed337', + # Amber-16-AT-17-use_CUSTOMBUILDFLAGS_for_nab.patch + '5de8b3e93bd1b36c5d57b64089fc40f14b00c6503fdc7437a005d545c4c16282', + # Amber-16-AT-17-fix_missing_do_parallel_in_checkrismunsupported.patch + '5cf41b908b730efee760e623465e180d8aa93f0c50b688093bd4258cf508eba7', + '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch + '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch + # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch + 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch + 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', + '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch + 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch + # Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch + '129752ba327559951d79abc3d7d15fe919897b063edcd29f79112861bdd8d9ec', +] + +builddependencies = [ + ('flex', '2.6.4') +] + +dependencies = [ + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.14'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('X11', '20171023'), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb new file mode 100644 index 00000000000..d15e0c510e4 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb @@ -0,0 +1,85 @@ +name = 'Amber' +version = '16' +ambertools_ver = '17' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (10, 15) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] +patches = [ + 'Amber-%%(version)s-AT-%s_fix-hardcoding.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_intel_mpi_compiler_version_detection.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_mkl_include_path.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_fftw_from_mkl_or_external.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_FFTW_FFT_instead_of_PUBFFT.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_sander_link_with_external_fftw.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix-cpptraj-dont-use-static.patch' % ambertools_ver, + # Must come after fix-cpptraj-dont-use-static.patch + 'Amber-%%(version)s-AT-%s_cpptraj_use_mkl_fft.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_incorrect_omp_directive_rism.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_openmp_at_link.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_CUSTOMBUILDFLAGS_for_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_do_parallel_in_checkrismunsupported.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_fixed_size_cmd_in_nab.patch' % ambertools_ver, + 'Amber-%(version)s-fix_missing_build_target.patch', + 'Amber-%(version)s-dont_use_ipo.patch', +] +checksums = [ + '3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d', # Amber16.tar.bz2 + '4fbb2cf57d27422949909cc6f7e434c9855333366196a1d539264617c8bc5dec', # AmberTools17.tar.bz2 + '5bf43acaa720815640e54f0872e119dd33bb223e7e1c2f01b459b86efc71ae6e', # Amber-16-AT-17_fix-hardcoding.patch + # Amber-16-AT-17-fix_intel_mpi_compiler_version_detection.patch + '43e79b40388caa2bc14f80acbe72e520b245459dde519d528c07928909dd3c08', + '35fc82573ede194d11090f1df8fdef36d681bf78d2107a495e57a7f1d5ca0b69', # Amber-16-AT-17-fix_mkl_include_path.patch + # Amber-16-AT-17-use_fftw_from_mkl_or_external.patch + 'dc42817ae02ba605a9a74044a0775e9be43fe9d5c8160977da01d68c533b9464', + # Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch + '8a377c87f95756bb072664a77d417eec66912872c4c02e354f4068104ee2a51c', + # Amber-16-AT-17-fix_sander_link_with_external_fftw.patch + '092d70bec83b4383fd2722095026e069acac0f6bf57a9ac8ae030fe537bc64f9', + # Amber-16-AT-17-fix-cpptraj-dont-use-static.patch + '9ae4d6ac172d30a9b3a48992ad4217e8e21336c94107ae2435850c0f77dc0993', + '17bb30c77e204c57cfb6e78f0a7a70994df206d6309f425d83ca0a026323b955', # Amber-16-AT-17_cpptraj_use_mkl_fft.patch + # Amber-16-AT-17-fix_incorrect_omp_directive_rism.patch + '46455dd23f93bdb657f27edc9f92fad503f12048184b926711ee41a6f28b916c', + # Amber-16-AT-17-fix_missing_openmp_at_link.patch + '2116f52b5051eb07cfe74fe5bd751e237d1792c248dc0e5a204a19aea25ed337', + # Amber-16-AT-17-use_CUSTOMBUILDFLAGS_for_nab.patch + '5de8b3e93bd1b36c5d57b64089fc40f14b00c6503fdc7437a005d545c4c16282', + # Amber-16-AT-17-fix_missing_do_parallel_in_checkrismunsupported.patch + '5cf41b908b730efee760e623465e180d8aa93f0c50b688093bd4258cf508eba7', + '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch + '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch + # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch + 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch + 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch +] + +builddependencies = [ + ('flex', '2.6.4') +] + +dependencies = [ + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.14'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('X11', '20171023'), +] + +moduleclass = 'chem' From c9472ce4ba736774186841b79d06ab5fa28b7907 Mon Sep 17 00:00:00 2001 From: jdemeul Date: Tue, 26 Feb 2019 17:39:48 +0000 Subject: [PATCH 0569/5331] removed toolchain specification for STAR --- .../s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb index c33f9318fa8..665b9b48970 100644 --- a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb @@ -24,7 +24,7 @@ checksums = ['229cbf7980496d72de0bfab5bde7148ff3111a99b72c6169d1a04120a52508b4'] dependencies = [ ('Perl', '5.28.0'), ('DB', '18.1.25'), - ('STAR', '2.6.1c', '', ('foss', '2018b')), + ('STAR', '2.6.1c'), ] # these are the perl libraries dependencies From 388fcf98973905a26f77774252e99396c3fbb1ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 19:28:11 +0100 Subject: [PATCH 0570/5331] allow Jellyfish 1.x as extra dep variant since it's required for Kraken 1.0 --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c0129534add..20780841067 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -239,6 +239,8 @@ def check_dep_vars(dep, dep_vars): 'libxc': r'[23]\.', # OPERA requires SAMtools 0.x 'SAMtools': r'0\.', + # Kraken 1.0 requires Jellyfish 1.x + 'Jellyfish': r'1\.', } if dep in old_dep_versions and len(dep_vars) > 1: for key in dep_vars.keys(): From 7c98f91e8b76440ea43803eb21b79b11109eabd4 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 26 Feb 2019 18:56:19 +0000 Subject: [PATCH 0571/5331] fixed wrong version in easyconfig --- .../a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb index 7f1484baf58..9155a701cd1 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'AUGUSTUS' -version = '3.2.3' +version = '3.3.2' versionsuffix = '-Python-2.7.13' homepage = 'http://bioinf.uni-greifswald.de/augustus/' From 79dbc2c0f21ebf5f3bbef0f24425673f558157c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 20:24:19 +0100 Subject: [PATCH 0572/5331] add description + authorship to patch for AUGUSTUS 3.3.2, add SHA256 checksums to easyconfig --- .../a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb | 4 ++++ .../a/AUGUSTUS/AUGUSTUS-3.3.2_fix-hardcoding.patch | 2 ++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb index 9155a701cd1..1e7cdc3b857 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb @@ -15,6 +15,10 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch'] +checksums = [ + '989a95fe3a83d62af4d323a9727d11b2c566adcf4d789d5d86d7b842d83e7671', # augustus-3.3.2.tar.gz + '96e8d72b67e820dca0d6fdbda5b9735dc8259e27fe06167462f2bdbfef5ed7d7', # AUGUSTUS-3.3.2_fix-hardcoding.patch +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_fix-hardcoding.patch b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_fix-hardcoding.patch index 0173fae980b..18bc6ccb967 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_fix-hardcoding.patch +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_fix-hardcoding.patch @@ -1,3 +1,5 @@ +fix hardcoded compiler names in Makefile + don't try to link binaries in /usr/local/bin +author: Kenneth Hoste (HPC-UGent), ported by Maxime Boissonneault (ComputeCanada) diff -ru augustus-3.3.2.orig/auxprogs/bam2wig/Makefile augustus-3.3.2/auxprogs/bam2wig/Makefile --- augustus-3.3.2.orig/auxprogs/bam2wig/Makefile 2019-02-26 14:52:06.899673626 +0000 +++ augustus-3.3.2/auxprogs/bam2wig/Makefile 2019-02-26 15:20:39.258854823 +0000 From df48aa603922f2aa23871cde7c6f3c70b1b02399 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 26 Feb 2019 19:51:56 +0000 Subject: [PATCH 0573/5331] added missing dependencies --- .../a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb index 9155a701cd1..435d8cc00e8 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb @@ -24,6 +24,8 @@ dependencies = [ ('SuiteSparse', '4.5.5', '-ParMETIS-4.0.3'), ('lpsolve', '5.5.2.5'), ('BamTools', '2.4.1'), + ('SAMtools', '1.5'), + ('HTSlib','1.4.1'), ] skipsteps = ['configure'] From 6acdda7bf2523936b2d4145cb73dc667037dcc0e Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 26 Feb 2019 15:09:14 -0600 Subject: [PATCH 0574/5331] Move source_urls within eack package --- ...orch-0.3.1-fosscuda-2017b-Python-2.7.14.eb | 98 +++++++++++++++++++ ...Torch-0.3.1-fosscuda-2017b-Python-3.6.3.eb | 98 +++++++++++++++++++ 2 files changed, 196 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..ef346abc74c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,98 @@ +easyblock = 'PythonPackage' + +name = 'PyTorch' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +pytorchdir = 'pytorch-%(version)s' +extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' + +source_urls = ['https://github.com/pytorch/pytorch/archive'] + +# PyTorch pulls in a bunch of submodules which don't have releases. +# We download the submodule revisions from their repos. +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], + 'download_filename': 'cb002e4eb8d167c2c60fc3bdaae4e1844e0f9353.tar.gz', + 'filename': 'gloo-20180105.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo'), + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': 'ec44c6c1675c25b9827aacd08c02433cccde7780.tar.gz', + 'filename': 'googletest-20160714.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo/third-party/googletest'), + }, + { + 'source_urls': ['https://github.com/nanopb/nanopb/archive'], + 'download_filename': '14efb1a47a496652ab08b1ebcefb0ea24ae4a5e4.tar.gz', + 'filename': 'nanopb-20170723.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/nanopb'), + }, + { + 'source_urls': ['https://github.com/pybind/pybind11/archive'], + 'download_filename': '9f6a636e547fc70a02fa48436449aad67080698f.tar.gz', + 'filename': 'pybind11-20170821.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11'), + }, + { + 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], + 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', + 'filename': 'clang-cindex-python3-20170330.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11/tools/clang'), + }, +] +patches = [ + '%(name)s-%(version)s-cmake.patch', + '%(name)s-%(version)s_skip_MPI_tests.patch', + '%(name)s-%(version)s_fix_findAVX.patch', +] +checksums = [ + 'ee7e5633382bcf9866852e6eaa7bae9000ffb92d6f35605b0031b8d836c4cd94', # v0.3.1.tar.gz + 'c470bccdef90b300e8b50d27e7850cc5789ecd1045a85bd8625088c7c7e47a36', # gloo-20180105.tar.gz + '175a22300b3450e27e5f2e6f95cc9abca74617cbc21a1e0ed19bdfbd22ea0305', # googletest-20160714.tar.gz + '7d18b9bdc10de382da1643c2b1b0227131db47eef89998050b5e0a829d3bd0af', # nanopb-20170723.tar.gz + '3a53dac15e87056a9724b9b6403343b47bb71fec26c090979562f71d7ec9ee98', # pybind11-20170821.tar.gz + '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz + '710bbd38973a94c5c20695d25b819c4b41565bd4723ee4e07542d9537fa2bf18', # PyTorch-0.3.1-cmake.patch + '72c8d6804bff568c2a49b1b7019171c93309a1853a90d5e3abe778f8aa80ca4f', # PyTorch-0.3.1_skip_MPI_tests.patch + '951d5fde89df3be98c1bc6750546259c1b3d0c77574fa3f9e67d9e8fe5b08161', # PyTorch-0.3.1_fix_findAVX.patch +] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('Python', '2.7.14'), + ('PyYAML', '3.12', versionsuffix), + ('magma', '2.3.0'), + ('cuDNN', '7.0.5.15'), +] + +download_dep_fail = True + +# This environment is needed to prevent setup.py from invoking git to determine version. +prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1' + +# you can choice here: either give a list of CUDA cc version or tell it All +# by default it does autodetect of the GPU on the local machine +prebuildopts += ' TORCH_CUDA_ARCH_LIST="3.0 3.2 3.5 3.7 5.0 5.2 5.3 6.0 6.1 7.0"' + +runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' +runtest += '&& cd test && bash run_test.sh' + +options = {'modulename': 'torch'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..38fe1b992bf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,98 @@ +easyblock = 'PythonPackage' + +name = 'PyTorch' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +pytorchdir = 'pytorch-%(version)s' +extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' + +source_urls = ['https://github.com/pytorch/pytorch/archive'] + +# PyTorch pulls in a bunch of submodules which don't have releases. +# We download the submodule revisions from their repos. +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], + 'download_filename': 'cb002e4eb8d167c2c60fc3bdaae4e1844e0f9353.tar.gz', + 'filename': 'gloo-20180105.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo'), + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': 'ec44c6c1675c25b9827aacd08c02433cccde7780.tar.gz', + 'filename': 'googletest-20160714.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo/third-party/googletest'), + }, + { + 'source_urls': ['https://github.com/nanopb/nanopb/archive'], + 'download_filename': '14efb1a47a496652ab08b1ebcefb0ea24ae4a5e4.tar.gz', + 'filename': 'nanopb-20170723.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/nanopb'), + }, + { + 'source_urls': ['https://github.com/pybind/pybind11/archive'], + 'download_filename': '9f6a636e547fc70a02fa48436449aad67080698f.tar.gz', + 'filename': 'pybind11-20170821.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11'), + }, + { + 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], + 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', + 'filename': 'clang-cindex-python3-20170330.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11/tools/clang'), + }, +] +patches = [ + '%(name)s-%(version)s-cmake.patch', + '%(name)s-%(version)s_skip_MPI_tests.patch', + '%(name)s-%(version)s_fix_findAVX.patch', +] +checksums = [ + 'ee7e5633382bcf9866852e6eaa7bae9000ffb92d6f35605b0031b8d836c4cd94', # v0.3.1.tar.gz + 'c470bccdef90b300e8b50d27e7850cc5789ecd1045a85bd8625088c7c7e47a36', # gloo-20180105.tar.gz + '175a22300b3450e27e5f2e6f95cc9abca74617cbc21a1e0ed19bdfbd22ea0305', # googletest-20160714.tar.gz + '7d18b9bdc10de382da1643c2b1b0227131db47eef89998050b5e0a829d3bd0af', # nanopb-20170723.tar.gz + '3a53dac15e87056a9724b9b6403343b47bb71fec26c090979562f71d7ec9ee98', # pybind11-20170821.tar.gz + '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz + '710bbd38973a94c5c20695d25b819c4b41565bd4723ee4e07542d9537fa2bf18', # PyTorch-0.3.1-cmake.patch + '72c8d6804bff568c2a49b1b7019171c93309a1853a90d5e3abe778f8aa80ca4f', # PyTorch-0.3.1_skip_MPI_tests.patch + '951d5fde89df3be98c1bc6750546259c1b3d0c77574fa3f9e67d9e8fe5b08161', # PyTorch-0.3.1_fix_findAVX.patch +] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('Python', '3.6.3'), + ('PyYAML', '3.12', versionsuffix), + ('magma', '2.3.0'), + ('cuDNN', '7.0.5.15'), +] + +download_dep_fail = True + +# This environment is needed to prevent setup.py from invoking git to determine version. +prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1' + +# you can choice here: either give a list of CUDA cc version or tell it All +# by default it does autodetect of the GPU on the local machine +prebuildopts += ' TORCH_CUDA_ARCH_LIST="3.0 3.2 3.5 3.7 5.0 5.2 5.3 6.0 6.1 7.0"' + +runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' +runtest += '&& cd test && bash run_test.sh' + +options = {'modulename': 'torch'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' From 01fc5bda351a62fa10b92c40f92bf43594f44488 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 26 Feb 2019 15:10:42 -0600 Subject: [PATCH 0575/5331] Move source_urls within eack package --- .../PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb | 14 ++++++-------- .../PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb | 14 ++++++-------- 2 files changed, 12 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb index 002c195faa7..ef346abc74c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb @@ -13,40 +13,38 @@ toolchain = {'name': 'fosscuda', 'version': '2017b'} pytorchdir = 'pytorch-%(version)s' extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' -source_urls = [ - 'https://github.com/pytorch/pytorch/archive', - "https://github.com/facebookincubator/gloo/archive", - "https://github.com/google/googletest/archive", - "https://github.com/nanopb/nanopb/archive", - "https://github.com/pybind/pybind11/archive", - "https://github.com/wjakob/clang-cindex-python3/archive", -] +source_urls = ['https://github.com/pytorch/pytorch/archive'] # PyTorch pulls in a bunch of submodules which don't have releases. # We download the submodule revisions from their repos. sources = [ 'v%(version)s.tar.gz', # PyTorch { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], 'download_filename': 'cb002e4eb8d167c2c60fc3bdaae4e1844e0f9353.tar.gz', 'filename': 'gloo-20180105.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo'), }, { + 'source_urls': ['https://github.com/google/googletest/archive'], 'download_filename': 'ec44c6c1675c25b9827aacd08c02433cccde7780.tar.gz', 'filename': 'googletest-20160714.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo/third-party/googletest'), }, { + 'source_urls': ['https://github.com/nanopb/nanopb/archive'], 'download_filename': '14efb1a47a496652ab08b1ebcefb0ea24ae4a5e4.tar.gz', 'filename': 'nanopb-20170723.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/nanopb'), }, { + 'source_urls': ['https://github.com/pybind/pybind11/archive'], 'download_filename': '9f6a636e547fc70a02fa48436449aad67080698f.tar.gz', 'filename': 'pybind11-20170821.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11'), }, { + 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', 'filename': 'clang-cindex-python3-20170330.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11/tools/clang'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb index 4bc5422fdcd..38fe1b992bf 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb @@ -13,40 +13,38 @@ toolchain = {'name': 'fosscuda', 'version': '2017b'} pytorchdir = 'pytorch-%(version)s' extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' -source_urls = [ - 'https://github.com/pytorch/pytorch/archive', - "https://github.com/facebookincubator/gloo/archive", - "https://github.com/google/googletest/archive", - "https://github.com/nanopb/nanopb/archive", - "https://github.com/pybind/pybind11/archive", - "https://github.com/wjakob/clang-cindex-python3/archive", -] +source_urls = ['https://github.com/pytorch/pytorch/archive'] # PyTorch pulls in a bunch of submodules which don't have releases. # We download the submodule revisions from their repos. sources = [ 'v%(version)s.tar.gz', # PyTorch { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], 'download_filename': 'cb002e4eb8d167c2c60fc3bdaae4e1844e0f9353.tar.gz', 'filename': 'gloo-20180105.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo'), }, { + 'source_urls': ['https://github.com/google/googletest/archive'], 'download_filename': 'ec44c6c1675c25b9827aacd08c02433cccde7780.tar.gz', 'filename': 'googletest-20160714.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo/third-party/googletest'), }, { + 'source_urls': ['https://github.com/nanopb/nanopb/archive'], 'download_filename': '14efb1a47a496652ab08b1ebcefb0ea24ae4a5e4.tar.gz', 'filename': 'nanopb-20170723.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/nanopb'), }, { + 'source_urls': ['https://github.com/pybind/pybind11/archive'], 'download_filename': '9f6a636e547fc70a02fa48436449aad67080698f.tar.gz', 'filename': 'pybind11-20170821.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11'), }, { + 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', 'filename': 'clang-cindex-python3-20170330.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11/tools/clang'), From c56ce031cb90fa7133aff25499b9ffdd9524ecac Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 26 Feb 2019 15:11:41 -0600 Subject: [PATCH 0576/5331] Remove accidentally added file --- ...orch-0.3.1-fosscuda-2017b-Python-2.7.14.eb | 98 ------------------- 1 file changed, 98 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb deleted file mode 100644 index ef346abc74c..00000000000 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-2.7.14.eb +++ /dev/null @@ -1,98 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyTorch' -version = '0.3.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://pytorch.org/' -description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. -PyTorch is a deep learning framework that puts Python first.""" - -toolchain = {'name': 'fosscuda', 'version': '2017b'} - -pytorchdir = 'pytorch-%(version)s' -extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' - -source_urls = ['https://github.com/pytorch/pytorch/archive'] - -# PyTorch pulls in a bunch of submodules which don't have releases. -# We download the submodule revisions from their repos. -sources = [ - 'v%(version)s.tar.gz', # PyTorch - { - 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], - 'download_filename': 'cb002e4eb8d167c2c60fc3bdaae4e1844e0f9353.tar.gz', - 'filename': 'gloo-20180105.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo'), - }, - { - 'source_urls': ['https://github.com/google/googletest/archive'], - 'download_filename': 'ec44c6c1675c25b9827aacd08c02433cccde7780.tar.gz', - 'filename': 'googletest-20160714.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo/third-party/googletest'), - }, - { - 'source_urls': ['https://github.com/nanopb/nanopb/archive'], - 'download_filename': '14efb1a47a496652ab08b1ebcefb0ea24ae4a5e4.tar.gz', - 'filename': 'nanopb-20170723.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/nanopb'), - }, - { - 'source_urls': ['https://github.com/pybind/pybind11/archive'], - 'download_filename': '9f6a636e547fc70a02fa48436449aad67080698f.tar.gz', - 'filename': 'pybind11-20170821.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11'), - }, - { - 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], - 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', - 'filename': 'clang-cindex-python3-20170330.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11/tools/clang'), - }, -] -patches = [ - '%(name)s-%(version)s-cmake.patch', - '%(name)s-%(version)s_skip_MPI_tests.patch', - '%(name)s-%(version)s_fix_findAVX.patch', -] -checksums = [ - 'ee7e5633382bcf9866852e6eaa7bae9000ffb92d6f35605b0031b8d836c4cd94', # v0.3.1.tar.gz - 'c470bccdef90b300e8b50d27e7850cc5789ecd1045a85bd8625088c7c7e47a36', # gloo-20180105.tar.gz - '175a22300b3450e27e5f2e6f95cc9abca74617cbc21a1e0ed19bdfbd22ea0305', # googletest-20160714.tar.gz - '7d18b9bdc10de382da1643c2b1b0227131db47eef89998050b5e0a829d3bd0af', # nanopb-20170723.tar.gz - '3a53dac15e87056a9724b9b6403343b47bb71fec26c090979562f71d7ec9ee98', # pybind11-20170821.tar.gz - '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz - '710bbd38973a94c5c20695d25b819c4b41565bd4723ee4e07542d9537fa2bf18', # PyTorch-0.3.1-cmake.patch - '72c8d6804bff568c2a49b1b7019171c93309a1853a90d5e3abe778f8aa80ca4f', # PyTorch-0.3.1_skip_MPI_tests.patch - '951d5fde89df3be98c1bc6750546259c1b3d0c77574fa3f9e67d9e8fe5b08161', # PyTorch-0.3.1_fix_findAVX.patch -] - -builddependencies = [('CMake', '3.9.5')] - -dependencies = [ - ('Python', '2.7.14'), - ('PyYAML', '3.12', versionsuffix), - ('magma', '2.3.0'), - ('cuDNN', '7.0.5.15'), -] - -download_dep_fail = True - -# This environment is needed to prevent setup.py from invoking git to determine version. -prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1' - -# you can choice here: either give a list of CUDA cc version or tell it All -# by default it does autodetect of the GPU on the local machine -prebuildopts += ' TORCH_CUDA_ARCH_LIST="3.0 3.2 3.5 3.7 5.0 5.2 5.3 6.0 6.1 7.0"' - -runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' -runtest += '&& cd test && bash run_test.sh' - -options = {'modulename': 'torch'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' From dd3ddde189c72a9f80c74feb7924994c41f4230f Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 26 Feb 2019 15:12:09 -0600 Subject: [PATCH 0577/5331] Remove accidentally added file --- ...Torch-0.3.1-fosscuda-2017b-Python-3.6.3.eb | 98 ------------------- 1 file changed, 98 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb deleted file mode 100644 index 38fe1b992bf..00000000000 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-fosscuda-2017b-Python-3.6.3.eb +++ /dev/null @@ -1,98 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyTorch' -version = '0.3.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://pytorch.org/' -description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. -PyTorch is a deep learning framework that puts Python first.""" - -toolchain = {'name': 'fosscuda', 'version': '2017b'} - -pytorchdir = 'pytorch-%(version)s' -extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' - -source_urls = ['https://github.com/pytorch/pytorch/archive'] - -# PyTorch pulls in a bunch of submodules which don't have releases. -# We download the submodule revisions from their repos. -sources = [ - 'v%(version)s.tar.gz', # PyTorch - { - 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], - 'download_filename': 'cb002e4eb8d167c2c60fc3bdaae4e1844e0f9353.tar.gz', - 'filename': 'gloo-20180105.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo'), - }, - { - 'source_urls': ['https://github.com/google/googletest/archive'], - 'download_filename': 'ec44c6c1675c25b9827aacd08c02433cccde7780.tar.gz', - 'filename': 'googletest-20160714.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/gloo/third-party/googletest'), - }, - { - 'source_urls': ['https://github.com/nanopb/nanopb/archive'], - 'download_filename': '14efb1a47a496652ab08b1ebcefb0ea24ae4a5e4.tar.gz', - 'filename': 'nanopb-20170723.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/nanopb'), - }, - { - 'source_urls': ['https://github.com/pybind/pybind11/archive'], - 'download_filename': '9f6a636e547fc70a02fa48436449aad67080698f.tar.gz', - 'filename': 'pybind11-20170821.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11'), - }, - { - 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], - 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', - 'filename': 'clang-cindex-python3-20170330.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'torch/lib/pybind11/tools/clang'), - }, -] -patches = [ - '%(name)s-%(version)s-cmake.patch', - '%(name)s-%(version)s_skip_MPI_tests.patch', - '%(name)s-%(version)s_fix_findAVX.patch', -] -checksums = [ - 'ee7e5633382bcf9866852e6eaa7bae9000ffb92d6f35605b0031b8d836c4cd94', # v0.3.1.tar.gz - 'c470bccdef90b300e8b50d27e7850cc5789ecd1045a85bd8625088c7c7e47a36', # gloo-20180105.tar.gz - '175a22300b3450e27e5f2e6f95cc9abca74617cbc21a1e0ed19bdfbd22ea0305', # googletest-20160714.tar.gz - '7d18b9bdc10de382da1643c2b1b0227131db47eef89998050b5e0a829d3bd0af', # nanopb-20170723.tar.gz - '3a53dac15e87056a9724b9b6403343b47bb71fec26c090979562f71d7ec9ee98', # pybind11-20170821.tar.gz - '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz - '710bbd38973a94c5c20695d25b819c4b41565bd4723ee4e07542d9537fa2bf18', # PyTorch-0.3.1-cmake.patch - '72c8d6804bff568c2a49b1b7019171c93309a1853a90d5e3abe778f8aa80ca4f', # PyTorch-0.3.1_skip_MPI_tests.patch - '951d5fde89df3be98c1bc6750546259c1b3d0c77574fa3f9e67d9e8fe5b08161', # PyTorch-0.3.1_fix_findAVX.patch -] - -builddependencies = [('CMake', '3.9.5')] - -dependencies = [ - ('Python', '3.6.3'), - ('PyYAML', '3.12', versionsuffix), - ('magma', '2.3.0'), - ('cuDNN', '7.0.5.15'), -] - -download_dep_fail = True - -# This environment is needed to prevent setup.py from invoking git to determine version. -prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1' - -# you can choice here: either give a list of CUDA cc version or tell it All -# by default it does autodetect of the GPU on the local machine -prebuildopts += ' TORCH_CUDA_ARCH_LIST="3.0 3.2 3.5 3.7 5.0 5.2 5.3 6.0 6.1 7.0"' - -runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' -runtest += '&& cd test && bash run_test.sh' - -options = {'modulename': 'torch'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' From b4d90fac6a00b12ed1c7f9667754e404a6087491 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Tue, 26 Feb 2019 21:55:53 +0000 Subject: [PATCH 0578/5331] fixed styling issues and sanity_check_paths --- .../a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb index 2428b761a4c..7bb040de739 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb @@ -29,7 +29,7 @@ dependencies = [ ('lpsolve', '5.5.2.5'), ('BamTools', '2.4.1'), ('SAMtools', '1.5'), - ('HTSlib','1.4.1'), + ('HTSlib', '1.4.1'), ] skipsteps = ['configure'] @@ -39,7 +39,7 @@ buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CX installopts = 'INSTALLDIR=%(installdir)s' sanity_check_paths = { - 'files': ['bin/aln2wig', 'bin/augustus', 'bin/bam2hints', 'bin/bam2wig', 'bin/espoca', 'bin/etraining', + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/espoca', 'bin/etraining', 'bin/fastBlockSearch', 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', 'bin/load2sqlitedb', 'bin/prepareAlign'], 'dirs': ['config', 'scripts'], From 0d694dc3d82946269751f4aeeac026e14dc39d1d Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 26 Feb 2019 16:12:42 -0600 Subject: [PATCH 0579/5331] adding easyconfigs: RELION-2.1-foss-2017b.eb, RELION-2.1-intel-2017b.eb --- .../r/RELION/RELION-2.1-foss-2017b.eb | 31 ++++++++++++++++++ .../r/RELION/RELION-2.1-intel-2017b.eb | 32 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2017b.eb create mode 100644 easybuild/easyconfigs/r/RELION/RELION-2.1-intel-2017b.eb diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2017b.eb new file mode 100644 index 00000000000..0f43b7a07c4 --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2017b.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'RELION' +version = '2.1' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/3dem/relion/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['08729aac4fa0841e08df2c90a2c26cfe2aef52af2f5fb94a770ed2c11373b886'] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('X11', '20171023'), + ('FLTK', '1.3.4'), +] + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-lpthread' " + +sanity_check_paths = { + 'files': ['bin/relion', 'lib/librelion_gui_lib.%s' % SHLIB_EXT, 'lib/librelion_lib.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.1-intel-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-2.1-intel-2017b.eb new file mode 100644 index 00000000000..0a66dc0fafd --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-2.1-intel-2017b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'RELION' +version = '2.1' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://github.com/3dem/relion/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['08729aac4fa0841e08df2c90a2c26cfe2aef52af2f5fb94a770ed2c11373b886'] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('X11', '20171023'), + ('FLTK', '1.3.4'), + ('FFTW', '3.3.6'), +] + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-lpthread' " + +sanity_check_paths = { + 'files': ['bin/relion', 'lib/librelion_gui_lib.%s' % SHLIB_EXT, 'lib/librelion_lib.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'bio' From b35c15802fc2c22bd1f9ed22e8dcaf0dca8dadb9 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 26 Feb 2019 17:42:31 -0600 Subject: [PATCH 0580/5331] adding easyconfigs: Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb, Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb --- ...da-2017b-AmberTools-17-patchlevel-10-15.eb | 93 +++++++++++++++++++ ...da-2017b-AmberTools-17-patchlevel-10-15.eb | 90 ++++++++++++++++++ 2 files changed, 183 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb new file mode 100644 index 00000000000..75821d5dce7 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb @@ -0,0 +1,93 @@ +name = 'Amber' +version = '16' +ambertools_ver = '17' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (10, 15) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] +patches = [ + 'Amber-%%(version)s-AT-%s_fix-hardcoding.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_intel_mpi_compiler_version_detection.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_mkl_include_path.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_fftw_from_mkl_or_external.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_FFTW_FFT_instead_of_PUBFFT.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_sander_link_with_external_fftw.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix-cpptraj-dont-use-static.patch' % ambertools_ver, + # Must come after fix-cpptraj-dont-use-static.patch + 'Amber-%%(version)s-AT-%s_cpptraj_use_mkl_fft.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_incorrect_omp_directive_rism.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_openmp_at_link.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_CUSTOMBUILDFLAGS_for_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_do_parallel_in_checkrismunsupported.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_fixed_size_cmd_in_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch' % ambertools_ver, + 'Amber-%(version)s-fix_missing_build_target.patch', + 'Amber-%(version)s-dont_use_ipo.patch', + 'Amber-%%(version)s-AT-%s_use_FFTW_FFT_instead_of_PUBFFT_part2.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_allow_cuda9.patch' % ambertools_ver, + 'Amber-%(version)s_test_cuda.patch', +] +checksums = [ + '3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d', # Amber16.tar.bz2 + '4fbb2cf57d27422949909cc6f7e434c9855333366196a1d539264617c8bc5dec', # AmberTools17.tar.bz2 + '5bf43acaa720815640e54f0872e119dd33bb223e7e1c2f01b459b86efc71ae6e', # Amber-16-AT-17_fix-hardcoding.patch + # Amber-16-AT-17-fix_intel_mpi_compiler_version_detection.patch + '43e79b40388caa2bc14f80acbe72e520b245459dde519d528c07928909dd3c08', + '35fc82573ede194d11090f1df8fdef36d681bf78d2107a495e57a7f1d5ca0b69', # Amber-16-AT-17-fix_mkl_include_path.patch + # Amber-16-AT-17-use_fftw_from_mkl_or_external.patch + 'dc42817ae02ba605a9a74044a0775e9be43fe9d5c8160977da01d68c533b9464', + # Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch + '8a377c87f95756bb072664a77d417eec66912872c4c02e354f4068104ee2a51c', + # Amber-16-AT-17-fix_sander_link_with_external_fftw.patch + '092d70bec83b4383fd2722095026e069acac0f6bf57a9ac8ae030fe537bc64f9', + # Amber-16-AT-17-fix-cpptraj-dont-use-static.patch + '9ae4d6ac172d30a9b3a48992ad4217e8e21336c94107ae2435850c0f77dc0993', + '17bb30c77e204c57cfb6e78f0a7a70994df206d6309f425d83ca0a026323b955', # Amber-16-AT-17_cpptraj_use_mkl_fft.patch + # Amber-16-AT-17-fix_incorrect_omp_directive_rism.patch + '46455dd23f93bdb657f27edc9f92fad503f12048184b926711ee41a6f28b916c', + # Amber-16-AT-17-fix_missing_openmp_at_link.patch + '2116f52b5051eb07cfe74fe5bd751e237d1792c248dc0e5a204a19aea25ed337', + # Amber-16-AT-17-use_CUSTOMBUILDFLAGS_for_nab.patch + '5de8b3e93bd1b36c5d57b64089fc40f14b00c6503fdc7437a005d545c4c16282', + # Amber-16-AT-17-fix_missing_do_parallel_in_checkrismunsupported.patch + '5cf41b908b730efee760e623465e180d8aa93f0c50b688093bd4258cf508eba7', + '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch + '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch + # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch + 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch + 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', + '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch + 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch + # Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch + '129752ba327559951d79abc3d7d15fe919897b063edcd29f79112861bdd8d9ec', + '9f57711fe607920a48fcff2f2523230a13fbbb354ab683795247fc6dd8848192', # Amber-16-AT-17_allow_cuda9.patch + 'b870417a0aad5b220dca9f590ec5cf857e06f44b7ee43165c4ace9901ae9a0f7', # Amber-16_test_cuda.patch +] + +builddependencies = [('flex', '2.6.4')] + +dependencies = [ + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.14'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('X11', '20171023'), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb new file mode 100644 index 00000000000..706f5eea615 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb @@ -0,0 +1,90 @@ +name = 'Amber' +version = '16' +ambertools_ver = '17' +# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html +patchlevels = (10, 15) # (AmberTools, Amber) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy + Refinement) is software for performing molecular dynamics and structure + prediction.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] +patches = [ + 'Amber-%%(version)s-AT-%s_fix-hardcoding.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_intel_mpi_compiler_version_detection.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_mkl_include_path.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_fftw_from_mkl_or_external.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_FFTW_FFT_instead_of_PUBFFT.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_sander_link_with_external_fftw.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix-cpptraj-dont-use-static.patch' % ambertools_ver, + # Must come after fix-cpptraj-dont-use-static.patch + 'Amber-%%(version)s-AT-%s_cpptraj_use_mkl_fft.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_incorrect_omp_directive_rism.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_openmp_at_link.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-use_CUSTOMBUILDFLAGS_for_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s-fix_missing_do_parallel_in_checkrismunsupported.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_rism_fftw_lib.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_ignore_X11_checks.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_fix_fixed_size_cmd_in_nab.patch' % ambertools_ver, + 'Amber-%%(version)s-AT-%s_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch' % ambertools_ver, + 'Amber-%(version)s-fix_missing_build_target.patch', + 'Amber-%(version)s-dont_use_ipo.patch', + 'Amber-%%(version)s-AT-%s_allow_cuda9.patch' % ambertools_ver, + 'Amber-%(version)s_test_cuda.patch', +] +checksums = [ + '3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d', # Amber16.tar.bz2 + '4fbb2cf57d27422949909cc6f7e434c9855333366196a1d539264617c8bc5dec', # AmberTools17.tar.bz2 + '5bf43acaa720815640e54f0872e119dd33bb223e7e1c2f01b459b86efc71ae6e', # Amber-16-AT-17_fix-hardcoding.patch + # Amber-16-AT-17-fix_intel_mpi_compiler_version_detection.patch + '43e79b40388caa2bc14f80acbe72e520b245459dde519d528c07928909dd3c08', + '35fc82573ede194d11090f1df8fdef36d681bf78d2107a495e57a7f1d5ca0b69', # Amber-16-AT-17-fix_mkl_include_path.patch + # Amber-16-AT-17-use_fftw_from_mkl_or_external.patch + 'dc42817ae02ba605a9a74044a0775e9be43fe9d5c8160977da01d68c533b9464', + # Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch + '8a377c87f95756bb072664a77d417eec66912872c4c02e354f4068104ee2a51c', + # Amber-16-AT-17-fix_sander_link_with_external_fftw.patch + '092d70bec83b4383fd2722095026e069acac0f6bf57a9ac8ae030fe537bc64f9', + # Amber-16-AT-17-fix-cpptraj-dont-use-static.patch + '9ae4d6ac172d30a9b3a48992ad4217e8e21336c94107ae2435850c0f77dc0993', + '17bb30c77e204c57cfb6e78f0a7a70994df206d6309f425d83ca0a026323b955', # Amber-16-AT-17_cpptraj_use_mkl_fft.patch + # Amber-16-AT-17-fix_incorrect_omp_directive_rism.patch + '46455dd23f93bdb657f27edc9f92fad503f12048184b926711ee41a6f28b916c', + # Amber-16-AT-17-fix_missing_openmp_at_link.patch + '2116f52b5051eb07cfe74fe5bd751e237d1792c248dc0e5a204a19aea25ed337', + # Amber-16-AT-17-use_CUSTOMBUILDFLAGS_for_nab.patch + '5de8b3e93bd1b36c5d57b64089fc40f14b00c6503fdc7437a005d545c4c16282', + # Amber-16-AT-17-fix_missing_do_parallel_in_checkrismunsupported.patch + '5cf41b908b730efee760e623465e180d8aa93f0c50b688093bd4258cf508eba7', + '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch + '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch + # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch + 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch + 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', + '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch + 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch + '9f57711fe607920a48fcff2f2523230a13fbbb354ab683795247fc6dd8848192', # Amber-16-AT-17_allow_cuda9.patch + 'b870417a0aad5b220dca9f590ec5cf857e06f44b7ee43165c4ace9901ae9a0f7', # Amber-16_test_cuda.patch +] + +builddependencies = [('flex', '2.6.4')] + +dependencies = [ + ('netCDF', '4.4.1.1'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.14'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('X11', '20171023'), +] + +moduleclass = 'chem' From e7c55a33e0ebd50185cb2f26bc35b42b5b87ac8d Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 26 Feb 2019 17:44:01 -0600 Subject: [PATCH 0581/5331] Add dependencies --- .../h/HDF5/HDF5-1.10.1-intelcuda-2017b.eb | 21 ++++++++++++ .../netCDF-Fortran-4.4.4-fosscuda-2017b.eb | 18 ++++++++++ .../netCDF-Fortran-4.4.4-intelcuda-2017b.eb | 18 ++++++++++ .../n/netCDF/netCDF-4.4.1.1-fosscuda-2017b.eb | 34 +++++++++++++++++++ .../netCDF/netCDF-4.4.1.1-intelcuda-2017b.eb | 34 +++++++++++++++++++ 5 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intelcuda-2017b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-fosscuda-2017b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intelcuda-2017b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-fosscuda-2017b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intelcuda-2017b.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intelcuda-2017b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intelcuda-2017b.eb new file mode 100644 index 00000000000..f3d31ffc2fd --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-intelcuda-2017b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.1' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-fosscuda-2017b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-fosscuda-2017b.eb new file mode 100644 index 00000000000..e75ab580b10 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-fosscuda-2017b.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.4.4' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['44b1986c427989604df9925dcdbf6c1a977e4ecbde6dd459114bca20bf5e9e67'] + +dependencies = [('netCDF', '4.4.1.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intelcuda-2017b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intelcuda-2017b.eb new file mode 100644 index 00000000000..87cdcddd5d1 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intelcuda-2017b.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.4.4' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['44b1986c427989604df9925dcdbf6c1a977e4ecbde6dd459114bca20bf5e9e67'] + +dependencies = [('netCDF', '4.4.1.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-fosscuda-2017b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-fosscuda-2017b.eb new file mode 100644 index 00000000000..e9020c6e512 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-fosscuda-2017b.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.1.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7f040a0542ed3f6d27f3002b074e509614e18d6c515b2005d1537fec01b24909'] + +dependencies = [ + ('HDF5', '1.10.1'), + ('cURL', '7.56.0'), + ('Szip', '2.1.1'), +] + +builddependencies = [ + ('Autotools', '20170619'), + ('CMake', '3.9.4'), + ('Doxygen', '1.8.13'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intelcuda-2017b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intelcuda-2017b.eb new file mode 100644 index 00000000000..a61613491e4 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1.1-intelcuda-2017b.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.1.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7f040a0542ed3f6d27f3002b074e509614e18d6c515b2005d1537fec01b24909'] + +dependencies = [ + ('HDF5', '1.10.1'), + ('cURL', '7.56.0'), + ('Szip', '2.1.1'), +] + +builddependencies = [ + ('Autotools', '20170619'), + ('CMake', '3.9.4'), + ('Doxygen', '1.8.13'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' From fda8d4ef37e90e88a93ef11c0c4660eaec99ac21 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 26 Feb 2019 18:32:42 -0600 Subject: [PATCH 0582/5331] adding easyconfigs: HTSlib-1.9-iccifort-2017.4.196-GCC-6.4.0-2.28.eb, LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb, LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb --- ...-1.9-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 36 +++++++++++++++++ ...LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb | 40 +++++++++++++++++++ ...oFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb | 40 +++++++++++++++++++ 3 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.9-iccifort-2017.4.196-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.9-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.9-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..95c0b4d2e3d --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.9-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,36 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +## + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.9' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['e04b877057e8b3b8425d957f057b42f0e8509173621d3eccaedd0da607d9929a'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('cURL', '7.56.1'), +] + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..3fa2ff94502 --- /dev/null +++ b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'LoFreq' +version = '2.1.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://csb5.github.io/lofreq' +description = "Fast and sensitive variant calling from next-gen sequencing data" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/CSB5/lofreq/raw/master/dist/'] +sources = ['lofreq_star-%(version)s.tar.gz'] +patches = ['LoFreq-2.1.2_SAMtools-HTSlib.patch'] +checksums = [ + '0caddc6163641993a71c8b94a145debcbf3b63ac969eeaf4fab297ff50817623', # lofreq_star-2.1.3.1.tar.gz + 'aaf195c236eee30ed06efeeea47e8abc3e5dd6eeae8cb69c56c5e128360038e4', # LoFreq-2.1.2_SAMtools-HTSlib.patch +] + +builddependencies = [('HTSlib', '1.9')] +dependencies = [ + ('Python', '2.7.14'), + ('SAMtools', '1.6'), + ('cURL', '7.56.1'), + ('XZ', '5.2.3'), + ('bzip2', '1.0.6'), +] + +# required to fix linking issues with libhts.a +buildopts = 'LIBS="$LIBS -lz -lm -lcurl -llzma -lbz2"' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/lofreq'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('python', "-c 'import lofreq_star'")] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..23d39ac43f0 --- /dev/null +++ b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'LoFreq' +version = '2.1.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://csb5.github.io/lofreq' +description = "Fast and sensitive variant calling from next-gen sequencing data" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://github.com/CSB5/lofreq/raw/master/dist/'] +sources = ['lofreq_star-%(version)s.tar.gz'] +patches = ['LoFreq-2.1.2_SAMtools-HTSlib.patch'] +checksums = [ + '0caddc6163641993a71c8b94a145debcbf3b63ac969eeaf4fab297ff50817623', # lofreq_star-2.1.3.1.tar.gz + 'aaf195c236eee30ed06efeeea47e8abc3e5dd6eeae8cb69c56c5e128360038e4', # LoFreq-2.1.2_SAMtools-HTSlib.patch +] + +builddependencies = [('HTSlib', '1.9')] +dependencies = [ + ('Python', '2.7.14'), + ('SAMtools', '1.6'), + ('cURL', '7.56.1'), + ('XZ', '5.2.3'), + ('bzip2', '1.0.6'), +] + +# required to fix linking issues with libhts.a +buildopts = 'LIBS="$LIBS -lz -lm -lcurl -llzma -lbz2"' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/lofreq'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('python', "-c 'import lofreq_star'")] + +moduleclass = 'bio' From 054723f84971d1732157532e84703adb753b6436 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 27 Feb 2019 09:01:06 +0100 Subject: [PATCH 0583/5331] add comment on version requirement for Jellyfish --- .../easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb index 681800b893d..2f589c1e56f 100644 --- a/easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/k/Kraken/Kraken-1.1-foss-2018b-Perl-5.28.0.eb @@ -28,6 +28,7 @@ checksums = [ dependencies = [ ('Perl', '5.28.0'), + # Jellyfish 1.x is required, see https://github.com/DerrickWood/kraken/issues/69 ('Jellyfish', '1.1.12'), ('wget', '1.20.1'), ] From 9fe3856665c270b8749f56011cd79257bf963fde Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Feb 2019 09:31:17 +0100 Subject: [PATCH 0584/5331] run various checks on easyconfigs that are touched in pull requests and involve Python packages --- test/easyconfigs/easyconfigs.py | 46 +++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c0129534add..178909e7311 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -359,6 +359,51 @@ def check_sha256_checksums(self, changed_ecs): checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) + def check_python_packages(self, changed_ecs): + """Several checks for easyconfigs that install (bundles of) Python packages.""" + + failing_checks = [] + + for ec in changed_ecs: + + ec_fn = os.path.basename(ec.path) + easyblock = ec.get('easyblock') + exts_defaultclass = ec.get('exts_defaultclass') + + download_dep_fail = ec.get('download_dep_fail') + exts_download_dep_fail = ec.get('exts_download_dep_fail') + use_pip = ec.get('use_pip') + + if easyblock == 'PythonPackage': + if not download_dep_fail: + failing_checks.append("'download_dep_fail' set in %s" % ec_fn) + + # download_dep_fail is enabled automatically in PythonBundle easyblock + elif easyblock in ['PythonBundle', 'PythonPackage']: + if not use_pip: + failing_checks.append("'use_pip' set in %s" % ec_fn) + + if download_dep_fail or exts_download_dep_fail: + fail = "'*download_dep_fail' set in %s (shouldn't, since PythonBundle easyblock is used)" % ec_fn + failing_checks.append(fail) + + elif exts_defaultclass == 'PythonPackage': + if easyblock == 'Bundle': + fail = "'PythonBundle' easyblock is used for bundle of Python packages in %s" % ec_fn + failing_checks.append(fail) + else: + exts_default_options = ec.get('exts_default_options', {}) + for key in ['download_dep_fail', 'use_pip']: + if not exts_default_options.get(key): + failing_checks.append("'%s' set in exts_default_options in %s" % (key, ec_fn)) + + # if Python is a dependency, that should be reflected in the versionsuffix + if any(dep['name'] == 'Python' for dep in ec['dependencies']): + if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): + failing_checks.append("'-Python-%(pyver)s' included in versionsuffix in %s" % ec_fn) + + self.assertFalse(failing_checks, '\n'.join(failing_checks)) + def test_changed_files_pull_request(self): """Specific checks only done for the (easyconfig) files that were changed in a pull request.""" @@ -395,6 +440,7 @@ def test_changed_files_pull_request(self): # run checks on changed easyconfigs self.check_sha256_checksums(changed_ecs) + self.check_python_packages(changed_ecs) def test_zzz_cleanup(self): """Dummy test to clean up global temporary directory.""" From 646533c05d0e448601f35a174540ad9adc649c3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Feb 2019 10:16:51 +0100 Subject: [PATCH 0585/5331] cache parsed easyconfig earlier, so checks that rely on cached easyconfigs can always run --- test/easyconfigs/easyconfigs.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 178909e7311..61216386301 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -459,6 +459,9 @@ def template_easyconfig_test(self, spec): ecs = process_easyconfig(spec) if len(ecs) == 1: ec = ecs[0]['ec'] + + # cache the parsed easyconfig, to avoid that it is parsed again + self.parsed_easyconfigs.append(ecs[0]) else: self.assertTrue(False, "easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) @@ -617,9 +620,6 @@ def template_easyconfig_test(self, spec): else: self.assertEqual(orig_val, dumped_val) - # cache the parsed easyconfig, to avoid that it is parsed again - self.parsed_easyconfigs.append(ecs[0]) - # test passed, so set back to True single_tests_ok = True and prev_single_tests_ok From 2a79d0ca8113999df65479f676446d370efa4a1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Feb 2019 10:19:53 +0100 Subject: [PATCH 0586/5331] make sure a parsed easyconfig is found for every changed easyconfig file --- test/easyconfigs/easyconfigs.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 61216386301..32d7608047f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -426,18 +426,24 @@ def test_changed_files_pull_request(self): cmd = "git diff --name-only --diff-filter=AM %s...HEAD" % travis_branch out, ec = run_cmd(cmd, simple=False) changed_ecs_filenames = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith('.eb')] - print("List of changed easyconfig files in this PR: %s" % changed_ecs_filenames) + print("\nList of changed easyconfig files in this PR: %s" % '\n'.join(changed_ecs_filenames)) change_dir(cwd) # grab parsed easyconfigs for changed easyconfig files changed_ecs = [] for ec_fn in changed_ecs_filenames: + match = None for ec in self.parsed_easyconfigs: if os.path.basename(ec['spec']) == ec_fn: - changed_ecs.append(ec['ec']) + match = ec['ec'] break + if match: + changed_ecs.append(match) + else: + self.assertTrue(False, "Failed to find parsed easyconfig for %s" % ec_fn) + # run checks on changed easyconfigs self.check_sha256_checksums(changed_ecs) self.check_python_packages(changed_ecs) From ab6e2a751f2e1b1944c1b9fb3f524e026eb751ce Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 27 Feb 2019 10:41:08 +0100 Subject: [PATCH 0587/5331] Addressed reviewer comments regarding sanity-ckecks in Plumed configs --- .../p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb | 2 +- .../p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb index da556116bef..e7d566d81fe 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb @@ -37,7 +37,7 @@ preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' sanity_check_paths = { 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT, 'lib/plumed/python/plumed.%s' % SHLIB_EXT], - 'dirs': ['lib/plumed'], + 'dirs': , } sanity_check_commands = ["python -c 'import plumed'"] diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb index 58b9a0fbd3c..565914975e6 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb @@ -37,7 +37,7 @@ preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' sanity_check_paths = { 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT, 'lib/plumed/python/plumed.%s' % SHLIB_EXT], - 'dirs': ['lib/plumed'], + 'dirs': , } sanity_check_commands = ["python -c 'import plumed'"] From 8e72251712360f63ad011a04877d9e5f77fd9028 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 27 Feb 2019 10:45:12 +0100 Subject: [PATCH 0588/5331] Second fix for reviewer comment in Plumed configs. --- .../p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb | 2 +- .../p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb index e7d566d81fe..44f0396da97 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-foss-2018b-Python-2.7.15.eb @@ -37,7 +37,7 @@ preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' sanity_check_paths = { 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT, 'lib/plumed/python/plumed.%s' % SHLIB_EXT], - 'dirs': , + 'dirs': [], } sanity_check_commands = ["python -c 'import plumed'"] diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb index 565914975e6..6155652bd02 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.0-fosscuda-2018b-Python-2.7.15.eb @@ -37,7 +37,7 @@ preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' sanity_check_paths = { 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT, 'lib/plumed/python/plumed.%s' % SHLIB_EXT], - 'dirs': , + 'dirs': [], } sanity_check_commands = ["python -c 'import plumed'"] From ef3c98f5d127a5ea55bd86d2b8d5d2985dc1819c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 27 Feb 2019 11:48:20 +0100 Subject: [PATCH 0589/5331] use BLAST+ 2.7.1 for consistency --- easybuild/easyconfigs/c/ChimPipe/ChimPipe-0.9.5-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ChimPipe/ChimPipe-0.9.5-foss-2018b.eb b/easybuild/easyconfigs/c/ChimPipe/ChimPipe-0.9.5-foss-2018b.eb index ed339f69d2e..b96db93c07a 100644 --- a/easybuild/easyconfigs/c/ChimPipe/ChimPipe-0.9.5-foss-2018b.eb +++ b/easybuild/easyconfigs/c/ChimPipe/ChimPipe-0.9.5-foss-2018b.eb @@ -22,7 +22,7 @@ checksums = ['0ab55a0a38dd86845334125459b3961e11e427564ed14b22185c9cc17467c000'] dependencies = [ ('BEDTools', '2.27.1'), ('SAMtools', '0.1.20'), - ('BLAST+', '2.8.1'), + ('BLAST+', '2.7.1'), ] sanity_check_paths = { From 1c92a7e2a41511bd810182dda6108ebcbe29f9e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Feb 2019 13:48:08 +0100 Subject: [PATCH 0590/5331] escaping fix in check_python_packages function --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 32d7608047f..3dc11bbcb22 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -400,7 +400,7 @@ def check_python_packages(self, changed_ecs): # if Python is a dependency, that should be reflected in the versionsuffix if any(dep['name'] == 'Python' for dep in ec['dependencies']): if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): - failing_checks.append("'-Python-%(pyver)s' included in versionsuffix in %s" % ec_fn) + failing_checks.append("'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn) self.assertFalse(failing_checks, '\n'.join(failing_checks)) From c10d91d88a05de9d453b8947f251c6e67fc1d227 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 27 Feb 2019 07:31:16 -0600 Subject: [PATCH 0591/5331] update the cURL version to avoid the conflict --- .../l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb | 2 +- .../l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb index 3fa2ff94502..63b7217d558 100644 --- a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb @@ -21,7 +21,7 @@ builddependencies = [('HTSlib', '1.9')] dependencies = [ ('Python', '2.7.14'), ('SAMtools', '1.6'), - ('cURL', '7.56.1'), + ('cURL', '7.58.0'), ('XZ', '5.2.3'), ('bzip2', '1.0.6'), ] diff --git a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb index 23d39ac43f0..83109b38f03 100644 --- a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb @@ -21,7 +21,7 @@ builddependencies = [('HTSlib', '1.9')] dependencies = [ ('Python', '2.7.14'), ('SAMtools', '1.6'), - ('cURL', '7.56.1'), + ('cURL', '7.58.0'), ('XZ', '5.2.3'), ('bzip2', '1.0.6'), ] From 7d781bebd4bf9d9b0f304f1172de4f5e29b3fcc1 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 08:19:34 -0600 Subject: [PATCH 0592/5331] Add openmp toolchain option --- easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2017b.eb | 1 + easybuild/easyconfigs/r/RELION/RELION-2.1-intel-2017b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2017b.eb index 0f43b7a07c4..42455eed7f7 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2017b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2017b.eb @@ -9,6 +9,7 @@ description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely averages in electron cryo-microscopy (cryo-EM).""" toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'openmp': True} source_urls = ['https://github.com/3dem/relion/archive'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.1-intel-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-2.1-intel-2017b.eb index 0a66dc0fafd..a122d56f5da 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-2.1-intel-2017b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-2.1-intel-2017b.eb @@ -9,6 +9,7 @@ description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely averages in electron cryo-microscopy (cryo-EM).""" toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'openmp': True} source_urls = ['https://github.com/3dem/relion/archive'] sources = ['%(version)s.tar.gz'] From f507d8294dd07c527f556807329b977deec60b04 Mon Sep 17 00:00:00 2001 From: dugan Date: Wed, 27 Feb 2019 15:09:06 +0000 Subject: [PATCH 0593/5331] Added use_pip and changed version to include post0. --- ...MD-5.3.0.post0-intel-2018b-Python-3.6.6.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0.post0-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0.post0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0.post0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..77422c65cd6 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0.post0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '5.3.0.post0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0086cea17590587e8041fe35a2c0c8680975198d798c2b39cdf277354b3b16c8'] + +dependencies = [ + ('Python', '3.6.6'), + ('libjpeg-turbo', '2.0.0'), + ('libpng', '1.6.34'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.9'), + ('freetype', '2.9.1') +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' From 414bd31251b15a657d8de701ef54a68ec3ae163a Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Wed, 27 Feb 2019 15:10:39 +0000 Subject: [PATCH 0594/5331] Delete Pillow-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb Removed file with missing post0 in version. --- ...low-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb deleted file mode 100644 index 76599d0f98b..00000000000 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-5.3.0-intel-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pillow-SIMD' -version = '5.3.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/uploadcare/pillow-simd' -description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. - PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" - -toolchain = {'name': 'intel', 'version': '2018b'} - -source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] -sources = ['v%(version)s.post0.tar.gz'] -checksums = ['0086cea17590587e8041fe35a2c0c8680975198d798c2b39cdf277354b3b16c8'] - -dependencies = [ - ('Python', '3.6.6'), - ('libjpeg-turbo', '2.0.0'), - ('libpng', '1.6.34'), - ('zlib', '1.2.11'), - ('LibTIFF', '4.0.9'), - ('freetype', '2.9.1') -] - -options = {'modulename': 'PIL'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'vis' From 42345cb21f87f56a7eb9c27091644d5d5cc898ec Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 27 Feb 2019 18:12:10 +0200 Subject: [PATCH 0595/5331] adding easyconfigs: gnuplot-5.2.6-foss-2018b.eb --- .../g/gnuplot/gnuplot-5.2.6-foss-2018b.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-foss-2018b.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-foss-2018b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-foss-2018b.eb new file mode 100644 index 00000000000..46ac519c67d --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-foss-2018b.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.2.6' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['35dd8f013139e31b3028fac280ee12d4b1346d9bb5c501586d1b5a04ae7a94ee'] + +dependencies = [ + ('cairo', '1.14.12'), + ('libjpeg-turbo', '2.0.0'), + ('libpng', '1.6.34'), + ('libgd', '2.2.5'), + ('Pango', '1.42.4'), + ('libcerf', '1.7'), + ('Qt5', '5.10.1'), +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' + From 5c0cde6f679630476983998014cf23aae6794fc8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Feb 2019 09:43:46 +0100 Subject: [PATCH 0596/5331] {devel}[foss/2018b] SCons 3.0.4 w/ Python 2.7.15 --- .../SCons-3.0.4-foss-2018b-Python-2.7.15.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-3.0.4-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-3.0.4-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SCons/SCons-3.0.4-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..9f12c717012 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-3.0.4-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '3.0.4' +#versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e2b8b36e25492720a05c0f0a92a219b42d11ce0c51e3397a1e8296dfea1d9b1a'] + +dependencies = [('Python', '2.7.15')] + +#download_dep_fail = True +#use_pip = True + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s/%(name)s'], +} + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' From be5e7d16c5f9e574331258556709294103f66bc6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Feb 2019 14:24:00 +0100 Subject: [PATCH 0597/5331] add patch for SCons to fix installation using 'pip install' --- .../SCons-3.0.4-foss-2018b-Python-2.7.15.eb | 12 ++++--- .../s/SCons/SCons-3.0.4_fix-pip-install.patch | 36 +++++++++++++++++++ 2 files changed, 44 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-3.0.4_fix-pip-install.patch diff --git a/easybuild/easyconfigs/s/SCons/SCons-3.0.4-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SCons/SCons-3.0.4-foss-2018b-Python-2.7.15.eb index 9f12c717012..cda825da254 100644 --- a/easybuild/easyconfigs/s/SCons/SCons-3.0.4-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SCons/SCons-3.0.4-foss-2018b-Python-2.7.15.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'SCons' version = '3.0.4' -#versionsuffix = '-Python-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.scons.org/' description = "SCons is a software construction tool." @@ -11,12 +11,16 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['e2b8b36e25492720a05c0f0a92a219b42d11ce0c51e3397a1e8296dfea1d9b1a'] +patches = ['SCons-%(version)s_fix-pip-install.patch'] +checksums = [ + 'e2b8b36e25492720a05c0f0a92a219b42d11ce0c51e3397a1e8296dfea1d9b1a', # scons-3.0.4.tar.gz + 'c632a50184edbb0dc032943fd717e832577d4ad407eb7743e5331eddb842a69f', # SCons-3.0.4_fix-pip-install.patch +] dependencies = [('Python', '2.7.15')] -#download_dep_fail = True -#use_pip = True +download_dep_fail = True +use_pip = True sanity_check_paths = { 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], diff --git a/easybuild/easyconfigs/s/SCons/SCons-3.0.4_fix-pip-install.patch b/easybuild/easyconfigs/s/SCons/SCons-3.0.4_fix-pip-install.patch new file mode 100644 index 00000000000..ba45cdf7cd6 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-3.0.4_fix-pip-install.patch @@ -0,0 +1,36 @@ +fix installation with pip by using setuptools.{install,setup} rather than distutils.* +author: Kenneth Hoste (HPC-UGent) +loosely inspired by https://bitbucket.org/scons/scons/pull-requests/113 +cfr. https://github.com/SCons/scons/issues/2769 +--- scons-3.0.4/setup.py.orig 2019-01-23 18:30:57.000000000 +0100 ++++ scons-3.0.4/setup.py 2019-02-27 14:07:50.139560710 +0100 +@@ -27,9 +27,8 @@ + import distutils.command.install_scripts + import distutils.command.install_lib + import distutils.command.install_data +-import distutils.command.install +-import distutils.core +-import distutils ++import setuptools.command.install ++import setuptools + # import setuptools + """ + NOTE: Installed SCons is not importable like usual Python packages. It is +@@ -77,7 +76,7 @@ + is_win32 = 1 + + +-_install = distutils.command.install.install ++_install = setuptools.command.install.install + _install_data = distutils.command.install_data.install_data + _install_lib = distutils.command.install_lib.install_lib + _install_scripts = distutils.command.install_scripts.install_scripts +@@ -510,7 +509,7 @@ + 'build_scripts': build_scripts}, + } + +-distutils.core.setup(**arguments) ++setuptools.setup(**arguments) + + if Installed: + for i in Installed: From 062dbb39390078449c294ff76bd00defbf1f49f0 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 27 Feb 2019 18:07:08 +0100 Subject: [PATCH 0598/5331] Update gnuplot-5.2.6-foss-2018b.eb removed blank lines at the end of the file --- easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-foss-2018b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-foss-2018b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-foss-2018b.eb index 46ac519c67d..9c2b6564671 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-foss-2018b.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-foss-2018b.eb @@ -47,4 +47,3 @@ sanity_check_paths = { sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] moduleclass = 'vis' - From 81904935dfae74e5292121cb8f2cebee1bec7f06 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Feb 2019 18:27:29 +0100 Subject: [PATCH 0599/5331] {vis}[intel/2018b] basemap v1.2.0 w/ Python 3.6.6 (+ deps) --- .../basemap-1.2.0-intel-2018b-Python-3.6.6.eb | 42 +++++++++++++++++++ .../GEOS-3.6.2-intel-2018b-Python-3.6.6.eb | 33 +++++++++++++++ .../SWIG-3.0.12-intel-2018b-Python-3.6.6.eb | 21 ++++++++++ 3 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/b/basemap/basemap-1.2.0-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.6.2-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/b/basemap/basemap-1.2.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/basemap/basemap-1.2.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..93282d13a55 --- /dev/null +++ b/easybuild/easyconfigs/b/basemap/basemap-1.2.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'basemap' +version = '1.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org/basemap/' +description = """The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('matplotlib', '3.0.0', versionsuffix), + ('GEOS', '3.6.2', versionsuffix), + ('Pillow', '5.3.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('pyshp', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyshp'], + 'checksums': ['e65c7f24d372b97d0920b864bbeb78322bb37b83f2606e2a2212631d5d51e5c0'], + 'modulename': 'shapefile', + }), + ('pyproj', '1.9.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyproj'], + 'checksums': ['e0c02b1554b20c710d16d673817b2a89ff94738b0b537aead8ecb2edc4c4487b'], + }), + (name, version, { + 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], + 'source_tmpl': 'v%(version)srel.tar.gz', + 'checksums': ['bd5bf305918a2eb675939873b735238f9e3dfe6b5c290e37c41e5b082ff3639a'], + 'prebuildopts': 'GEOS_DIR=$EBROOTGEOS', + 'preinstallopts': 'GEOS_DIR=$EBROOTGEOS', + 'modulename': 'mpl_toolkits.basemap', + }), +] + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.6.2-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.2-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..5528e8c4a44 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.6.2-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.6.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['GEOS-%(version)s_fix-Python3.patch'] +checksums = [ + '045a13df84d605a866602f6020fc6cbf8bf4c42fb50de237a08926e1d7d7652a', # geos-3.6.2.tar.bz2 + 'ce320e5533e407807c0e0599b6cf06e207bc993204b27250bf7e1d0f24160029', # GEOS-3.6.2_fix-Python3.patch +] + +dependencies = [('Python', '3.6.6')] + +builddependencies = [('SWIG', '3.0.12', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..8a2705a2ddd --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,21 @@ +name = 'SWIG' +version = '3.0.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7cf9f447ae7ed1c51722efc45e7f14418d15d7a1e143ac9f09a668999f4fc94d'] + +dependencies = [ + ('Python', '3.6.6'), + ('PCRE', '8.41'), +] + +moduleclass = 'devel' From a9d2ace30a6ccee9a7e4c969fcec80f740dfbefb Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 27 Feb 2019 12:45:29 -0600 Subject: [PATCH 0600/5331] adding easyconfigs: BCFtools-1.6-foss-2017b.eb, HTSlib-1.6-foss-2017b.eb, AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb, AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb and patches: AUGUSTUS-3.3.2_additional_fix_hardcoding.patch --- ...AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb | 55 ++++++++++++++++++ ...UGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb | 58 +++++++++++++++++++ ...STUS-3.3.2_additional_fix_hardcoding.patch | 33 +++++++++++ .../b/BCFtools/BCFtools-1.6-foss-2017b.eb | 31 ++++++++++ .../h/HTSlib/HTSlib-1.6-foss-2017b.eb | 37 ++++++++++++ 5 files changed, 214 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_additional_fix_hardcoding.patch create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.6-foss-2017b.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.6-foss-2017b.eb diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..2b293acc73e --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.3.2' +versionsuffix = '-Python-2.7.14' + +homepage = 'http://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://bioinf.uni-greifswald.de/augustus/binaries/'] +sources = ['augustus-%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fix-hardcoding.patch', + '%(name)s-%(version)s_additional_fix_hardcoding.patch', +] +checksums = [ + '989a95fe3a83d62af4d323a9727d11b2c566adcf4d789d5d86d7b842d83e7671', # augustus-3.3.2.tar.gz + '96e8d72b67e820dca0d6fdbda5b9735dc8259e27fe06167462f2bdbfef5ed7d7', # AUGUSTUS-3.3.2_fix-hardcoding.patch + # AUGUSTUS-3.3.2_additional_fix_hardcoding.patch + 'c42b14d52f4b98584ac9bcf2568c73feca987f563d40628be143ada326e9dccc', +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.65.1', versionsuffix), + ('GSL', '2.4'), + ('SAMtools', '1.6'), + ('HTSlib', '1.6'), + ('BCFtools', '1.6'), + ('tabix', '0.2.6'), + ('lpsolve', '5.5.2.5'), + ('SuiteSparse', '5.1.2', '-METIS-5.1.0'), + ('BamTools', '2.5.1'), + ('SQLite', '3.21.0'), +] + +skipsteps = ['configure'] + +prebuildopts = "make clean && " +buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX"' +installopts = 'INSTALLDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/espoca', 'bin/etraining', + 'bin/fastBlockSearch', 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} + +modextrapaths = {'PATH': 'scripts'} +modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..7ada555706b --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.3.2' +versionsuffix = '-Python-2.7.14' + +homepage = 'http://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [ + 'http://bioinf.uni-greifswald.de/augustus/binaries/', + 'http://bioinf.uni-greifswald.de/augustus/binaries/old/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_fix-hardcoding.patch', + '%(name)s-%(version)s_additional_fix_hardcoding.patch', +] +checksums = [ + '989a95fe3a83d62af4d323a9727d11b2c566adcf4d789d5d86d7b842d83e7671', # augustus-3.3.2.tar.gz + '96e8d72b67e820dca0d6fdbda5b9735dc8259e27fe06167462f2bdbfef5ed7d7', # AUGUSTUS-3.3.2_fix-hardcoding.patch + # AUGUSTUS-3.3.2_additional_fix_hardcoding.patch + 'c42b14d52f4b98584ac9bcf2568c73feca987f563d40628be143ada326e9dccc', +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.65.1', versionsuffix), + ('GSL', '2.4'), + ('SAMtools', '1.6'), + ('HTSlib', '1.6'), + ('BCFtools', '1.6'), + ('tabix', '0.2.6'), + ('lpsolve', '5.5.2.5'), + ('SuiteSparse', '5.1.2', '-METIS-5.1.0'), + ('BamTools', '2.5.1'), + ('SQLite', '3.21.0'), +] + +skipsteps = ['configure'] + +prebuildopts = "unset LDFLAGS && unset LIBS && " +buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX"' +installopts = 'INSTALLDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/espoca', 'bin/etraining', + 'bin/fastBlockSearch', 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} + +modextrapaths = {'PATH': 'scripts'} +modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_additional_fix_hardcoding.patch b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_additional_fix_hardcoding.patch new file mode 100644 index 00000000000..8f1ea64fe25 --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_additional_fix_hardcoding.patch @@ -0,0 +1,33 @@ +fix the additional hardcoded compiler options that are making trouble. + +diff -Naur augustus-3.3.2.ori/auxprogs/bam2hints/Makefile augustus-3.3.2/auxprogs/bam2hints/Makefile +--- augustus-3.3.2.ori/auxprogs/bam2hints/Makefile 2019-02-26 13:31:59.005083190 -0600 ++++ augustus-3.3.2/auxprogs/bam2hints/Makefile 2019-02-27 11:58:22.100807318 -0600 +@@ -8,13 +8,13 @@ + # Last modified: 09-October-2015 by Katharina J. Hoff + + # Variable definition +-INCLUDES = /usr/include/bamtools ++INCLUDES = $(EBROOTBAMTOOLS)/include/bamtools + LIBS = -lbamtools -lz + SOURCES = bam2hints.cc + OBJECTS = $(SOURCES:.cc=.o) + CXXFLAGS += -Wall -O2 # -g -p -g -ggdb + +-LINK.cc = g++ ++LINK.cc = $(CXX) + + # Recipe(s) + # $@: full target name of current target. +diff -Naur augustus-3.3.2.ori/auxprogs/filterBam/src/Makefile augustus-3.3.2/auxprogs/filterBam/src/Makefile +--- augustus-3.3.2.ori/auxprogs/filterBam/src/Makefile 2019-02-26 13:31:59.004083210 -0600 ++++ augustus-3.3.2/auxprogs/filterBam/src/Makefile 2019-02-27 12:23:43.812006140 -0600 +@@ -8,7 +8,7 @@ + printElapsedTime.cc sumMandIOperations.cc sumDandIOperations.cc PairednessCoverage.cc + PROGRAM = filterBam + OBJECTS = $(SOURCES:.cc=.o) +-BAMTOOLS = /usr/include/bamtools ++BAMTOOLS = $(EBROOTBAMTOOLS)/include/bamtools + INCLUDES = -I$(BAMTOOLS) -Iheaders -I./bamtools + LIBS = -lbamtools -lz + CFLAGS = -std=c++0x diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.6-foss-2017b.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.6-foss-2017b.eb new file mode 100644 index 00000000000..c38d6e3237c --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.6-foss-2017b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.6' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['293010736b076cf684d2873928924fcc3d2c231a091084c2ac23a8045c7df982'] + +dependencies = [ + ('zlib', '1.2.11'), + ('HTSlib', '1.6'), + ('GSL', '2.4'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['libexec/bcftools'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.6-foss-2017b.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.6-foss-2017b.eb new file mode 100644 index 00000000000..b9902791427 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.6-foss-2017b.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.6' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9588be8be0c2390a87b7952d644e7a88bead2991b3468371347965f2e0504ccb'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('cURL', '7.56.0'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From c000c2fc59af29ced99740618d5aa3280916529e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Feb 2019 16:39:06 +0100 Subject: [PATCH 0601/5331] {bio,devel}[foss/2018b] MetaBAT v2.12.1, SCons v3.0.4 w/ Python 2.7.15 --- ...MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb | 36 +++++++++++++++++++ .../MetaBAT-2.12.1_fix-prepend-PATH.patch | 14 ++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1_fix-prepend-PATH.patch diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..ef0c0f0fd99 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,36 @@ +easyblock = 'SCons' + +name = 'MetaBAT' +version = '2.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/berkeleylab/metabat' +description = "An efficient tool for accurately reconstructing single genomes from complex microbial communities" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] +sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-%(version)s_fix-prepend-PATH.patch'] +checksums = [ + 'e3aca0656f56f815135521360dc56667ec26af25143c3a31d645fef1a96abbc2', # v2.12.1.tar.gz + '5735d2661f1b890688029ccccf24d278c71ece9d6c603ced442327010de1287b', # MetaBAT-2.12.1_fix-prepend-PATH.patch +] + +builddependencies = [('SCons', '3.0.4', versionsuffix)] + +dependencies = [ + ('Python', '2.7.15'), + ('Boost', '1.67.0'), + ('zlib', '1.2.11'), + ('SAMtools', '1.9'), +] + +prebuildopts = "ln -s $EBROOTSAMTOOLS samtools && " + +sanity_check_paths = { + 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1_fix-prepend-PATH.patch b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1_fix-prepend-PATH.patch new file mode 100644 index 00000000000..0f0d328931e --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1_fix-prepend-PATH.patch @@ -0,0 +1,14 @@ +prepend to $PATH rather than append, to avoid picking up system compiler (g++) +author: Kenneth Hoste (HPC-UGent) +see also https://bitbucket.org/berkeleylab/metabat/issues/52 +--- berkeleylab-metabat-37db58fe3fda/SConstruct.orig 2017-09-01 07:28:02.000000000 +0200 ++++ berkeleylab-metabat-37db58fe3fda/SConstruct 2019-02-26 16:13:03.150132631 +0100 +@@ -7,7 +7,7 @@ + def ENV_update(tgt_ENV, src_ENV): + for K in src_ENV.keys(): + if K in tgt_ENV.keys() and K in [ 'PATH', 'LD_LIBRARY_PATH', 'LIB', 'INCLUDE' ]: +- tgt_ENV[K]=SCons.Util.AppendPath(tgt_ENV[K], src_ENV[K]) ++ tgt_ENV[K]=SCons.Util.PrependPath(tgt_ENV[K], src_ENV[K]) + else: + tgt_ENV[K]=src_ENV[K] + From da25df66525e23454aa8b7b2ba2630a0c5812825 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 14:38:21 -0600 Subject: [PATCH 0602/5331] adding easyconfigs: MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb, MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb --- ...-Engine-R2018b-foss-2017b-Python-2.7.14.eb | 35 +++++++++++++++++++ ...B-Engine-R2018b-foss-2017b-Python-3.6.3.eb | 35 +++++++++++++++++++ .../easyconfigs/m/MATLAB/MATLAB-2018b.eb | 24 +++++++++++++ 3 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..86cd4fe9460 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = 'R2018b' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [ + ('Python', '2.7.14'), + ('MATLAB', '2018b', '', True) +] + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. + +prebuildopts = 'cd $EBROOTMATLAB/extern/engines/python && ' +buildopts = '--build-base=%(builddir)s install --prefix=%(installdir)s' + +skipsteps = ['install'] + +options = {'modulename': 'matlab.engine'} + +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..043aae0dc70 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = 'R2018b' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [ + ('Python', '3.6.3'), + ('MATLAB', '2018b', '', True) +] + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. + +prebuildopts = 'cd $EBROOTMATLAB/extern/engines/python && ' +buildopts = '--build-base=%(builddir)s install --prefix=%(installdir)s' + +skipsteps = ['install'] + +options = {'modulename': 'matlab.engine'} + +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb new file mode 100644 index 00000000000..c93645d2d0f --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb @@ -0,0 +1,24 @@ +name = 'MATLAB' +version = '2018b' + +homepage = 'http://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# be sure to copy both DVD content to the SAME directory, +# including the hidden files, especially .dvd1 and .dvd2 +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ba2b6c2c5af656d317df7c8478f5568bfe89f39c193d49a2b17949d009759622'] + +dependencies = [('Java', '1.8')] + +license_server = 'my-license-server' +license_server_port = '1234' +key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} + +moduleclass = 'math' From 5cdd3da10c45977bfd0f82ba92fe4c442d604dbd Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 14:40:58 -0600 Subject: [PATCH 0603/5331] Corrected version --- easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb index c93645d2d0f..f28bcf43901 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb @@ -1,5 +1,5 @@ name = 'MATLAB' -version = '2018b' +version = 'R2018b' homepage = 'http://www.mathworks.com/products/matlab' description = """MATLAB is a high-level language and interactive environment From f28b3c8d18b4d10d605c27b44091492f81f5bc0c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 14:44:51 -0600 Subject: [PATCH 0604/5331] Delete file for replacement --- .../easyconfigs/m/MATLAB/MATLAB-2018b.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb deleted file mode 100644 index f28bcf43901..00000000000 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'MATLAB' -version = 'R2018b' - -homepage = 'http://www.mathworks.com/products/matlab' -description = """MATLAB is a high-level language and interactive environment - that enables you to perform computationally intensive tasks faster than with - traditional programming languages such as C, C++, and Fortran.""" - -toolchain = {'name': 'dummy', 'version': ''} - -# be sure to copy both DVD content to the SAME directory, -# including the hidden files, especially .dvd1 and .dvd2 -sources = [SOURCELOWER_TAR_GZ] -checksums = ['ba2b6c2c5af656d317df7c8478f5568bfe89f39c193d49a2b17949d009759622'] - -dependencies = [('Java', '1.8')] - -license_server = 'my-license-server' -license_server_port = '1234' -key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' - -modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} - -moduleclass = 'math' From c9e86a316b7f6dbda474093fa5f9969e57059467 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 14:47:31 -0600 Subject: [PATCH 0605/5331] Added correct MATLAB easyconfig file --- .../easyconfigs/m/MATLAB/MATLAB-R2018b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb new file mode 100644 index 00000000000..b32089d2eb4 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb @@ -0,0 +1,23 @@ +name = 'MATLAB' +version = 'R2018b' + +homepage = 'http://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# be sure to copy both DVD content to the SAME directory, +# including the hidden files, especially .dvd1 and .dvd2 +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Java', '1.8')] + +license_server = 'my-license-server' +license_server_port = '1234' +key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} + +moduleclass = 'math' From da14fe5192197468a3a7625c96b4f04e62f2b753 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 14:48:12 -0600 Subject: [PATCH 0606/5331] Use same version for MATLAB --- .../MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb | 2 +- .../MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb index 86cd4fe9460..2aa91866b2a 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('MATLAB', '2018b', '', True) + ('MATLAB', version, '', True) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb index 043aae0dc70..a8fedb1365b 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('MATLAB', '2018b', '', True) + ('MATLAB', version, '', True) ] # Since this setup.py does not provide a separate --build-base for the install From 63609848a2007249ec690b1734b82b3496f086c0 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 14:50:54 -0600 Subject: [PATCH 0607/5331] Flesh out MATLAB easyconfig file --- .../easyconfigs/m/MATLAB/MATLAB-R2018b.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb deleted file mode 100644 index b32089d2eb4..00000000000 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'MATLAB' -version = 'R2018b' - -homepage = 'http://www.mathworks.com/products/matlab' -description = """MATLAB is a high-level language and interactive environment - that enables you to perform computationally intensive tasks faster than with - traditional programming languages such as C, C++, and Fortran.""" - -toolchain = {'name': 'dummy', 'version': ''} - -# be sure to copy both DVD content to the SAME directory, -# including the hidden files, especially .dvd1 and .dvd2 -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('Java', '1.8')] - -license_server = 'my-license-server' -license_server_port = '1234' -key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' - -modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} - -moduleclass = 'math' From 1b400af3b10b287b3f2c71c6a89f2cffa69b5cb8 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 14:52:33 -0600 Subject: [PATCH 0608/5331] Add intel versions --- ...Engine-R2018b-intel-2017b-Python-2.7.14.eb | 35 +++++++++++++++++++ ...-Engine-R2018b-intel-2017b-Python-3.6.3.eb | 35 +++++++++++++++++++ .../easyconfigs/m/MATLAB/MATLAB-R2018b.eb | 23 ++++++++++++ 3 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..e39e592445f --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = 'R2018b' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [ + ('Python', '2.7.14'), + ('MATLAB', version, '', True) +] + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. + +prebuildopts = 'cd $EBROOTMATLAB/extern/engines/python && ' +buildopts = '--build-base=%(builddir)s install --prefix=%(installdir)s' + +skipsteps = ['install'] + +options = {'modulename': 'matlab.engine'} + +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..3798c7c47c7 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = 'R2018b' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [ + ('Python', '3.6.3'), + ('MATLAB', version, '', True) +] + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. + +prebuildopts = 'cd $EBROOTMATLAB/extern/engines/python && ' +buildopts = '--build-base=%(builddir)s install --prefix=%(installdir)s' + +skipsteps = ['install'] + +options = {'modulename': 'matlab.engine'} + +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb new file mode 100644 index 00000000000..b32089d2eb4 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb @@ -0,0 +1,23 @@ +name = 'MATLAB' +version = 'R2018b' + +homepage = 'http://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# be sure to copy both DVD content to the SAME directory, +# including the hidden files, especially .dvd1 and .dvd2 +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Java', '1.8')] + +license_server = 'my-license-server' +license_server_port = '1234' +key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} + +moduleclass = 'math' From 6865a282ecbba83e41e140f6e7b4160a3b536468 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 14:52:59 -0600 Subject: [PATCH 0609/5331] Getting rid of MATLAB again --- .../easyconfigs/m/MATLAB/MATLAB-R2018b.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb deleted file mode 100644 index b32089d2eb4..00000000000 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'MATLAB' -version = 'R2018b' - -homepage = 'http://www.mathworks.com/products/matlab' -description = """MATLAB is a high-level language and interactive environment - that enables you to perform computationally intensive tasks faster than with - traditional programming languages such as C, C++, and Fortran.""" - -toolchain = {'name': 'dummy', 'version': ''} - -# be sure to copy both DVD content to the SAME directory, -# including the hidden files, especially .dvd1 and .dvd2 -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('Java', '1.8')] - -license_server = 'my-license-server' -license_server_port = '1234' -key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' - -modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} - -moduleclass = 'math' From 2be71e301d2f3fa837a4a2f929cc54a1cea02dc6 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 14:53:43 -0600 Subject: [PATCH 0610/5331] adding easyconfigs: MATLAB-R2018b.eb --- .../easyconfigs/m/MATLAB/MATLAB-R2018b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb new file mode 100644 index 00000000000..b32089d2eb4 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb @@ -0,0 +1,23 @@ +name = 'MATLAB' +version = 'R2018b' + +homepage = 'http://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = {'name': 'dummy', 'version': ''} + +# be sure to copy both DVD content to the SAME directory, +# including the hidden files, especially .dvd1 and .dvd2 +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Java', '1.8')] + +license_server = 'my-license-server' +license_server_port = '1234' +key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} + +moduleclass = 'math' From a63b2264c8ca00c1cb321155e541350f3c7e9959 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 16:08:00 -0600 Subject: [PATCH 0611/5331] adding easyconfigs: RAxML-8.2.11-foss-2017b-hybrid-avx2.eb, RAxML-8.2.11-foss-2017b-hybrid-avx.eb, RAxML-8.2.11-foss-2017b-hybrid-sse3.eb, RAxML-8.2.11-intel-2017b-hybrid-avx.eb, RAxML-8.2.11-intel-2017b-hybrid-sse3.eb --- .../RAxML-8.2.11-foss-2017b-hybrid-avx.eb | 28 +++++++++++++++++++ .../RAxML-8.2.11-foss-2017b-hybrid-avx2.eb | 28 +++++++++++++++++++ .../RAxML-8.2.11-foss-2017b-hybrid-sse3.eb | 28 +++++++++++++++++++ .../RAxML-8.2.11-intel-2017b-hybrid-avx.eb | 28 +++++++++++++++++++ .../RAxML-8.2.11-intel-2017b-hybrid-sse3.eb | 28 +++++++++++++++++++ 5 files changed, 140 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-avx.eb create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-avx2.eb create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-sse3.eb create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-intel-2017b-hybrid-avx.eb create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-intel-2017b-hybrid-sse3.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-avx.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-avx.eb new file mode 100644 index 00000000000..4524b7c8106 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-avx.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.11' +versionsuffix = '-hybrid-avx' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['23470ddd1f96255b28f1d2bd0462c9c232122fa4a8f996dd10a6371c80b16f0b'] + +buildopts = '-f Makefile.AVX.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-avx2.eb new file mode 100644 index 00000000000..6f70125328a --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-avx2.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.11' +versionsuffix = '-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['23470ddd1f96255b28f1d2bd0462c9c232122fa4a8f996dd10a6371c80b16f0b'] + +buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-sse3.eb new file mode 100644 index 00000000000..7561795ba98 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-foss-2017b-hybrid-sse3.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.11' +versionsuffix = '-hybrid-sse3' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['23470ddd1f96255b28f1d2bd0462c9c232122fa4a8f996dd10a6371c80b16f0b'] + +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-SSE3"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-SSE3 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-intel-2017b-hybrid-avx.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-intel-2017b-hybrid-avx.eb new file mode 100644 index 00000000000..28dd1f888c6 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-intel-2017b-hybrid-avx.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.11' +versionsuffix = '-hybrid-avx' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['23470ddd1f96255b28f1d2bd0462c9c232122fa4a8f996dd10a6371c80b16f0b'] + +buildopts = '-f Makefile.AVX.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-intel-2017b-hybrid-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-intel-2017b-hybrid-sse3.eb new file mode 100644 index 00000000000..da63bc9f2c0 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.11-intel-2017b-hybrid-sse3.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.11' +versionsuffix = '-hybrid-sse3' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['23470ddd1f96255b28f1d2bd0462c9c232122fa4a8f996dd10a6371c80b16f0b'] + +buildopts = '-f Makefile.SSE3.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-SSE3"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-SSE3 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +moduleclass = 'bio' From 14fd996a85afed90963fd31edf913c845fd787d4 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 27 Feb 2019 17:50:17 -0600 Subject: [PATCH 0612/5331] Make Travis happy --- easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb index b32089d2eb4..2d4d57aa5f8 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb @@ -16,7 +16,7 @@ dependencies = [('Java', '1.8')] license_server = 'my-license-server' license_server_port = '1234' -key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' +key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} From 3bd776511d20510ad3693d546dabc6b1632fe0e2 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Thu, 28 Feb 2019 11:38:23 +0100 Subject: [PATCH 0613/5331] Attempt to write eb for recent PCMSolver --- ...PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..730cb4b72e6 --- /dev/null +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'PCMSolver' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pcmsolver.readthedocs.org' +description = """An API for the Polarizable Continuum Model.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +#toolchainopts = {'cstd': 'c99'} + +source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d1ef6bdc268a2e719b36c85125c3543df7a26e1a738daf4483f4ded0c76f5b60'] + +dependencies = [ + ('Python', '3.6.6'), + ('zlib', '1.2.11'), + ('Boost', '1.67.0'), +] + +builddependencies = [ + ('CMake', '3.12.1'), + ('Eigen', '3.3.7', '', True), +] + +configopts = '-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN' +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS $LIBLAPACK_MT"' + +separate_build_dir = True + +runtest = 'test' + +postinstallcmds = ["chmod +x %(installdir)s/bin/pcmsolver.py"] + +sanity_check_paths = { + 'files': ['bin/pcmsolver.py', 'lib/libpcm.a', 'lib/libpcm.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'chem' From 3dcd6e3a0a4318f1d789ab383ec391a331e8e771 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Thu, 28 Feb 2019 12:11:52 +0100 Subject: [PATCH 0614/5331] Dependencies for upcomming PSI4-1.3 --- .../c/CheMPS2/CheMPS2-1.8.9-foss-2018b.eb | 31 ++++++++++ .../c/CheMPS2/CheMPS2-1.8.9-intel-2018b.eb | 31 ++++++++++ .../deepdiff-3.3.0-foss-2018b-Python-3.6.6.eb | 32 +++++++++++ ...deepdiff-3.3.0-intel-2018b-Python-3.6.6.eb | 32 +++++++++++ .../networkx-2.2-foss-2018b-Python-3.3.6.eb | 24 ++++++++ .../networkx-2.2-intel-2018b-Python-3.3.6.eb | 24 ++++++++ .../pytest-4.3.0-foss-2018b-Python-3.6.6.eb | 56 +++++++++++++++++++ .../pytest-4.3.0-intel-2018b-Python-3.6.6.eb | 56 +++++++++++++++++++ 8 files changed, 286 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2018b.eb create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2018b.eb create mode 100644 easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.3.6.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.3.6.eb create mode 100644 easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2018b.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2018b.eb new file mode 100644 index 00000000000..90f6c396925 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2018b.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.8.9' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ccd4c0d9432759d97690bf37a0333440f93513960c62d1f75842f090406a224d'] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('HDF5', '1.10.2') +] + +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2018b.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2018b.eb new file mode 100644 index 00000000000..c3c7728d4b1 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2018b.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.8.9' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ccd4c0d9432759d97690bf37a0333440f93513960c62d1f75842f090406a224d'] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('HDF5', '1.10.2') +] + +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..8780f5f56e1 --- /dev/null +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'deepdiff' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://deepdiff.readthedocs.io/en/latest/' +description = """DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [('Python', '3.6.6')] + +use_pip = True + +exts_list = [ + ('jsonpickle', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpickle/'], + 'checksums': ['d43ede55b3d9b5524a8e11566ea0b11c9c8109116ef6a509a1b619d2041e7397'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/deepdiff/'], + 'checksums': ['ecad8e16a96ffd27e8f40c9801a6ab16ec6a7e7e6e6859a7710ba4695f22702c'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..e89c0c39417 --- /dev/null +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-3.3.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'deepdiff' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://deepdiff.readthedocs.io/en/latest/' +description = """DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [('Python', '3.6.6')] + +use_pip = True + +exts_list = [ + ('jsonpickle', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpickle/'], + 'checksums': ['d43ede55b3d9b5524a8e11566ea0b11c9c8109116ef6a509a1b619d2041e7397'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/deepdiff/'], + 'checksums': ['ecad8e16a96ffd27e8f40c9801a6ab16ec6a7e7e6e6859a7710ba4695f22702c'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.3.6.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.3.6.eb new file mode 100644 index 00000000000..3c92fd21541 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.3.6.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] +checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] + +dependencies = [('Python', '3.6.6')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.3.6.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.3.6.eb new file mode 100644 index 00000000000..508508d61f8 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.3.6.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] +checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] + +dependencies = [('Python', '3.6.6')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..4f596e9570a --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'pytest' +version = '4.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [('Python', '3.6.6')] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('py', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], + }), + ('attrs', '18.2.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], + }), + ('pluggy', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], + }), + ('atomicwrites', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], + }), + ('more-itertools', '5.0.0', { + 'modulename': 'more_itertools', + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + 'checksums': ['067a1d4bf827ffdd56ad21bd46674703fce77c5957f6c1eef731f6146bfcef1c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..143b517439e --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'pytest' +version = '4.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [('Python', '3.6.6')] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('py', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], + }), + ('attrs', '18.2.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], + }), + ('pluggy', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], + }), + ('atomicwrites', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], + }), + ('more-itertools', '5.0.0', { + 'modulename': 'more_itertools', + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + 'checksums': ['067a1d4bf827ffdd56ad21bd46674703fce77c5957f6c1eef731f6146bfcef1c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' From 2d15411a7b70a9c2a9e3707ec0bc6300cf1c0f0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Feb 2019 12:32:10 +0100 Subject: [PATCH 0615/5331] {bio}[intel/2018b] MinPath v1.4 w/ Python 2.7.15 --- .../MinPath-1.4-intel-2018b-Python-2.7.15.eb | 45 +++++++++++++++++++ .../MinPath/MinPath-1.4_fix-glpsol-path.patch | 21 +++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/m/MinPath/MinPath-1.4_fix-glpsol-path.patch diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..b42977cad42 --- /dev/null +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.4-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,45 @@ +easyblock = 'Tarball' + +name = 'MinPath' +version = '1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://omics.informatics.indiana.edu/MinPath' +description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions + using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological + pathways for a query dataset.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['http://omics.informatics.indiana.edu/mg/get.php?justdoit=yes&software='] +sources = ['minpath%(version)s.tar.gz'] +patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] +checksums = [ + '665e90b5ee7fa5837d13b1145cdf3eafa691d25c1ce4bb76847dfa771ff24551', # minpath1.4.tar.gz + '35ac9d18ec5e2d6e2345de708236ed12cddcccbd8fc0c5a3652ecd838dc57822', # MinPath-1.4_fix-glpsol-path.patch +] + +dependencies = [ + ('Python', '2.7.15'), + ('GLPK', '4.65'), +] + +# remove included old GLPK copy +postinstallcmds = ["rm -rf %(installdir)s/glpk-*"] + +sanity_check_paths = { + 'files': ['MinPath%(version)s.py'], + 'dirs': [], +} + +sanity_check_commands = [ + "MinPath%(version)s.py -ko examples/demo.ko -report /dev/null -details /dev/null", + "MinPath%(version)s.py -fig examples/demo.fig -report /dev/null -details /dev/null", + "MinPath%(version)s.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", +] + +modextrapaths = {'PATH': ''} + +modextravars = {'MinPath': '%(installdir)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.4_fix-glpsol-path.patch b/easybuild/easyconfigs/m/MinPath/MinPath-1.4_fix-glpsol-path.patch new file mode 100644 index 00000000000..820835d3136 --- /dev/null +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.4_fix-glpsol-path.patch @@ -0,0 +1,21 @@ +patch MinPath*.py script to use glpsol provided through GLPK dependency rather than included one +author: Kenneth Hoste (HPC-UGent) +--- MinPath/MinPath1.4.py.orig 2019-02-28 12:23:26.875861180 +0100 ++++ MinPath/MinPath1.4.py 2019-02-28 12:22:47.142287000 +0100 +@@ -19,6 +19,7 @@ + import math + + minpath = os.environ.get('MinPath') ++glpkroot = os.getenv("EBROOTGLPK") + path0 = "/u/yye/Pathways/MinPath" + if minpath or os.path.exists(path0): + if os.path.exists(path0): +@@ -26,7 +27,7 @@ + else: + sys.exit("Environment variable MinPath not set") + +-keggPath0, seedPath0, mapPath0, glpsol0 = minpath + "/data", minpath + "/data", minpath + "/data", minpath + "/glpk-4.6/examples/glpsol" ++keggPath0, seedPath0, mapPath0, glpsol0 = minpath + "/data", minpath + "/data", minpath + "/data", glpkroot + "/bin/glpsol" + + def intmatrix(dim1, dim2): + mat = [] From 1e0c7dc16ccea0c6631e47d8f98e5c0f04373523 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Feb 2019 12:37:30 +0100 Subject: [PATCH 0616/5331] also include easyconfig for MinPath 1.4 using foss/2018b --- .../MinPath-1.4-foss-2018b-Python-2.7.15.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/MinPath/MinPath-1.4-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.4-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.4-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..e514b613d9e --- /dev/null +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.4-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,45 @@ +easyblock = 'Tarball' + +name = 'MinPath' +version = '1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://omics.informatics.indiana.edu/MinPath' +description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions + using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological + pathways for a query dataset.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://omics.informatics.indiana.edu/mg/get.php?justdoit=yes&software='] +sources = ['minpath%(version)s.tar.gz'] +patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] +checksums = [ + '665e90b5ee7fa5837d13b1145cdf3eafa691d25c1ce4bb76847dfa771ff24551', # minpath1.4.tar.gz + '35ac9d18ec5e2d6e2345de708236ed12cddcccbd8fc0c5a3652ecd838dc57822', # MinPath-1.4_fix-glpsol-path.patch +] + +dependencies = [ + ('Python', '2.7.15'), + ('GLPK', '4.65'), +] + +# remove included old GLPK copy +postinstallcmds = ["rm -rf %(installdir)s/glpk-*"] + +sanity_check_paths = { + 'files': ['MinPath%(version)s.py'], + 'dirs': [], +} + +sanity_check_commands = [ + "MinPath%(version)s.py -ko examples/demo.ko -report /dev/null -details /dev/null", + "MinPath%(version)s.py -fig examples/demo.fig -report /dev/null -details /dev/null", + "MinPath%(version)s.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", +] + +modextrapaths = {'PATH': ''} + +modextravars = {'MinPath': '%(installdir)s'} + +moduleclass = 'bio' From 6dcd99adc6594e75ff2ec9ab00b0109c5e884cfe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Feb 2019 12:58:22 +0100 Subject: [PATCH 0617/5331] adding easyconfigs: PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb --- .../PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb | 100 ++++++++++++++++++ 1 file changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..caba299740c --- /dev/null +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,100 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'PRINSEQ' +version = '0.20.4' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://prinseq.sourceforge.net' +description = """A bioinformatics tool to PRe-process and show INformation of SEQuence data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/'] +sources = ['%(namelower)s-lite-%(version)s.tar.gz'] +checksums = ['9b5e0dce3b7f02f09e1cc7e8a2dd77c0b133e5e35529d570ee901f53ebfeb56f'] + +dependencies = [ + ('Perl', '5.28.0'), +] + +# these are the perl libraries dependencies +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::Depends', '0.405', { + 'source_tmpl': 'ExtUtils-Depends-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['8ad6401ad7559b03ceda1fe4b191c95f417bdec7c542a984761a4656715a8a2c'], + }), + ('ExtUtils::PkgConfig', '1.16', { + 'source_tmpl': 'ExtUtils-PkgConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e'], + }), + ('Pod::Usage', '1.69', { + 'source_tmpl': 'Pod-Usage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + 'checksums': ['1a920c067b3c905b72291a76efcdf1935ba5423ab0187b9a5a63cfc930965132'], + }), + ('Cairo', '1.106', { + 'source_tmpl': 'Cairo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['e64803018bc7cba49e73e258547f5378cc4249797beafec524852140f49c45c4'], + }), + ('Statistics::PCA', '0.0.1', { + 'source_tmpl': 'Statistics-PCA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSTH/'], + 'checksums': ['f8adb10b00232123d103a5b49161ad46370f47fe0f752e5462a4dc15f9d46bc4'], + }), + ('MIME::Base64', '3.15', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + 'checksums': ['7f863566a6a9cb93eda93beadb77d9aa04b9304d769cea3bb921b9a91b3a1eb9'], + }), + ('Math::Cephes::Matrix', '0.5305', { + 'source_tmpl': 'Math-Cephes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['561a800a4822e748d2befc366baa4b21e879a40cc00c22293c7b8736caeb83a1'], + }), + ('Math::MatrixReal', '2.13', { + 'source_tmpl': 'Math-MatrixReal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LETO/'], + 'checksums': ['4f9fa1a46dd34d2225de461d9a4ed86932cdd821c121fa501a15a6d4302fb4b2'], + }), + ('Text::SimpleTable', '2.07', { + 'source_tmpl': 'Text-SimpleTable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRAMBERG/'], + 'checksums': ['256d3f38764e96333158b14ab18257b92f3155c60d658cafb80389f72f4619ed'], + }), + ('Contextual::Return', '0.004014', { + 'source_tmpl': 'Contextual-Return-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'], + 'checksums': ['09fe1415e16e49a69e13c0ef6e6a4a3fd8b856f389d3f3e624d7ab3b71719f78'], + }), +] + +# this is the script which relies in many extra Perl libraries so we verify it's working fine +sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl'] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +postinstallcmds = [ + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", + "chmod +x %(installdir)s/*.pl", +] + +sanity_check_paths = { + 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], + 'dirs': [] +} + +moduleclass = 'bio' From cb83e185ce35fc7821e099df2f54aafa08592c69 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 28 Feb 2019 12:59:23 +0100 Subject: [PATCH 0618/5331] Update the fix in nab.c for fixed sized buffers. There where more buffers that needed fixing. --- ...r-16-AT-17_fix_fixed_size_cmd_in_nab.patch | 172 +++++++++++++++--- 1 file changed, 148 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch index 6f7205f0625..b4873564377 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch +++ b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch @@ -1,61 +1,105 @@ -Fix the size command in nab. +Fix incorrect use of fixed sized buffers. -Åke Sandgren, 20180405 -diff -ru amber16.orig.patched/AmberTools/src/nab/nab.c amber16/AmberTools/src/nab/nab.c ---- amber16.orig.patched/AmberTools/src/nab/nab.c 2017-04-13 15:00:53.000000000 +0200 -+++ amber16/AmberTools/src/nab/nab.c 2018-04-05 10:20:55.267295948 +0200 -@@ -233,8 +233,9 @@ +Åke Sandgren, 20190228 +diff -ru amber16.orig/AmberTools/src/nab/nab.c amber16/AmberTools/src/nab/nab.c +--- amber16.orig/AmberTools/src/nab/nab.c 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/nab/nab.c 2019-02-28 12:51:07.844183899 +0100 +@@ -128,8 +128,8 @@ + char cpp_ofname[ 256 ]; + + char cmd[ 1024 ]; +- char *fields[ 256 ]; +- int nfields; ++ char **fields; ++ int nfields, i; + int cpp_ofd, n2c_ofd; + int status; + char *amberhome; +@@ -169,7 +169,7 @@ + amberhome, cppstring, amberhome, + argv[ ac ] ? argv[ ac ] : "" ); + if( cgdopt ) fprintf( stderr, "cpp cmd: %s\n", cmd ); +- nfields = split( cmd, fields, " " ); ++ nfields = split( cmd, &fields, " " ); + + #ifndef USE_MKSTEMP + if( (cpp_ofd = +@@ -205,7 +205,7 @@ + nodebug ? "-nodebug" : "", + argv[ ac ] ? argv[ ac ] : "" ); + if( cgdopt ) fprintf( stderr, "nab2c cmd: %s\n", cmd ); +- nfields = split( cmd, fields, " " ); ++ nfields = split( cmd, &fields, " " ); + + status = execute( fields, cpp_ofd, n2c_ofd, 2 ); + unlink( cpp_ofname ); +@@ -213,6 +213,10 @@ + unlink( n2c_ofname ); + fprintf( stderr, "nab2c failed!\n" ); exit(1); + } ++ for (i = 0; i < nfields; i++) { ++ free(fields[i]); ++ } ++ free(fields); + } + } + unlink( n2c_ofname ); +@@ -233,20 +237,28 @@ { int ac; char *dotp, *amberhome; - char cmd[ 1024 ], word[ 1024 ]; -+ char *cmd, word[ 1024 ]; - char *fields[256]; +- char *fields[256]; ++#define WORDSZ 1024 ++ char *cmd, word[ WORDSZ ]; ++ char **fields; + int cmd_sz; int status; - int nfields; +- int nfields; ++ int nfields, i; -@@ -243,10 +244,16 @@ + amberhome = (char *) getenv("AMBERHOME"); + if( amberhome == NULL ){ fprintf( stderr, "AMBERHOME is not set!\n" ); exit(1); } -+ cmd_sz = 1024; ++ cmd_sz = WORDSZ; + cmd = malloc(cmd_sz); sprintf( cmd, "%s -I%s/include", CC, amberhome ); if( aopt ){ #ifdef AVSDIR sprintf( word, " -I%s/include", AVSDIR ); + if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { -+ cmd_sz += 1024; ++ cmd_sz += WORDSZ; + cmd = realloc(cmd, cmd_sz); + } strcat( cmd, word ); #else fprintf( stderr, "-avs not supported.\n" ); -@@ -257,9 +264,17 @@ +@@ -257,9 +269,17 @@ dotp = strrchr( argv[ ac ], '.' ); strcpy( &dotp[ 1 ], "c" ); sprintf( word, " %s", argv[ ac ] ); + if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { -+ cmd_sz += 1024; ++ cmd_sz += WORDSZ; + cmd = realloc(cmd, cmd_sz); + } strcat( cmd, word ); }else if( argv[ ac ] ){ sprintf( word, " %s", argv[ ac ] ); + if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { -+ cmd_sz += 1024; ++ cmd_sz += WORDSZ; + cmd = realloc(cmd, cmd_sz); + } strcat( cmd, word ); } } -@@ -268,12 +283,25 @@ +@@ -268,71 +288,100 @@ if( aopt ){ sprintf( word, " -L%s/lib -lflow_c -lgeom -lutil", AVSDIR ); + if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { -+ cmd_sz += 1024; ++ cmd_sz += WORDSZ; + cmd = realloc(cmd, cmd_sz); + } strcat( cmd, word ); @@ -63,24 +107,104 @@ diff -ru amber16.orig.patched/AmberTools/src/nab/nab.c amber16/AmberTools/src/na #endif sprintf( word, " -L%s/lib -lnab -lcifparse", amberhome ); + if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { -+ cmd_sz += 1024; ++ cmd_sz += WORDSZ; + cmd = realloc(cmd, cmd_sz); + } strcat( cmd, word ); - sprintf( word, " %s ", FLIBS ); +- sprintf( word, " %s ", FLIBS ); +- strcat( cmd, word ); ++ /* FLIBS can be very big and there is no need to copy it into word first. */ + /* Make sure there is space enough for the " -lm" too */ -+ if (strlen(cmd) + strlen(word) + 5 > cmd_sz) { -+ cmd_sz += 1024; ++ if (strlen(cmd) + strlen(FLIBS) + 6 > cmd_sz) { ++ cmd_sz += strlen(FLIBS) + 6; + cmd = realloc(cmd, cmd_sz); + } - strcat( cmd, word ); ++ strcat( cmd, " " ); ++ strcat( cmd, FLIBS ); strcat( cmd, " -lm" ); } -@@ -283,6 +311,7 @@ + if( cgdopt ) fprintf( stderr, "cc cmd: %s\n", cmd ); +- nfields = split(cmd,fields," "); ++ nfields = split(cmd, &fields, " "); + status = execute(fields, 0, 1, 2); if (status != 0) { fprintf(stderr,"cc failed!\n"); exit (1); } ++ for (i = 0; i < nfields; i++) { ++ free(fields[i]); ++ } ++ free(fields); + free(cmd); } - static int split( char str[], char *fields[], char *fsep ) +-static int split( char str[], char *fields[], char *fsep ) ++static int split( char str[], char ***fields, char *fsep ) + { +- int nf, flen; ++ int nf, flen, maxnf; + char *sp, *fp, *efp, *nfp; + + if( !str ) + return( 0 ); + ++ maxnf = 10; ++ *fields = (char **) malloc(sizeof(char *) * maxnf); + /* Use fsep of white space is special */ + if( strspn( fsep, " \t\n" ) ){ + for( nf = 0, sp = str; ; ){ + fp = sp + strspn( sp, fsep ); + if( !*fp ) + return( nf ); ++ if (nf + 1 > maxnf) { ++ maxnf += 10; ++ *fields = (char **) realloc(*fields, sizeof(char *) * maxnf); ++ } + if( (efp = strpbrk( fp, fsep )) ){ + if( !( flen = efp - fp ) ) + return( nf ); + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strncpy( nfp, fp, flen ); + nfp[ flen ] = '\0'; +- fields[ nf ] = nfp; ++ (*fields)[ nf ] = nfp; + sp = efp; +- fields[++nf] = NULL; ++ (*fields)[++nf] = NULL; + }else{ + flen = strlen( fp ); + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strcpy( nfp, fp ); +- fields[ nf ] = nfp; +- fields[++nf]=NULL; ++ (*fields)[ nf ] = nfp; ++ (*fields)[++nf]=NULL; + return( nf ); + } + } + }else{ + for( nf = 0, sp = str; ; ){ ++ if (nf + 1 > maxnf) { ++ maxnf += 10; ++ *fields = (char **) realloc(*fields, sizeof(char *) * maxnf); ++ } + if( (fp = strchr( sp, *fsep )) ){ + flen = fp - sp; + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strncpy( nfp, sp, flen ); + nfp[ flen ] = '\0'; +- fields[ nf ] = nfp; +- fields[++nf]=NULL; ++ (*fields)[ nf ] = nfp; ++ (*fields)[++nf]=NULL; + sp = fp + 1; + }else{ + flen = strlen( sp ); + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strcpy( nfp, sp ); +- fields[ nf ] = nfp; +- fields[++nf] = NULL; ++ (*fields)[ nf ] = nfp; ++ (*fields)[++nf] = NULL; + return( nf ); + } + } From 3bd7bb87d6f7f53f85a19c4b88a0476d1cfe5b1d Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Thu, 28 Feb 2019 13:05:49 +0100 Subject: [PATCH 0619/5331] Removed wrong files --- .../networkx-2.2-foss-2018b-Python-3.3.6.eb | 24 ------------------- .../networkx-2.2-intel-2018b-Python-3.3.6.eb | 24 ------------------- 2 files changed, 48 deletions(-) delete mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.3.6.eb delete mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.3.6.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.3.6.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.3.6.eb deleted file mode 100644 index 3c92fd21541..00000000000 --- a/easybuild/easyconfigs/n/networkx/networkx-2.2-foss-2018b-Python-3.3.6.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'networkx' -version = '2.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/networkx' -description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, - and functions of complex networks.""" - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_ZIP] -checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] - -dependencies = [('Python', '3.6.6')] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.3.6.eb b/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.3.6.eb deleted file mode 100644 index 508508d61f8..00000000000 --- a/easybuild/easyconfigs/n/networkx/networkx-2.2-intel-2018b-Python-3.3.6.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'networkx' -version = '2.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/networkx' -description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, - and functions of complex networks.""" - -toolchain = {'name': 'intel', 'version': '2018b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_ZIP] -checksums = ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'] - -dependencies = [('Python', '3.6.6')] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' From e7e904a78b5eedd9aaf1ca9ad3db189e9cfc9442 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Feb 2019 13:18:02 +0100 Subject: [PATCH 0620/5331] adding easyconfigs: AMOS-3.1.0-foss-2018b.eb --- .../a/AMOS/AMOS-3.1.0-foss-2018b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2018b.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2018b.eb new file mode 100644 index 00000000000..aa2a5d0b010 --- /dev/null +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2018b.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'AMOS' +version = '3.1.0' + +homepage = 'http://amos.sourceforge.net' +description = """The AMOS consortium is committed to the development of open-source whole genome assembly software""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True, 'cstd': 'c++98'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['AMOS-%(version)s_GCC-4.7.patch'] +checksums = [ + '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b', # amos-3.1.0.tar.gz + '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844', # AMOS-3.1.0_GCC-4.7.patch +] + +dependencies = [ + ('expat', '2.2.5'), + ('MUMmer', '4.0.0beta2'), +] + +sanity_check_paths = { + 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], + 'dirs': [] +} + +parallel = 1 # make crashes otherwise + +moduleclass = 'bio' From ad798cb6e72378188440827542518f6c861247e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Feb 2019 13:36:24 +0100 Subject: [PATCH 0621/5331] adding easyconfigs: MaxBin-2.2.6-foss-2018b-Perl-5.28.0.eb, FragGeneScan-1.31-foss-2018b.eb --- .../FragGeneScan-1.31-foss-2018b.eb | 26 ++++++++++++++ .../MaxBin-2.2.6-foss-2018b-Perl-5.28.0.eb | 36 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-foss-2018b.eb create mode 100644 easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.6-foss-2018b-Perl-5.28.0.eb diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-foss-2018b.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-foss-2018b.eb new file mode 100644 index 00000000000..599bdfc11a5 --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-foss-2018b.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.31' + +homepage = 'http://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' + +files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FragGeneScan', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.6-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.6-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..b4a2bbcb4e0 --- /dev/null +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.6-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'MaxBin' +version = '2.2.6' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html' +description = """MaxBin is software for binning assembled metagenomic sequences based on + an Expectation-Maximization algorithm.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2fdef85a7af175c605be51dd7b410087bf2602945ca692521c06c24d0c90cd30'] + +dependencies = [ + ('Perl', '5.28.0'), + ('Bowtie2', '2.3.4.2'), + ('FragGeneScan', '1.31'), + ('HMMER', '3.2.1'), + ('IDBA-UD', '1.1.3'), +] + +prebuildopts = "cd src && " + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['run_MaxBin.pl', 'src/MaxBin'], + 'dirs': [], +} + +modextrapaths = {'PATH': ['', 'src']} + +moduleclass = 'bio' From 7bba9987139674f9fb2d87261845dbe3f7bd1620 Mon Sep 17 00:00:00 2001 From: ebtest Date: Thu, 28 Feb 2019 12:51:34 +0000 Subject: [PATCH 0622/5331] adding easyconfigs: StringTie-1.3.5-GCCcore-8.2.0.eb --- .../StringTie-1.3.5-GCCcore-8.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..9721dbb7e51 --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '1.3.5' + +homepage = 'http://ccb.jhu.edu/software/%(namelower)/' +description = "StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://ccb.jhu.edu/software/%(namelower)s/dl/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f16ec07d4869b7656bc1a9b6eb662fd9404c122d18431c845e93d810840c5db9'] + +builddependencies = [('binutils', '2.31.1', '', True)] + +dependencies = [ + ('zlib', '1.2.11'), +] + +# release option must be given to 'make' otherwise a DEBUG version is built by default +buildopts = " release" + +files_to_copy = [(['%(namelower)s'], 'bin'), 'README', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 38f8238c51e2354e46f1c1c51d77a839d5c68604 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Thu, 28 Feb 2019 14:01:06 +0100 Subject: [PATCH 0623/5331] Change Bundle to PythonBundle --- .../p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb | 2 +- .../p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb index 4f596e9570a..92755ba6186 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'pytest' version = '4.3.0' diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb index 143b517439e..db21839705a 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'pytest' version = '4.3.0' From 198c61ac52ed159132da75d4aeea8f252d6fee7d Mon Sep 17 00:00:00 2001 From: ebtest Date: Thu, 28 Feb 2019 13:16:33 +0000 Subject: [PATCH 0624/5331] adding easyconfigs: gffcompare-0.10.6-GCCcore-7.3.0.eb, gffread-0.10.6-GCCcore-7.3.0.eb --- .../gffcompare-0.10.6-GCCcore-7.3.0.eb | 31 +++++++++++++++++++ .../g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..00c2c78b719 --- /dev/null +++ b/easybuild/easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'gffcompare' +version = '0.10.6' + +homepage = 'https://github.com/gpertea/%(namelower)s' +description = """gffcompare provides classification and reference annotation mapping and + matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['e75cc9fff42cea2d02752bd96e0e0451b268384247606e0e27193d15f4a54477'] + +buildopts = " release" + +files_to_copy = ['%(namelower)s', 'LICENSE', 'README.md'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s -v'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..97984d513f6 --- /dev/null +++ b/easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'gffread' +version = '0.10.6' + +homepage = 'https://github.com/gpertea/%(name)s' +description = """GFF/GTF parsing utility providing format conversions, +region filtering, FASTA sequence extraction and more.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['760b7c61542dc65caec0e7551e51fa43c0b2e0da536d8e2f37a472ac285a04e1'] + +buildopts = " release" + +files_to_copy = ['%(namelower)s', 'LICENSE'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s '] + +moduleclass = 'bio' From 1ca320766cf3d9acd434723a8d42862f738070ae Mon Sep 17 00:00:00 2001 From: ebtest Date: Thu, 28 Feb 2019 15:35:36 +0000 Subject: [PATCH 0625/5331] add binutils as builddep --- .../easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb | 2 ++ easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb index 00c2c78b719..dea44605fe8 100644 --- a/easybuild/easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb @@ -15,6 +15,8 @@ source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] sources = ['%(namelower)s-%(version)s.tar.gz'] checksums = ['e75cc9fff42cea2d02752bd96e0e0451b268384247606e0e27193d15f4a54477'] +builddependencies = [('binutils', '2.30')] + buildopts = " release" files_to_copy = ['%(namelower)s', 'LICENSE', 'README.md'] diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb index 97984d513f6..4d8b5173e3c 100644 --- a/easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb @@ -15,6 +15,8 @@ source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] sources = ['%(namelower)s-%(version)s.tar.gz'] checksums = ['760b7c61542dc65caec0e7551e51fa43c0b2e0da536d8e2f37a472ac285a04e1'] +builddependencies = [('binutils', '2.30')] + buildopts = " release" files_to_copy = ['%(namelower)s', 'LICENSE'] From 66f733e08f6fa937e9793dc13557f624f65e4b2e Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Thu, 28 Feb 2019 16:44:33 +0100 Subject: [PATCH 0626/5331] Fix old bundle lines for pytest --- .../p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb | 6 +----- .../p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb | 6 +----- 2 files changed, 2 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb index 92755ba6186..afa87efe8b5 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-foss-2018b-Python-3.6.6.eb @@ -11,11 +11,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [('Python', '3.6.6')] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('py', '1.8.0', { diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb index db21839705a..00903c9ef46 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.3.0-intel-2018b-Python-3.6.6.eb @@ -11,11 +11,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} dependencies = [('Python', '3.6.6')] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('py', '1.8.0', { From 1f6b7fe344357040629dc1f2a92798cf4187d742 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Thu, 28 Feb 2019 17:32:17 +0100 Subject: [PATCH 0627/5331] Add libxc 4.3.3 --- .../l/libxc/libxc-4.3.3-foss-2018b.eb | 26 +++++++++++++++++++ .../l/libxc/libxc-4.3.3-intel-2018b.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb new file mode 100644 index 00000000000..782a22b3efb --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '4.3.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +sources = [SOURCE_TAR_GZ] + +configopts = '--enable-static --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb new file mode 100644 index 00000000000..fb1340a035a --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '4.3.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] + +configopts = '--enable-static --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' From 52920e10dcb687b8f48867f8405aee386dd38516 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Feb 2019 18:09:12 +0100 Subject: [PATCH 0628/5331] {bio}[foss/2018b] SqueezeMeta v0.4.3 w/ Python 2.7.15 (WIP) --- ...eezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb | 70 +++++++++++++++++++ .../SqueezeMeta-0.4.3_fix-hardcoding.patch | 54 ++++++++++++++ 2 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3_fix-hardcoding.patch diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..81d52b96174 --- /dev/null +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,70 @@ +easyblock = 'Tarball' + +name = 'SqueezeMeta' +version = '0.4.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jtamames/SqueezeMeta' +description = """SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, + covering all steps of the analysis.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/jtamames/SqueezeMeta/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['SqueezeMeta-%(version)s_fix-hardcoding.patch'] +checksums = [ + 'd08911dcbfd4c244118e6414f36639781b9bb84ddfba83cba1157825f9a93a87', # v0.4.3.tar.gz + '91e9116ec63a9a655be3706530e6ce710826186ed6b7aa245ee189888cc77463', # SqueezeMeta-0.4.3_fix-hardcoding.patch +] + +dependencies = [ + ('Perl', '5.28.0'), + ('XML-LibXML', '2.0132', '-Perl-%(perlver)s'), + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), + ('Pysam', '0.15.1', versionsuffix), + ('R', '3.5.1', '-Python-%(pyver)s'), + ('BLAST+', '2.7.1'), + ('BWA', '0.7.17'), + ('barrnap', '0.9'), + ('CD-HIT', '4.6.8'), + ('CheckM', '1.0.13', '-Python-%(pyver)s'), + ('DAS_Tool', '1.1.1', '-R-%(rver)s-Python-%(pyver)s'), # depends on prodigal & pullseq + ('DIAMOND', '0.9.22'), + ('MEGAHIT', '1.1.4', versionsuffix), + ('minimap2', '2.13'), + ('Java', '1.8', '', True), + ('RDP-Classifier', '2.12', '-Java-%(javaver)s', True), + ('MetaBAT', '2.12.1', versionsuffix), + ('MinPath', '1.4', versionsuffix), # depends on GPLK (which provides glpsol) + ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), + ('Trimmomatic', '0.38', '-Java-%(javaver)s', True), + ('AMOS', '3.1.0'), + ('MaxBin', '2.2.6', '-Perl-%(perlver)s'), + ('SPAdes', '3.13.0'), + ('Bowtie2', '2.3.4.2'), + ('canu', '1.8', '-Perl-%(perlver)s'), + ('HMMER', '3.2.1'), + ('MEGAHIT', '1.1.4', versionsuffix), + ('MUMmer', '4.0.0beta2'), + ('pplacer', '1.1.alpha19', '', True), +] + +keepsymlinks = True + +postinstallcmds = [ + # remove vendored tools that are include as dependencies + "rm -r %(installdir)s/bin/*", + # fix shebang in Perl scripts + "ls %(installdir)s/scripts/*.pl | xargs sed -i 's@#!/usr/bin/perl@#!/usr/bin/env perl@g'", +] + +sanity_check_paths = { + 'files': ['scripts/SqueezeMeta.pl'], + 'dirs': ['scripts/preparing_databases'], +} + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3_fix-hardcoding.patch b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3_fix-hardcoding.patch new file mode 100644 index 00000000000..ed896b7b651 --- /dev/null +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3_fix-hardcoding.patch @@ -0,0 +1,54 @@ +fix hardcoded paths, rely on specified dependencies via $PATH and $EBROOT* +author: Kenneth Hoste (HPC-UGent) +--- scripts/SqueezeMeta_conf_original.pl.orig 2019-02-28 15:28:10.248411000 +0100 ++++ scripts/SqueezeMeta_conf_original.pl 2019-02-28 17:31:01.568977000 +0100 +@@ -78,26 +78,26 @@ + + #-- External software + +-$metabat_soft="$installpath/bin/metabat2"; +-$maxbin_soft="$installpath/bin/MaxBin/run_MaxBin.pl"; +-$spades_soft="$installpath/bin/SPAdes/spades.py"; +-$barrnap_soft="$installpath/bin/barrnap"; +-$rdpclassifier_soft="java -jar $installpath/bin/classifier.jar"; +-$bowtie2_build_soft="$installpath/bin/bowtie2/bowtie2-build"; +-$bowtie2_x_soft="$installpath/bin/bowtie2/bowtie2"; +-$bwa_soft = "$installpath/bin/bwa"; +-$minimap2_soft = "$installpath/bin/minimap2"; +-$bedtools_soft="$installpath/bin/bedtools"; #-- IMPORTANT! Needs version <0.24 +-$diamond_soft="$installpath/bin/diamond"; +-$hmmer_soft="$installpath/bin/hmmer/hmmsearch"; +-$megahit_soft="$installpath/bin/megahit/megahit"; +-$prinseq_soft="$installpath/bin/prinseq-lite.pl"; +-$prodigal_soft="$installpath/bin/prodigal"; +-$cdhit_soft="$installpath/bin/cd-hit-est"; +-$toamos_soft="$installpath/bin/AMOS/toAmos"; +-$minimus2_soft="$installpath/bin/AMOS/minimus2"; +-$checkm_soft="$installpath/bin/checkm"; +-$minpath_soft="python $installpath/bin/MinPath1.4.py"; +-$canu_soft="$installpath/bin/canu/canu"; +-$trimmomatic_soft="java -jar $installpath/bin/trimmomatic-0.38.jar"; +-$dastool_soft="$installpath/bin/DAS_Tool/DAS_Tool"; ++$metabat_soft="metabat2"; ++$maxbin_soft="run_MaxBin.pl"; ++$spades_soft="spades.py"; ++$barrnap_soft="barrnap"; ++$rdpclassifier_soft="java -jar $ENV{'EBROOTRDPMINCLASSIFIER'}/dist/classifier.jar"; ++$bowtie2_build_soft="bowtie2-build"; ++$bowtie2_x_soft="bowtie2"; ++$bwa_soft = "bwa"; ++$minimap2_soft = "minimap2"; ++$bedtools_soft="bedtools"; #-- IMPORTANT! Needs version <0.24 ++$diamond_soft="diamond"; ++$hmmer_soft="hmmsearch"; ++$megahit_soft="megahit"; ++$prinseq_soft="prinseq-lite.pl"; ++$prodigal_soft="prodigal"; ++$cdhit_soft="cd-hit-est"; ++$toamos_soft="toAmos"; ++$minimus2_soft="minimus2"; ++$checkm_soft="checkm"; ++$minpath_soft="MinPath$ENV{'EBVERSIONMINPATH'}.py"; ++$canu_soft="canu"; ++$trimmomatic_soft="java -jar $ENV{'EBROOTTRIMMOMATIC'}/trimmomatic-$ENV{'EBVERSIONTRIMMOMATIC'}.jar"; ++$dastool_soft="DAS_Tool"; From ed140920dc27406c0e4a0f4e384b4c1d117ee7ed Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 28 Feb 2019 11:29:29 -0600 Subject: [PATCH 0629/5331] Added float128 patch --- ...-17_Fix_intelcuda_undefined_float128.patch | 27 +++++++++++++++++++ ...da-2017b-AmberTools-17-patchlevel-10-15.eb | 2 +- ...da-2017b-AmberTools-17-patchlevel-10-15.eb | 7 +++-- 3 files changed, 33 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch new file mode 100644 index 00000000000..d24a533f133 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch @@ -0,0 +1,27 @@ +Force the compiler used by nvcc to use the C++11 standard to avoid: +error: identifier "__float128" is undefined +Author: Davide Vanzo (Vanderbilt University) +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2019-02-28 10:41:07.185332187 -0600 ++++ amber16/AmberTools/src/configure2 2019-02-28 10:54:54.313355074 -0600 +@@ -1415,7 +1415,7 @@ + if [ "$optimise" = 'no' ]; then + nvcc="$nvcc -use_fast_math -O0 " + else +- nvcc="$nvcc -use_fast_math -O3 " ++ nvcc="$nvcc -use_fast_math -O3" + fi + if [ "$mpi" = 'yes' ]; then + mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` +@@ -1731,9 +1731,9 @@ + pmemd_cu_libs="./cuda/cuda.a -L\$(CUDA_HOME)/lib64 -L\$(CUDA_HOME)/lib -lcurand -lcufft -lcudart $fc_cxx_link_flag" + pbsa_cu_libs="-L\$(CUDA_HOME)/lib64 -L\$(CUDA_HOME)/lib -lcublas -lcusparse -lcudart -lcuda $fc_cxx_link_flag" + if [ "$optimise" = 'yes' ]; then +- nvcc="$nvcc -use_fast_math -O3 " ++ nvcc="$nvcc -use_fast_math -O3 -Xcompiler '-std=c++11'" + else +- nvcc="$nvcc -use_fast_math -O0 " ++ nvcc="$nvcc -use_fast_math -O0 -Xcompiler '-std=c++11'" + fi + + if [ "$mpi" = 'yes' ]; then diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb index 75821d5dce7..bd30bd435c7 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb @@ -68,7 +68,7 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + '5cb4d4c7ea6f95ec59ac20912d0223b278db92eef202ce70da34c558cbd6629e', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb index 706f5eea615..eed29869071 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb @@ -11,7 +11,7 @@ description = """Amber (originally Assisted Model Building with Energy prediction.""" toolchain = {'name': 'intelcuda', 'version': '2017b'} -toolchainopts = {'usempi': True, 'openmp': True} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11'} sources = [ 'Amber%(version)s.tar.bz2', @@ -39,6 +39,7 @@ patches = [ 'Amber-%(version)s-dont_use_ipo.patch', 'Amber-%%(version)s-AT-%s_allow_cuda9.patch' % ambertools_ver, 'Amber-%(version)s_test_cuda.patch', + 'Amber-%%(version)s-AT-%s_Fix_intelcuda_undefined_float128.patch' % ambertools_ver, ] checksums = [ '3b7ef281fd3c46282a51b6a6deed9ed174a1f6d468002649d84bfc8a2577ae5d', # Amber16.tar.bz2 @@ -67,13 +68,15 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + '5cb4d4c7ea6f95ec59ac20912d0223b278db92eef202ce70da34c558cbd6629e', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch '9f57711fe607920a48fcff2f2523230a13fbbb354ab683795247fc6dd8848192', # Amber-16-AT-17_allow_cuda9.patch 'b870417a0aad5b220dca9f590ec5cf857e06f44b7ee43165c4ace9901ae9a0f7', # Amber-16_test_cuda.patch + # Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch + '89502bacd38eb2060872548dc3924bf35fad22151266069eee6656e9b16e5fc8', ] builddependencies = [('flex', '2.6.4')] From f3959fe3479f6115ee6f06fb2d734900b2db06c8 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 28 Feb 2019 11:32:53 -0600 Subject: [PATCH 0630/5331] Correct patch --- ...er-16-AT-17_Fix_intelcuda_undefined_float128.patch | 11 +---------- ...-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb | 2 +- 2 files changed, 2 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch index d24a533f133..8e40f21f4ac 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch +++ b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch @@ -3,16 +3,7 @@ error: identifier "__float128" is undefined Author: Davide Vanzo (Vanderbilt University) diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 --- amber16.orig/AmberTools/src/configure2 2019-02-28 10:41:07.185332187 -0600 -+++ amber16/AmberTools/src/configure2 2019-02-28 10:54:54.313355074 -0600 -@@ -1415,7 +1415,7 @@ - if [ "$optimise" = 'no' ]; then - nvcc="$nvcc -use_fast_math -O0 " - else -- nvcc="$nvcc -use_fast_math -O3 " -+ nvcc="$nvcc -use_fast_math -O3" - fi - if [ "$mpi" = 'yes' ]; then - mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++++ amber16/AmberTools/src/configure2 2019-02-28 11:31:13.125415364 -0600 @@ -1731,9 +1731,9 @@ pmemd_cu_libs="./cuda/cuda.a -L\$(CUDA_HOME)/lib64 -L\$(CUDA_HOME)/lib -lcurand -lcufft -lcudart $fc_cxx_link_flag" pbsa_cu_libs="-L\$(CUDA_HOME)/lib64 -L\$(CUDA_HOME)/lib -lcublas -lcusparse -lcudart -lcuda $fc_cxx_link_flag" diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb index eed29869071..d0e7d0a78fe 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb @@ -76,7 +76,7 @@ checksums = [ '9f57711fe607920a48fcff2f2523230a13fbbb354ab683795247fc6dd8848192', # Amber-16-AT-17_allow_cuda9.patch 'b870417a0aad5b220dca9f590ec5cf857e06f44b7ee43165c4ace9901ae9a0f7', # Amber-16_test_cuda.patch # Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch - '89502bacd38eb2060872548dc3924bf35fad22151266069eee6656e9b16e5fc8', + 'b5033d84c4c34bf31f8cf7aadf38a6e31f69894c56ed84deb1bf21b41d83b53c', ] builddependencies = [('flex', '2.6.4')] From 94357127719d441579f540c25250172d36402e5b Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 28 Feb 2019 11:48:33 -0600 Subject: [PATCH 0631/5331] update cURL version to solve the conflict problem reported by Travis --- .../l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb | 2 +- .../l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb index 63b7217d558..3fa2ff94502 100644 --- a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb @@ -21,7 +21,7 @@ builddependencies = [('HTSlib', '1.9')] dependencies = [ ('Python', '2.7.14'), ('SAMtools', '1.6'), - ('cURL', '7.58.0'), + ('cURL', '7.56.1'), ('XZ', '5.2.3'), ('bzip2', '1.0.6'), ] diff --git a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb index 83109b38f03..23d39ac43f0 100644 --- a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb @@ -21,7 +21,7 @@ builddependencies = [('HTSlib', '1.9')] dependencies = [ ('Python', '2.7.14'), ('SAMtools', '1.6'), - ('cURL', '7.58.0'), + ('cURL', '7.56.1'), ('XZ', '5.2.3'), ('bzip2', '1.0.6'), ] From 9883d383f44a81b76edb2593bfdb2ec2633b20d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Feb 2019 19:15:15 +0100 Subject: [PATCH 0632/5331] {data}[intel/2018b] bitarray v0.8.3 w/ Python 2.7.15 & 3.6.6 --- ...itarray-0.8.3-intel-2018b-Python-2.7.15.eb | 26 +++++++++++++++++++ ...bitarray-0.8.3-intel-2018b-Python-3.6.6.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..7748a353739 --- /dev/null +++ b/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'bitarray' +version = '0.8.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ilanschnell/bitarray' +description = "bitarray provides an object type which efficiently represents an array of booleans" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['050cd30b810ddb3aa941e7ddfbe0d8065e793012d0a88cb5739ec23624b9895e'] + +dependencies = [('Python', '2.7.15')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..73e048151c3 --- /dev/null +++ b/easybuild/easyconfigs/b/bitarray/bitarray-0.8.3-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'bitarray' +version = '0.8.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ilanschnell/bitarray' +description = "bitarray provides an object type which efficiently represents an array of booleans" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['050cd30b810ddb3aa941e7ddfbe0d8065e793012d0a88cb5739ec23624b9895e'] + +dependencies = [('Python', '3.6.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' From 28a470470c29a9b639ad91fcee642d5ce89498ed Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 28 Feb 2019 13:21:28 -0600 Subject: [PATCH 0633/5331] update cURL version again to solve the conflict problem reported by Travis --- .../h/HTSlib/HTSlib-1.9-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- .../l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb | 2 +- .../l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.9-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.9-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 95c0b4d2e3d..8f5c27f76eb 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.9-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.9-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -25,7 +25,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), - ('cURL', '7.56.1'), + ('cURL', '7.58.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb index 3fa2ff94502..63b7217d558 100644 --- a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-foss-2017b-Python-2.7.14.eb @@ -21,7 +21,7 @@ builddependencies = [('HTSlib', '1.9')] dependencies = [ ('Python', '2.7.14'), ('SAMtools', '1.6'), - ('cURL', '7.56.1'), + ('cURL', '7.58.0'), ('XZ', '5.2.3'), ('bzip2', '1.0.6'), ] diff --git a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb index 23d39ac43f0..83109b38f03 100644 --- a/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/l/LoFreq/LoFreq-2.1.3.1-intel-2017b-Python-2.7.14.eb @@ -21,7 +21,7 @@ builddependencies = [('HTSlib', '1.9')] dependencies = [ ('Python', '2.7.14'), ('SAMtools', '1.6'), - ('cURL', '7.56.1'), + ('cURL', '7.58.0'), ('XZ', '5.2.3'), ('bzip2', '1.0.6'), ] From 55494f416f6064f9d4d1fd68ada8cb6be32d4027 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 28 Feb 2019 13:31:43 -0600 Subject: [PATCH 0634/5331] update SQLite version to solve the conflict problem reported by Travis --- .../a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb | 2 +- .../a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb index 2b293acc73e..497e1cfe48b 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb @@ -33,7 +33,7 @@ dependencies = [ ('lpsolve', '5.5.2.5'), ('SuiteSparse', '5.1.2', '-METIS-5.1.0'), ('BamTools', '2.5.1'), - ('SQLite', '3.21.0'), + ('SQLite', '3.20.1'), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb index 7ada555706b..355a9b08d25 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb @@ -36,7 +36,7 @@ dependencies = [ ('lpsolve', '5.5.2.5'), ('SuiteSparse', '5.1.2', '-METIS-5.1.0'), ('BamTools', '2.5.1'), - ('SQLite', '3.21.0'), + ('SQLite', '3.20.1'), ] skipsteps = ['configure'] From 8c8062e56bb7bd3e71516214a6fdba1dc7aee4eb Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 28 Feb 2019 14:03:01 -0600 Subject: [PATCH 0635/5331] Remove R from version --- .../easyconfigs/m/MATLAB/{MATLAB-R2018b.eb => MATLAB-2018b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/MATLAB/{MATLAB-R2018b.eb => MATLAB-2018b.eb} (97%) diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb similarity index 97% rename from easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb rename to easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb index 2d4d57aa5f8..b563c88928d 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-R2018b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb @@ -1,5 +1,5 @@ name = 'MATLAB' -version = 'R2018b' +version = '2018b' homepage = 'http://www.mathworks.com/products/matlab' description = """MATLAB is a high-level language and interactive environment From 60a5f43c0732f4bf62321c48294f0fd67521be60 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 28 Feb 2019 14:04:21 -0600 Subject: [PATCH 0636/5331] Remove R from version --- ....7.14.eb => MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/MATLAB-Engine/{MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb => MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb} (98%) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb similarity index 98% rename from easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb rename to easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb index 2aa91866b2a..92278ba4968 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'MATLAB-Engine' -version = 'R2018b' +version = '2018b' versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' From efd3c7660dac570d53a0493bec167cbab3b0f6ce Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 28 Feb 2019 14:04:35 -0600 Subject: [PATCH 0637/5331] Update and rename MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb to MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb --- ...-3.6.3.eb => MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/MATLAB-Engine/{MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb => MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb} (98%) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb similarity index 98% rename from easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb rename to easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb index a8fedb1365b..439ddce3d1d 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'MATLAB-Engine' -version = 'R2018b' +version = '2018b' versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' From 016eaecdbce628fb57765fe0fb36136b73a8ffcf Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 28 Feb 2019 14:05:03 -0600 Subject: [PATCH 0638/5331] Remove R from version --- ...7.14.eb => MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/MATLAB-Engine/{MATLAB-Engine-R2018b-intel-2017b-Python-2.7.14.eb => MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb} (98%) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb similarity index 98% rename from easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-2.7.14.eb rename to easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb index e39e592445f..0a065a74e60 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'MATLAB-Engine' -version = 'R2018b' +version = '2018b' versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' From 68e0d565ed3e98d663efd26927d6cb1304ba0f86 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 28 Feb 2019 14:05:27 -0600 Subject: [PATCH 0639/5331] Remove R from version --- ...3.6.3.eb => MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/MATLAB-Engine/{MATLAB-Engine-R2018b-intel-2017b-Python-3.6.3.eb => MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb} (98%) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb similarity index 98% rename from easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-3.6.3.eb rename to easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb index 3798c7c47c7..a00824b2ca4 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-R2018b-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'MATLAB-Engine' -version = 'R2018b' +version = '2018b' versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' From ab37098877c8a11579ce8440a1314d5f32be4ac2 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 28 Feb 2019 19:16:49 -0600 Subject: [PATCH 0640/5331] Fixed split function declaration --- .../Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch | 14 ++++++++++++-- ...osscuda-2017b-AmberTools-17-patchlevel-10-15.eb | 2 +- ...telcuda-2017b-AmberTools-17-patchlevel-10-15.eb | 2 +- 3 files changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch index b4873564377..c769972f756 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch +++ b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch @@ -2,8 +2,17 @@ Fix incorrect use of fixed sized buffers. Åke Sandgren, 20190228 diff -ru amber16.orig/AmberTools/src/nab/nab.c amber16/AmberTools/src/nab/nab.c ---- amber16.orig/AmberTools/src/nab/nab.c 2017-04-13 15:00:53.000000000 +0200 -+++ amber16/AmberTools/src/nab/nab.c 2019-02-28 12:51:07.844183899 +0100 +--- amber16.orig/AmberTools/src/nab/nab.c 2019-02-28 10:41:07.185332187 -0600 ++++ amber16/AmberTools/src/nab/nab.c 2019-02-28 19:12:13.618946740 -0600 +@@ -22,7 +22,7 @@ + + static void n2c( int, int, char *, int, int, int, char *[], char [], char * ); + static void cc( int, int, int, int, char [], int, char *[], char [] ); +-static int split( char [], char *[], char * ); ++static int split( char [], char ***, char * ); + static int execute( char **, int, int, int ); + + int main( int argc, char *argv[] ) @@ -128,8 +128,8 @@ char cpp_ofname[ 256 ]; @@ -208,3 +217,4 @@ diff -ru amber16.orig/AmberTools/src/nab/nab.c amber16/AmberTools/src/nab/nab.c return( nf ); } } +Only in amber16/AmberTools/src/nab: nab.c~ diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb index bd30bd435c7..aeefba265b3 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb @@ -68,7 +68,7 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - '5cb4d4c7ea6f95ec59ac20912d0223b278db92eef202ce70da34c558cbd6629e', + 'a73f5da964dbd52a12a8dc9cf2c7648ec3f00c1f18e37f8dc6c43c32e86e5776', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb index d0e7d0a78fe..4b8130b4bd0 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb @@ -68,7 +68,7 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - '5cb4d4c7ea6f95ec59ac20912d0223b278db92eef202ce70da34c558cbd6629e', + 'a73f5da964dbd52a12a8dc9cf2c7648ec3f00c1f18e37f8dc6c43c32e86e5776', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch From 70a77a193f23104bd5db242a4a71159593d389bd Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 28 Feb 2019 19:20:14 -0600 Subject: [PATCH 0641/5331] Removed spurious line --- .../a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch | 1 - .../Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb | 2 +- .../Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch index c769972f756..08d1a8c2282 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch +++ b/easybuild/easyconfigs/a/Amber/Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch @@ -217,4 +217,3 @@ diff -ru amber16.orig/AmberTools/src/nab/nab.c amber16/AmberTools/src/nab/nab.c return( nf ); } } -Only in amber16/AmberTools/src/nab: nab.c~ diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb index aeefba265b3..1bdc2d39adf 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb @@ -68,7 +68,7 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - 'a73f5da964dbd52a12a8dc9cf2c7648ec3f00c1f18e37f8dc6c43c32e86e5776', + 'c0c05bf4260c39c87fb57984d84853df01bfd054c389d58c2626c12c921ae4ce', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb index 4b8130b4bd0..1d35f12be86 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb @@ -68,7 +68,7 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - 'a73f5da964dbd52a12a8dc9cf2c7648ec3f00c1f18e37f8dc6c43c32e86e5776', + 'c0c05bf4260c39c87fb57984d84853df01bfd054c389d58c2626c12c921ae4ce', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch From 20c032260a73c8d417dd78f08cdc58a02aa5a676 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Fri, 1 Mar 2019 09:12:57 +0100 Subject: [PATCH 0642/5331] Add checksums for libxc --- easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb | 1 + easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb index 782a22b3efb..e8fe242e82f 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] sources = [SOURCE_TAR_GZ] +checksums = ['99ed7a31c7ae19e364d341e2d4a02b108a9b4f45c7f5c5926c6108612784aff0'] configopts = '--enable-static --enable-shared --enable-fortran' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb index fb1340a035a..a67619a822d 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb @@ -9,8 +9,9 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel', 'version': '2018b'} -sources = [SOURCE_TAR_GZ] source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['99ed7a31c7ae19e364d341e2d4a02b108a9b4f45c7f5c5926c6108612784aff0'] configopts = '--enable-static --enable-shared --enable-fortran' From ca7f467132c0b231436d7e8cbcb6af356272eeb0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 1 Mar 2019 14:52:57 +0200 Subject: [PATCH 0643/5331] adding easyconfigs: JasPer-2.0.14-GCCcore-8.2.0.eb --- .../j/JasPer/JasPer-2.0.14-GCCcore-8.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-8.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..ad882bc7e73 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-8.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.14' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2a1f61e55afe8b4ce8115e1508c5d7cb314d56dfcc2dd323f90c072f88ccf57b'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), +] + +separate_build_dir = True + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'vis' From 49f804bf8adb1d4e533e84a63e594932d2841755 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 1 Mar 2019 15:32:01 +0200 Subject: [PATCH 0644/5331] adding easyconfigs: HDF5-1.10.5-intel-2019a.eb --- .../h/HDF5/HDF5-1.10.5-intel-2019a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-intel-2019a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-intel-2019a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-intel-2019a.eb new file mode 100644 index 00000000000..e66cab5c6e3 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-intel-2019a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.5' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From 449cbaf3b2264a1120af064c0d5f8e677ec62f57 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 1 Mar 2019 16:03:39 +0200 Subject: [PATCH 0645/5331] adding easyconfigs: pkg-config-0.29.2-GCCcore-8.2.0.eb --- .../pkg-config-0.29.2-GCCcore-8.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..a86e1e73245 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-8.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' From d4badb6044a622e1b7b46ff0506078e3e2a794a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Mar 2019 15:07:32 +0100 Subject: [PATCH 0646/5331] also run easyconfigs tests with Python 3.6 --- .travis.yml | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 71f98d05283..a535c902b99 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,8 +5,8 @@ env: - ENV_MOD_VERSION=3.2.10 EASYBUILD_MODULES_TOOL=EnvironmentModulesC EASYBUILD_MODULE_SYNTAX=Tcl - LMOD_VERSION=6.6.3 - LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Tcl - - LMOD_VERSION=7.7.16 - - LMOD_VERSION=7.7.16 EASYBUILD_MODULE_SYNTAX=Tcl + - LMOD_VERSION=7.8.5 + - LMOD_VERSION=7.8.5 EASYBUILD_MODULE_SYNTAX=Tcl - ENV_MOD_VERSION=4.0.0 EASYBUILD_MODULES_TOOL=EnvironmentModules EASYBUILD_MODULE_SYNTAX=Tcl matrix: # mark build as finished as soon as job has failed @@ -15,6 +15,9 @@ matrix: # also test default configuration with Python 2.7 - python: 2.7 env: LMOD_VERSION=6.6.3 + # also test with Python 3.6 + - python: 3.6 + env: LMOD_VERSION=7.8.5 addons: apt: packages: @@ -28,8 +31,10 @@ install: # required for test_dep_graph - pip install pep8 python-graph-core python-graph-dot # install easybuild-framework/easybuild-easyblocks (and dependencies) - # use 'develop' branch of framework/easyblocks, except when testing 'master' - - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; else BRANCH=develop; fi + # use 'develop' branch of framework/easyblocks, except when testing 'master' or '4.x' branches + - BRANCH=develop + - if [ "x$TRAVIS_BRANCH" = 'xmaster' ]; then BRANCH=master; fi + - if [ "x$TRAVIS_BRANCH" = 'x4.x' ]; then BRANCH=4.x; fi - cd $HOME - git clone -b $BRANCH --depth 10 --single-branch https://github.com/hpcugent/easybuild-framework.git - cd easybuild-framework; git log -n 1; cd - From 991469c11031bbee13299c5955539954a4d23928 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 1 Mar 2019 16:18:49 +0200 Subject: [PATCH 0647/5331] adding easyconfigs: Doxygen-1.8.15-GCCcore-8.2.0.eb --- .../d/Doxygen/Doxygen-1.8.15-GCCcore-8.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.15-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.15-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.15-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..dcf50722de2 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.15-GCCcore-8.2.0.eb @@ -0,0 +1,26 @@ +name = 'Doxygen' +version = '1.8.15' + +homepage = 'http://www.doxygen.org' + +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['bd9c0ec462b6a9b5b41ede97bede5458e0d7bb40d4cfa27f6f622eb33c59245d'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Bison', '3.0.5'), + ('CMake', '3.13.3'), + ('flex', '2.6.4'), + ('pkg-config', '0.29.2'), +] + +moduleclass = 'devel' From 3b5cd6a4c30933c5fcef77b89f9379afd970f329 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 08:29:55 -0600 Subject: [PATCH 0648/5331] Update patch checksum --- .../Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb | 2 +- .../Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb index aff2b7082b3..d420ab7f177 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb @@ -66,7 +66,7 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + 'c0c05bf4260c39c87fb57984d84853df01bfd054c389d58c2626c12c921ae4ce', # Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch 'aa470f20442b17554ae8b0d6e9cb65c59f1833f1bd7c57c614cbc22f6bf911a7', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb index d15e0c510e4..9d7d2475ed7 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb @@ -64,7 +64,7 @@ checksums = [ '1f407b7b5ae2d1f291eebdd2bb7c4a120f96305a89a9028bc0307ca150bb20d6', # Amber-16-AT-17_fix_rism_fftw_lib.patch '648ed44518dfc8275a1ab229efedcac37d9119991e046fd39e1ccbbbaed874f3', # Amber-16-AT-17_ignore_X11_checks.patch # Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch - 'c07189677d960add1bdccf784a6e07175e3b5800e41f3f18770ef790c7a526a4', + 'c0c05bf4260c39c87fb57984d84853df01bfd054c389d58c2626c12c921ae4ce', '74f045ac33516c417955e894971956ee179045d4d304a55b9c6436035a924a41', # Amber-16-fix_missing_build_target.patch 'b29b44859f7e9ee629d3b1cf378f4eb0c02b69d15e6c041734c24ced234748e5', # Amber-16-dont_use_ipo.patch ] From 74af4490511207c1377cc2995365bc1292013764 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 1 Mar 2019 16:38:41 +0200 Subject: [PATCH 0649/5331] adding easyconfigs: netCDF-4.6.2-intel-2019a.eb --- .../n/netCDF/netCDF-4.6.2-intel-2019a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-intel-2019a.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-intel-2019a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-intel-2019a.eb new file mode 100644 index 00000000000..5162677e923 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-intel-2019a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.6.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['673936c76ae0c496f6dde7e077f5be480afc1e300adb2c200bf56fbe22e5a82a'] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.13.3'), + ('Doxygen', '1.8.15'), +] + +dependencies = [ + ('HDF5', '1.10.5'), + ('cURL', '7.63.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' From fb072fda40f1f7a68767962bc6830e5451f5ada9 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 08:44:25 -0600 Subject: [PATCH 0650/5331] Comment optional variables --- easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb index b563c88928d..8c6de7f01dc 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb @@ -14,10 +14,11 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('Java', '1.8')] -license_server = 'my-license-server' -license_server_port = '1234' -key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' - -modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} +# Uncomment and modify the following variables if needed +# for installation with floating license server +#license_server = 'my-license-server' +#license_server_port = '1234' +#key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' +#modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} moduleclass = 'math' From d44163e5059550e5b9e6941eae31e82aacd87102 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 1 Mar 2019 16:51:40 +0200 Subject: [PATCH 0651/5331] adding easyconfigs: netCDF-Fortran-4.4.5-intel-2019a.eb --- .../netCDF-Fortran-4.4.5-intel-2019a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-intel-2019a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-intel-2019a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-intel-2019a.eb new file mode 100644 index 00000000000..4127d0f2a56 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-intel-2019a.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.4.5' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['01643461ac42d1986e38a052eb021135bae5b6cd592373fb44cf832236791c03'] + +dependencies = [('netCDF', '4.6.2')] + +moduleclass = 'data' From 1bb382b4daf01a73a20b02546a8702675f3b30d8 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 09:10:04 -0600 Subject: [PATCH 0652/5331] Removed redundant download_dep_fail --- .../k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb | 1 - .../k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb index b0df131178e..4bd4c8b5e66 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-2.7.14.eb @@ -19,7 +19,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True exts_list = [ ('Keras-Applications', '1.0.4', { diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb index 598e8518591..de38ea3229f 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.0-fosscuda-2017b-Python-3.6.3.eb @@ -19,7 +19,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True exts_list = [ ('Keras-Applications', '1.0.4', { From 494ab5b151e444fabb514e7655b04cfab8c75ef9 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 1 Mar 2019 09:47:33 -0600 Subject: [PATCH 0653/5331] add author and email for the patch file --- .../a/AUGUSTUS/AUGUSTUS-3.3.2_additional_fix_hardcoding.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_additional_fix_hardcoding.patch b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_additional_fix_hardcoding.patch index 8f1ea64fe25..07d68af9d7a 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_additional_fix_hardcoding.patch +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2_additional_fix_hardcoding.patch @@ -1,5 +1,5 @@ fix the additional hardcoded compiler options that are making trouble. - +author: fenglai liu (fenglai@accre.vanderbilt.edu) diff -Naur augustus-3.3.2.ori/auxprogs/bam2hints/Makefile augustus-3.3.2/auxprogs/bam2hints/Makefile --- augustus-3.3.2.ori/auxprogs/bam2hints/Makefile 2019-02-26 13:31:59.005083190 -0600 +++ augustus-3.3.2/auxprogs/bam2hints/Makefile 2019-02-27 11:58:22.100807318 -0600 From fcc158149bea73ed2ff62e7bfba96e76dd4e2782 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 1 Mar 2019 09:54:28 -0600 Subject: [PATCH 0654/5331] add additional space the buildopts and installopts --- .../a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb | 4 ++-- .../a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb index 497e1cfe48b..5193b3cbd74 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb @@ -39,8 +39,8 @@ dependencies = [ skipsteps = ['configure'] prebuildopts = "make clean && " -buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX"' -installopts = 'INSTALLDIR=%(installdir)s' +buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX" ' +installopts = 'INSTALLDIR=%(installdir)s ' sanity_check_paths = { 'files': ['bin/augustus', 'bin/bam2hints', 'bin/espoca', 'bin/etraining', diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb index 355a9b08d25..5da5d21fff8 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb @@ -42,8 +42,8 @@ dependencies = [ skipsteps = ['configure'] prebuildopts = "unset LDFLAGS && unset LIBS && " -buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX"' -installopts = 'INSTALLDIR=%(installdir)s' +buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX" ' +installopts = 'INSTALLDIR=%(installdir)s ' sanity_check_paths = { 'files': ['bin/augustus', 'bin/bam2hints', 'bin/espoca', 'bin/etraining', From 3226fb0c283315bf2adac16f51d17657141e29e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Mar 2019 16:58:32 +0100 Subject: [PATCH 0655/5331] use https in most recent XZ easyconfigs --- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb | 4 ++-- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb | 4 ++-- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb index 51557fc3d81..34d93c09f7b 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'XZ' version = '5.2.4' -homepage = 'http://tukaani.org/xz/' +homepage = 'https://tukaani.org/xz/' description = "xz: XZ utilities" toolchain = {'name': 'GCCcore', 'version': '7.2.0'} -source_urls = ['http://tukaani.org/xz/'] +source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] patches = ['XZ-5.2.2_compat-libs.patch'] checksums = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb index 4d5c6a39b60..4807e850e05 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'XZ' version = '5.2.4' -homepage = 'http://tukaani.org/xz/' +homepage = 'https://tukaani.org/xz/' description = "xz: XZ utilities" toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -source_urls = ['http://tukaani.org/xz/'] +source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] patches = ['XZ-5.2.2_compat-libs.patch'] checksums = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb index dc3a62dd679..e082fd1cfcb 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'XZ' version = '5.2.4' -homepage = 'http://tukaani.org/xz/' +homepage = 'https://tukaani.org/xz/' description = "xz: XZ utilities" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['http://tukaani.org/xz/'] +source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] patches = ['XZ-5.2.2_compat-libs.patch'] checksums = [ From ff3b6dad56bb7535f791d3d4fbeeef2235bde1b5 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 10:07:53 -0600 Subject: [PATCH 0656/5331] adding easyconfigs: RELION-2.1-fosscuda-2017b.eb --- .../r/RELION/RELION-2.1-fosscuda-2017b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/RELION/RELION-2.1-fosscuda-2017b.eb diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.1-fosscuda-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-2.1-fosscuda-2017b.eb new file mode 100644 index 00000000000..8f4bb136fa9 --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-2.1-fosscuda-2017b.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'RELION' +version = '2.1' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = ['https://github.com/3dem/relion/archive'] +sources = ['%(version)s.tar.gz'] +patches = ['RELION-2.1_cuda_capabilities.patch'] +checksums = [ + '08729aac4fa0841e08df2c90a2c26cfe2aef52af2f5fb94a770ed2c11373b886', # 2.1.tar.gz + '541cdc484ab885353e1f79d205e55332df58df619229a131ef7811f5784d5d46', # RELION-2.1_cuda_capabilities.patch +] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('X11', '20171023'), + ('FLTK', '1.3.4'), +] + +# lowest supported capability is 3.5 +cuda_compute_capabilities = ['3.5', '3.7', '5.0', '5.2', '5.3', '6.0', '6.1', '6.2', '7.0'] +capabilities = [''.join(x.split('.')) for x in cuda_compute_capabilities] +cuda_arch = ';'.join(['-gencode arch=compute_%s,code=\"sm_%s,compute_%s\"' % (x, x, x) for x in capabilities]) + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-lpthread' " +configopts += '-DCUDA_ARCH=\'' + cuda_arch + '\'' + +sanity_check_paths = { + 'files': ['bin/relion'] + ['lib/librelion_%s.%s' % (x, SHLIB_EXT) for x in ['gpu_util', 'gui_lib', 'lib']], + 'dirs': [] +} + +moduleclass = 'bio' From f92d351b9fcb33b315c996663eac9b81c617058b Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 10:08:51 -0600 Subject: [PATCH 0657/5331] Add deps --- .../f/FLTK/FLTK-1.3.4-fosscuda-2017b.eb | 41 ++++++++++++ .../l/LLVM/LLVM-5.0.0-fosscuda-2017b.eb | 44 +++++++++++++ .../l/libGLU/libGLU-9.0.0-fosscuda-2017b.eb | 25 +++++++ ...Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb | 23 +++++++ .../m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb | 66 +++++++++++++++++++ 5 files changed, 199 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-fosscuda-2017b.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-fosscuda-2017b.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-fosscuda-2017b.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-fosscuda-2017b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-fosscuda-2017b.eb new file mode 100644 index 00000000000..590cc7eb60f --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-fosscuda-2017b.eb @@ -0,0 +1,41 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.4' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-%(version)s_fix-LDFLAGS.patch'] +checksums = [ + 'c8ab01c4e860d53e11d40dc28f98d2fe9c85aaf6dbb5af50fd6e66afec3dc58f', # fltk-1.3.4-source.tar.gz + 'b9d39f6dce92fdb34a149f686a5d56e72912f94fd09c4958f3bb12770603da7d', # FLTK-1.3.4_fix-LDFLAGS.patch +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '17.2.5'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.32'), + ('libjpeg-turbo', '1.5.2'), + ('xprop', '1.2.2'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-fosscuda-2017b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-fosscuda-2017b.eb new file mode 100644 index 00000000000..ef87d251b82 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-fosscuda-2017b.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '5.0.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] +checksums = ['e35dcbae6084adcf4abb32514127c5eabd7d63b733852ccdb31e06f1373136da'] + +builddependencies = [ + ('CMake', '3.9.5'), + ('Python', '2.7.14'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-fosscuda-2017b.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-fosscuda-2017b.eb new file mode 100644 index 00000000000..defb25480f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-fosscuda-2017b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] +checksums = ['1f7ad0d379a722fcbd303aa5650c6d7d5544fde83196b42a73d1193568a4df12'] + +dependencies = [ + ('Mesa', '17.2.5'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..5e55d37f12f --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] + +dependencies = [('Python', '2.7.14')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb new file mode 100644 index 00000000000..0e610cd1aa6 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb @@ -0,0 +1,66 @@ +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '17.2.5' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. +toolchainopts = {'optarch': False} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7f7f914b7b9ea0b15f2d9d01a4375e311b0e90e55683b8e8a67ce8691eb1070f'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('Autotools', '20170619'), + ('pkg-config', '0.29.2'), + ('Mako', '1.0.7', '-Python-2.7.14'), + ('libxml2', '2.9.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('nettle', '3.3'), + ('libdrm', '2.4.88'), + ('LLVM', '5.0.0'), + ('X11', '20171023'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' From 6bbab0cc3a79a122337477ae48d0ee3dc29b9c3d Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 10:29:46 -0600 Subject: [PATCH 0658/5331] Make Travis happy again --- easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb index 8c6de7f01dc..2f3b02aa9c1 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb @@ -16,9 +16,10 @@ dependencies = [('Java', '1.8')] # Uncomment and modify the following variables if needed # for installation with floating license server -#license_server = 'my-license-server' -#license_server_port = '1234' -#key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' -#modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} + +# license_server = 'my-license-server' +# license_server_port = '1234' +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' +# modextravars = {'LM_LICENSE_FILE': '%s@%s' % (license_server_port, license_server)} moduleclass = 'math' From 9ed0813bff6ffe5f961de03015c5e7af1a188358 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Mar 2019 17:45:42 +0100 Subject: [PATCH 0659/5331] fix 'vsc' imports in test modules, use easybuild.base instead --- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/styletests.py | 2 +- test/easyconfigs/suite.py | 3 +-- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index fa8bf72eeca..9c3e0008483 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -34,11 +34,11 @@ import sys import tempfile from distutils.version import LooseVersion -from vsc.utils import fancylogger from unittest import TestCase, TestLoader, main import easybuild.main as eb_main import easybuild.tools.options as eboptions +from easybuild.base import fancylogger from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.framework.easyblock import EasyBlock from easybuild.framework.easyconfig.default import DEFAULT_CONFIG diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index 652bc4fad85..92041a4baa7 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -31,8 +31,8 @@ import glob import sys from unittest import TestCase, TestLoader, main -from vsc.utils import fancylogger +from easybuild.base import fancylogger from easybuild.framework.easyconfig.tools import get_paths_for from easybuild.framework.easyconfig.style import check_easyconfigs_style diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 2c7fab64844..3f60af9abb7 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -36,11 +36,10 @@ import tempfile import unittest -from vsc.utils import fancylogger - import easybuild.tools.build_log # initialize EasyBuild logging, so we disable it import test.easyconfigs.easyconfigs as e import test.easyconfigs.styletests as s +from easybuild.base import fancylogger # disable all logging to significantly speed up tests fancylogger.disableDefaultHandlers() From 89aaaeef70b68f09e92f54626c2570d8247bc049 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 11:07:19 -0600 Subject: [PATCH 0660/5331] Add Python versionsuffix --- ...-foss-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/Amber/{Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb => Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb} (97%) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb similarity index 97% rename from easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb rename to easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb index d420ab7f177..ae3f6b2e36c 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-foss-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb @@ -3,7 +3,7 @@ version = '16' ambertools_ver = '17' # Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html patchlevels = (10, 15) # (AmberTools, Amber) -versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-Python-%%(pyver)s' % (ambertools_ver, patchlevels[0], patchlevels[1]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy From 73bb234e79615891d1794ef037b3c459e95c8232 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 11:10:01 -0600 Subject: [PATCH 0661/5331] Add Python versionsuffix --- ...intel-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/Amber/{Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb => Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb} (97%) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb similarity index 97% rename from easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb rename to easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb index 9d7d2475ed7..59cdb974c8a 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intel-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb @@ -3,7 +3,7 @@ version = '16' ambertools_ver = '17' # Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html patchlevels = (10, 15) # (AmberTools, Amber) -versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-Python-%%(pyver)s' % (ambertools_ver, patchlevels[0], patchlevels[1]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy From 6dcd9954bdfdc5a3a16f0f627fbe7bbb5befb922 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 11:12:51 -0600 Subject: [PATCH 0662/5331] Add Python versionsuffix --- ...scuda-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/Amber/{Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb => Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb} (97%) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb similarity index 97% rename from easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb rename to easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb index 1bdc2d39adf..b575813d6ff 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-fosscuda-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb @@ -3,7 +3,7 @@ version = '16' ambertools_ver = '17' # Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html patchlevels = (10, 15) # (AmberTools, Amber) -versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-Python-%%(pyver)s' % (ambertools_ver, patchlevels[0], patchlevels[1]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy From 566c6a72243c444b138aced16de750f2f549ad5b Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 11:13:46 -0600 Subject: [PATCH 0663/5331] Add Python versionsuffix --- ...lcuda-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/Amber/{Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb => Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb} (97%) diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb similarity index 97% rename from easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb rename to easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb index 1d35f12be86..8deed90b9b5 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-intelcuda-2017b-AmberTools-17-patchlevel-10-15-Python-2.7.14.eb @@ -3,7 +3,7 @@ version = '16' ambertools_ver = '17' # Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html patchlevels = (10, 15) # (AmberTools, Amber) -versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' % (ambertools_ver, patchlevels[0], patchlevels[1]) +versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-Python-%%(pyver)s' % (ambertools_ver, patchlevels[0], patchlevels[1]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy From 2bf40916d8967012d9616b795ef66e6843208dca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Mar 2019 18:18:32 +0100 Subject: [PATCH 0664/5331] adding easyconfigs: TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb, Bazel-0.20.0-GCCcore-7.3.0.eb --- .../b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb | 21 ++++ ...nsorFlow-1.13.1-foss-2018b-Python-3.6.6.eb | 104 ++++++++++++++++++ 2 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..ed2f9ae9dbd --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb @@ -0,0 +1,21 @@ +name = 'Bazel' +version = '0.20.0' + +homepage = 'http://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = ['Bazel-0.18.0_remove_define_DATE.patch'] +checksums = [ + '1945afa84fd8858b0a3c68c09915a4bc81065c61df2591387b2985e2297d30bd', # bazel-0.20.0-dist.zip + '55fd52c512a578dc8242fbf204cf42f28aa93611910a5a791e0dda4c3a1c7d60', # Bazel-0.18.0_remove_define_DATE.patch +] + +builddependencies = [('binutils', '2.30')] +dependencies = [('Java', '1.8', '', True)] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..47ab80905ce --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,104 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '1.13.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True} + +builddependencies = [ + # must be Bazel <= 0.21, and Bazel 0.21.0 fails to install... + ('Bazel', '0.20.0'), + ('protobuf', '3.6.1'), +] + +dependencies = [ + ('Python', '3.6.6'), + ('wheel', '0.31.1', versionsuffix), + ('h5py', '2.8.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('protobuf-python', '3.6.1', { + 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', + 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + 'use_pip': False, + 'start_dir': 'python', + 'modulename': 'google.protobuf', + }), + ('absl-py', '0.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], + 'checksums': ['8718189e4bd6013bf79910b9d1cb0a76aecad8ce664f78e1144980fabdd2cd23'], + 'modulename': 'absl', + }), + ('astor', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], + 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], + }), + ('gast', '0.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], + 'checksums': ['fe939df4583692f0512161ec1c880e0a10e71e6a232da045ab8edd3756fbadf0'], + }), + ('grpcio', '1.19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], + 'checksums': ['2ddbca16c2e7b3f2ffc6e34c7cfa6886fb01de9f156ad3f77b72ad652d632097'], + 'modulename': 'grpc', + }), + ('Markdown', '3.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], + 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], + }), + ('tensorboard', '1.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'checksums': ['82c9c711b76949b7b3794fc319dc3d3b0fad25f7c0c5260ec4a8371b02d23da6'], + 'unpack_sources': False, + }), + ('termcolor', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('Werkzeug', '0.14.1', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], + 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], + }), + ('Keras-Applications', '1.0.7', { + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', + 'checksums': ['60607b2b98868983e5153bf1cc6aa468ba73adc93bc977a90edaa4bc595e69fa'], + 'modulename': 'keras_applications', + }), + ('Keras-Preprocessing', '1.0.9', { + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['5e3700117981c2db762e512ed6586638124fac5842170701628088a11aeb51ac'], + 'modulename': 'keras_preprocessing', + }), + # FIXME new dep, should be installed from source rather using .whl? + ('tensorflow-estimator', '1.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow-estimator'], + 'source_tmpl': 'tensorflow_estimator-1.13.0-py2.py3-none-any.whl', + 'unpack_sources': False, + }), + (name, version, { + 'patches': ['TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.13.1_lrt-flag.patch'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'checksums': [ + '7cd19978e6bc7edc2c847bce19f95515a742b34ea5e28e4389dade35348f58ed', # v1.13.1.tar.gz + 'aa53c7f6d42b4a9e91e0ba639d79f69a7db3c0a88c3b8e43d332479b6368391a', # TensorFlow-1.11.0_swig-env.patch + # TensorFlow-1.11.0_remove-msse-hardcoding.patch + 'a0f00ee4d03bb4fd3a645ee06045cedaf97d0b85675ec35187e9dd7e479d7bb6', + 'b388be35f2581786bcd533b1bfa375165d7f35e38a3aab74570019312816bf1b', # TensorFlow-1.13.1_lrt-flag.patch + ], + }), +] + +moduleclass = 'lib' From 0e3563959f7778e67a4ccc886cc98db1732e0a5d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Mar 2019 18:23:13 +0100 Subject: [PATCH 0665/5331] adding easyconfigs: VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb, MUSCLE-3.8.31-intel-2018b.eb --- .../m/MUSCLE/MUSCLE-3.8.31-intel-2018b.eb | 36 ++++++++ ...VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb | 92 +++++++++++++++++++ 2 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2018b.eb create mode 100644 easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2018b.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2018b.eb new file mode 100644 index 00000000000..4faf86b9765 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-intel-2018b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'http://drive5.com/muscle/' +description = """ MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['http://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + 'e108d1cc2d394236f839facc1304ff96c0e11f7fdd6d2444761808ec860cd58a', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..093d5479d1f --- /dev/null +++ b/easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,92 @@ +easyblock = 'PythonBundle' + +name = 'VCF-kit' +version = '0.1.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/AndersenLab/VCF-kit' +description = """VCF-kit is a command-line based collection of utilities for performing analysis on + Variant Call Format (VCF) files.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), + ('BWA', '0.7.17'), + ('SAMtools', '1.9'), + ('BCFtools', '1.9'), + ('BLAST+', '2.7.1'), + ('MUSCLE', '3.8.31'), + ('Biopython', '1.72', versionsuffix), + ('networkx', '2.2', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('tabulate', '0.8.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate'], + 'checksums': ['8af07a39377cee1103a5c8b3330a421c2d99b9141e9cc5ddd2e3263fea416943'], + }), + ('sortedcontainers', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], + 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], + }), + ('intervaltree', '3.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/intervaltree'], + 'checksums': ['cb4f61c81dcb4fea6c09903f3599015a83c9bdad1f0bbd232495e6681e19e273'], + }), + ('args', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/args'], + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('clint', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/clint'], + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('cyvcf2', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cyvcf2'], + 'checksums': ['62d950c940977243ab5d2d6e6eabad5fb0deb12012e8e0d2611da03384f118d9'], + }), + ('Unidecode', '0.04.21', { + 'source_urls': ['https://pypi.python.org/packages/source/U/Unidecode'], + 'checksums': ['280a6ab88e1f2eb5af79edff450021a0d3f0448952847cd79677e55e58bad051'], + }), + ('regex', '2019.02.21', { + 'source_urls': ['https://pypi.python.org/packages/source/r/regex'], + 'checksums': ['587bd4cad11c7294f89799c45778abca271d7c6668a0e85c41a6dbfa8096f9bb'], + }), + ('awesome-slugify', '1.6.5', { + 'source_urls': ['https://pypi.python.org/packages/source/a/awesome-slugify'], + 'checksums': ['bbdec3fa2187917473a2efad092b57f7125a55f841a7cf6a1773178d32ccfd71'], + 'modulename': 'slugify', + }), + ('yahmm', '1.1.3', { + 'source_tmpl': 'yahmm-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/y/yahmm'], + 'checksums': ['fe3614ef96da9410468976756fb93dc8235485242c05df01d8e5ed356a7dfb43'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/V/VCF-kit'], + 'checksums': ['e44319bc057ff4f90cc3a777bb6b1794e5dc3dcf56fe2753fee199f782fed6b6'], + # get rid of hardcoded versions for dependencies + 'prebuildopts': "sed -i 's/==[0-9.]*//g' requirements.txt && ", + 'modulename': 'vcfkit', + }), +] + +sanity_check_paths = { + 'files': ['bin/vk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 3edc4b95bbeb17574735dc20e25b160185f0f6d3 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 1 Mar 2019 12:15:22 -0600 Subject: [PATCH 0666/5331] update the checksum number --- .../a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb | 2 +- .../a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb index 5193b3cbd74..854004e05cf 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb @@ -19,7 +19,7 @@ checksums = [ '989a95fe3a83d62af4d323a9727d11b2c566adcf4d789d5d86d7b842d83e7671', # augustus-3.3.2.tar.gz '96e8d72b67e820dca0d6fdbda5b9735dc8259e27fe06167462f2bdbfef5ed7d7', # AUGUSTUS-3.3.2_fix-hardcoding.patch # AUGUSTUS-3.3.2_additional_fix_hardcoding.patch - 'c42b14d52f4b98584ac9bcf2568c73feca987f563d40628be143ada326e9dccc', + '2100c3c85a47228f1f2110b636f462305ba37a5f0c4b6f660d67f1696b25f79f', ] dependencies = [ diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb index 5da5d21fff8..05cb08c4ba2 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb @@ -22,7 +22,7 @@ checksums = [ '989a95fe3a83d62af4d323a9727d11b2c566adcf4d789d5d86d7b842d83e7671', # augustus-3.3.2.tar.gz '96e8d72b67e820dca0d6fdbda5b9735dc8259e27fe06167462f2bdbfef5ed7d7', # AUGUSTUS-3.3.2_fix-hardcoding.patch # AUGUSTUS-3.3.2_additional_fix_hardcoding.patch - 'c42b14d52f4b98584ac9bcf2568c73feca987f563d40628be143ada326e9dccc', + '2100c3c85a47228f1f2110b636f462305ba37a5f0c4b6f660d67f1696b25f79f', ] dependencies = [ From b110afcec96dfc9e9d3bbddea7ec7f3168498483 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Mar 2019 20:06:58 +0100 Subject: [PATCH 0667/5331] fix import/print/exec problems in easyconfig tests with Python 3 --- test/easyconfigs/easyconfigs.py | 12 ++++++------ test/easyconfigs/styletests.py | 2 +- test/easyconfigs/suite.py | 14 ++------------ 3 files changed, 9 insertions(+), 19 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9c3e0008483..c7b61379237 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -48,9 +48,8 @@ from easybuild.framework.easyconfig.tools import check_sha256_checksums, dep_graph, get_paths_for, process_easyconfig from easybuild.tools import config from easybuild.tools.build_log import EasyBuildError -from easybuild.tools.config import build_option +from easybuild.tools.config import GENERAL_CLASS, build_option from easybuild.tools.filetools import change_dir, remove_file, write_file -from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool from easybuild.tools.robot import check_conflicts, resolve_dependencies @@ -131,13 +130,13 @@ def test_dep_graph(self): remove_file(fn) else: - print "(skipped dep graph test)" + print("(skipped dep graph test)") def test_conflicts(self): """Check whether any conflicts occur in software dependency graphs.""" if not single_tests_ok: - print "(skipped conflicts test)" + print("(skipped conflicts test)") return if self.ordered_specs is None: @@ -645,13 +644,14 @@ def suite(): for spec in specs: if spec.endswith('.eb') and spec != 'TEMPLATE.eb': cnt += 1 - exec("def innertest(self): template_easyconfig_test(self, '%s')" % os.path.join(subpath, spec)) + code = "def innertest(self): template_easyconfig_test(self, '%s')" % os.path.join(subpath, spec) + exec(code, globals()) innertest.__doc__ = "Test for parsing of easyconfig %s" % spec # double underscore so parsing tests are run first innertest.__name__ = "test__parse_easyconfig_%s" % spec setattr(EasyConfigTest, innertest.__name__, innertest) - print "Found %s easyconfigs..." % cnt + print("Found %s easyconfigs..." % cnt) return TestLoader().loadTestsFromTestCase(EasyConfigTest) diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index 92041a4baa7..d054dcec5f3 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -48,7 +48,7 @@ class StyleTest(TestCase): def test_style_conformance(self): """Check the easyconfigs for style""" if 'pep8' not in sys.modules: - print "Skipping style checks (no pep8 available)" + print("Skipping style checks (no pep8 available)") return # all available easyconfig files diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 3f60af9abb7..b0028d1eb5c 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -36,7 +36,7 @@ import tempfile import unittest -import easybuild.tools.build_log # initialize EasyBuild logging, so we disable it +import easybuild.tools.build_log # noqa initialize EasyBuild logging, so we can disable it import test.easyconfigs.easyconfigs as e import test.easyconfigs.styletests as s from easybuild.base import fancylogger @@ -52,17 +52,7 @@ # call suite() for each module and then run them all SUITE = unittest.TestSuite([x.suite() for x in [e, s]]) - -# uses XMLTestRunner if possible, so we can output an XML file that can be supplied to Jenkins -xml_msg = "" -try: - import xmlrunner # requires unittest-xml-reporting package - xml_dir = 'test-reports' - res = xmlrunner.XMLTestRunner(output=xml_dir, verbosity=1).run(SUITE) - xml_msg = ", XML output of tests available in %s directory" % xml_dir -except ImportError, err: - sys.stderr.write("WARNING: xmlrunner module not available, falling back to using unittest...\n\n") - res = unittest.TextTestRunner().run(SUITE) +res = unittest.TextTestRunner().run(SUITE) shutil.rmtree(os.environ['EASYBUILD_TMP_LOGDIR']) del os.environ['EASYBUILD_TMP_LOGDIR'] From f0f9cd60914447e47b9be1b13701aa189ec0581b Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 13:42:32 -0600 Subject: [PATCH 0668/5331] Add required python package checks --- .../m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb index 5e55d37f12f..d645cfb1802 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb @@ -15,6 +15,9 @@ checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] dependencies = [('Python', '2.7.14')] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': ['bin/mako-render'], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], From d08ed4ef06dee1a4c1de385e7716da64435cb573 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 13:43:49 -0600 Subject: [PATCH 0669/5331] Add openmp flag --- easybuild/easyconfigs/r/RELION/RELION-2.1-fosscuda-2017b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.1-fosscuda-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-2.1-fosscuda-2017b.eb index 8f4bb136fa9..747433970b7 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-2.1-fosscuda-2017b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-2.1-fosscuda-2017b.eb @@ -9,6 +9,7 @@ description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely averages in electron cryo-microscopy (cryo-EM).""" toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'openmp': True} source_urls = ['https://github.com/3dem/relion/archive'] sources = ['%(version)s.tar.gz'] From ebc0a0fb4bfe2b9cd4cfd31f96189ff78140ed0a Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 13:45:18 -0600 Subject: [PATCH 0670/5331] adding easyconfigs: RELION-2.1-intelcuda-2017b.eb --- .../r/RELION/RELION-2.1-intelcuda-2017b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/r/RELION/RELION-2.1-intelcuda-2017b.eb diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.1-intelcuda-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-2.1-intelcuda-2017b.eb new file mode 100644 index 00000000000..95e6a23a112 --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-2.1-intelcuda-2017b.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'RELION' +version = '2.1' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/3dem/relion/archive'] +sources = ['%(version)s.tar.gz'] +patches = ['RELION-2.1_cuda_capabilities.patch'] +checksums = [ + '08729aac4fa0841e08df2c90a2c26cfe2aef52af2f5fb94a770ed2c11373b886', # 2.1.tar.gz + '541cdc484ab885353e1f79d205e55332df58df619229a131ef7811f5784d5d46', # RELION-2.1_cuda_capabilities.patch +] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('X11', '20171023'), + ('FLTK', '1.3.4'), + ('FFTW', '3.3.6'), +] + +# lowest supported capability is 3.5 +cuda_compute_capabilities = ['3.5', '3.7', '5.0', '5.2', '5.3', '6.0', '6.1', '6.2', '7.0'] +capabilities = [''.join(x.split('.')) for x in cuda_compute_capabilities] +cuda_arch = ';'.join(['-gencode arch=compute_%s,code=\"sm_%s,compute_%s\"' % (x, x, x) for x in capabilities]) + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-lpthread' " +configopts += '-DCUDA_ARCH=\'' + cuda_arch + '\'' + +sanity_check_paths = { + 'files': ['bin/relion'] + ['lib/librelion_%s.%s' % (x, SHLIB_EXT) for x in ['gpu_util', 'gui_lib', 'lib']], + 'dirs': [] +} + +moduleclass = 'bio' From afa21046fb00bf88d25da64ae2e8f460ec1f257a Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 13:46:28 -0600 Subject: [PATCH 0671/5331] Add deps --- .../f/FFTW/FFTW-3.3.6-intelcuda-2017b.eb | 25 +++++++ .../f/FLTK/FLTK-1.3.4-intelcuda-2017b.eb | 41 +++++++++++ .../l/LLVM/LLVM-5.0.0-intelcuda-2017b.eb | 44 ++++++++++++ .../l/libGLU/libGLU-9.0.0-intelcuda-2017b.eb | 25 +++++++ ...ako-1.0.7-intelcuda-2017b-Python-2.7.14.eb | 26 +++++++ .../m/Mesa/Mesa-17.2.4-intelcuda-2017b.eb | 70 +++++++++++++++++++ 6 files changed, 231 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intelcuda-2017b.eb create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intelcuda-2017b.eb create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intelcuda-2017b.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intelcuda-2017b.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intelcuda-2017b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intelcuda-2017b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intelcuda-2017b.eb new file mode 100644 index 00000000000..58fa737e8fa --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intelcuda-2017b.eb @@ -0,0 +1,25 @@ +name = 'FFTW' +version = '3.3.6' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl2.tar.gz'] +checksums = ['927e481edbb32575397eb3d62535a856'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intelcuda-2017b.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intelcuda-2017b.eb new file mode 100644 index 00000000000..eea0d70893a --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.4-intelcuda-2017b.eb @@ -0,0 +1,41 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.4' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-%(version)s_fix-LDFLAGS.patch'] +checksums = [ + 'c8ab01c4e860d53e11d40dc28f98d2fe9c85aaf6dbb5af50fd6e66afec3dc58f', # fltk-1.3.4-source.tar.gz + 'b9d39f6dce92fdb34a149f686a5d56e72912f94fd09c4958f3bb12770603da7d', # FLTK-1.3.4_fix-LDFLAGS.patch +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '17.2.4'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.32'), + ('libjpeg-turbo', '1.5.2'), + ('xprop', '1.2.2'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intelcuda-2017b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intelcuda-2017b.eb new file mode 100644 index 00000000000..38fcfaf3b0b --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intelcuda-2017b.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '5.0.0' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] +checksums = ['e35dcbae6084adcf4abb32514127c5eabd7d63b733852ccdb31e06f1373136da'] + +builddependencies = [ + ('CMake', '3.9.5'), + ('Python', '2.7.14'), +] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=1 " +configopts += "-DCMAKE_BUILD_TYPE=Release " + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intelcuda-2017b.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intelcuda-2017b.eb new file mode 100644 index 00000000000..89c2d2eb222 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-intelcuda-2017b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] +checksums = ['1f7ad0d379a722fcbd303aa5650c6d7d5544fde83196b42a73d1193568a4df12'] + +dependencies = [ + ('Mesa', '17.2.4'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..8a0bf7e1393 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] + +dependencies = [('Python', '2.7.14')] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intelcuda-2017b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intelcuda-2017b.eb new file mode 100644 index 00000000000..c82d2ed9dee --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.4-intelcuda-2017b.eb @@ -0,0 +1,70 @@ +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '17.2.4' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. +toolchainopts = {'optarch': False} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] +sources = [SOURCELOWER_TAR_XZ] +patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] +checksums = [ + '5ba408fecd6e1132e5490eec1a2f04466214e4c65c8b89b331be844768c2e550', # mesa-17.2.4.tar.xz + '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.2.4_fix-strip-llvm-flags.patch +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('Autotools', '20170619'), + ('pkg-config', '0.29.2'), + ('Mako', '1.0.7', '-Python-2.7.14'), + ('libxml2', '2.9.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('nettle', '3.3'), + ('libdrm', '2.4.88'), + ('LLVM', '5.0.0'), + ('X11', '20171023'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' From 44a1b290a45c6f12aee9b040cefadcd3ce540c89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Mar 2019 21:27:26 +0100 Subject: [PATCH 0672/5331] add patch for OpenMPI 3.1.x to fix ib-query 'Invalid argument' error --- .../o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb | 6 +++- .../o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb | 6 +++- .../o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb | 6 +++- ....1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb | 6 +++- .../OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb | 6 +++- .../OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb | 8 +++-- ....3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 8 +++-- .../o/OpenMPI/OpenMPI-3.1_fix-ib-query.patch | 36 +++++++++++++++++++ 8 files changed, 71 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1_fix-ib-query.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb index cd52676cc61..07291c638b4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['a72d5a3f64c7afa33fb6c795e1168de7f92b35fd1f97ef606cfcf7405273aedc'] +patches = ['OpenMPI-3.1_fix-ib-query.patch'] +checksums = [ + 'a72d5a3f64c7afa33fb6c795e1168de7f92b35fd1f97ef606cfcf7405273aedc', # openmpi-3.1.0.tar.gz + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch +] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb index 6679eb6e59f..8a9c2c25183 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce'] +patches = ['OpenMPI-3.1_fix-ib-query.patch'] +checksums = [ + '846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce', # openmpi-3.1.1.tar.gz + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch +] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb index f77cf79e6d0..1df7c075046 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'gcccuda', 'version': '2018b'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce'] +patches = ['OpenMPI-3.1_fix-ib-query.patch'] +checksums = [ + '846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce', # openmpi-3.1.1.tar.gz + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch +] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb index 44b0677262d..d24ba83eeb5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce'] +patches = ['OpenMPI-3.1_fix-ib-query.patch'] +checksums = [ + '846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce', # openmpi-3.1.1.tar.gz + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch +] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb index c38fc1d83da..9223fe6f024 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['363c8a1258d12df28657e9b13bfe41e30fc129a4cfb89fcf53ff68bbe1bd65b3'] +patches = ['OpenMPI-3.1_fix-ib-query.patch'] +checksums = [ + '363c8a1258d12df28657e9b13bfe41e30fc129a4cfb89fcf53ff68bbe1bd65b3', # openmpi-3.1.2.tar.gz + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch +] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb index a990de595f7..745d6879c13 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb @@ -10,13 +10,15 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] - +patches = [ + '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', + 'OpenMPI-3.1_fix-ib-query.patch', +] checksums = [ '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch ] # needed for --with-verbs diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 5d12763daa5..59f429004da 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -10,13 +10,15 @@ toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] - +patches = [ + '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', + 'OpenMPI-3.1_fix-ib-query.patch', +] checksums = [ '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch ] # needed for --with-verbs diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1_fix-ib-query.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1_fix-ib-query.patch new file mode 100644 index 00000000000..017b706561c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1_fix-ib-query.patch @@ -0,0 +1,36 @@ +fix for "error obtaining device attributes for mlx4_0 errno says Invalid argument" + +see also: +* https://github.com/open-mpi/ompi/issues/5810 +* https://github.com/open-mpi/ompi/pull/6038 + +From d70f27f9b209a00b89814fd11f7895eb82bec773 Mon Sep 17 00:00:00 2001 +From: Howard Pritchard +Date: Wed, 31 Oct 2018 14:50:15 -0600 +Subject: [PATCH] btl/openib: fix a problem with ib query + +Under certain circumstances, ibv_exp_query_device was +returning an error due to uninitialized fields in the +extended attributes struct. + +Fixes: #5810 +Fixes: #5914 + +Signed-off-by: Howard Pritchard +(cherry picked from commit 8126779a354b3e0c720d3e1790f7b936dd5b93b2) +--- + opal/mca/btl/openib/btl_openib_component.c | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/opal/mca/btl/openib/btl_openib_component.c b/opal/mca/btl/openib/btl_openib_component.c +index 44792a13ab8..8b86cbb587f 100644 +--- a/opal/mca/btl/openib/btl_openib_component.c ++++ b/opal/mca/btl/openib/btl_openib_component.c +@@ -1642,6 +1642,7 @@ static int init_one_device(opal_list_t *btl_list, struct ibv_device* ib_dev) + goto error; + } + #if HAVE_DECL_IBV_EXP_QUERY_DEVICE ++ memset(&device->ib_exp_dev_attr, 0, sizeof(device->ib_exp_dev_attr)); + device->ib_exp_dev_attr.comp_mask = IBV_EXP_DEVICE_ATTR_RESERVED - 1; + if(ibv_exp_query_device(device->ib_dev_context, &device->ib_exp_dev_attr)){ + BTL_ERROR(("error obtaining device attributes for %s errno says %s", From 778d9b59e1d316545abfe841d8bd616ba7fb51d0 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 14:54:45 -0600 Subject: [PATCH 0673/5331] Corrected sanity check path --- .../m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb index d645cfb1802..323b63bda50 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2017b-Python-2.7.14.eb @@ -20,7 +20,7 @@ download_dep_fail = True sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg-info'], } moduleclass = 'devel' From 41c95b5c02960a1853af491e64dcd44ebd1e55d2 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 15:08:17 -0600 Subject: [PATCH 0674/5331] Made additional check optional --- .../MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb index 92278ba4968..6bdafccb408 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb @@ -25,7 +25,8 @@ skipsteps = ['install'] options = {'modulename': 'matlab.engine'} -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] +# Test that connection with MATLAB can be established successfully +# sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] sanity_check_paths = { 'files': [], From c37d0ab39cca3ed51b8a850426fda7a1db8ea04b Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 15:08:54 -0600 Subject: [PATCH 0675/5331] Made additional check optional --- .../MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb index 439ddce3d1d..4bf529a2236 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb @@ -25,7 +25,8 @@ skipsteps = ['install'] options = {'modulename': 'matlab.engine'} -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] +# Test that connection with MATLAB can be established successfully +# sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] sanity_check_paths = { 'files': [], From e6ac1c5e6eea6218a2b52f69d6d18fce27150b68 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 15:09:27 -0600 Subject: [PATCH 0676/5331] Made additional check optional --- .../MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb index 0a065a74e60..bc318aabe88 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb @@ -25,7 +25,8 @@ skipsteps = ['install'] options = {'modulename': 'matlab.engine'} -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] +# Test that connection with MATLAB can be established successfully +# sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] sanity_check_paths = { 'files': [], From ef4f78a4f4444c7e74590d58ad14ed9e57579e22 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 15:09:59 -0600 Subject: [PATCH 0677/5331] Made additional check optional --- .../MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb index a00824b2ca4..992c2a55e76 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb @@ -25,7 +25,8 @@ skipsteps = ['install'] options = {'modulename': 'matlab.engine'} -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] +# Test that connection with MATLAB can be established successfully +# sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] sanity_check_paths = { 'files': [], From ceb6bf271ea38bf687fbbabc93b953387e651c95 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 1 Mar 2019 15:31:30 -0600 Subject: [PATCH 0678/5331] Corrected sanity check path --- .../m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb index 8a0bf7e1393..918a6d7e6bf 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-intelcuda-2017b-Python-2.7.14.eb @@ -20,7 +20,7 @@ download_dep_fail = True sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg-info'], } moduleclass = 'devel' From 1e519f299bfd2249e453a17f16b67be986bf08e2 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 1 Mar 2019 20:11:48 -0500 Subject: [PATCH 0679/5331] OpenBLAS: build with -fno-tree-vectorize (asm constraint bugs for <0.3.6) cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 --- .../o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb | 3 +++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb | 3 +++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb | 3 +++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb | 3 +++ .../o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb | 3 +++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb | 3 +++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb | 3 +++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb | 3 +++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb | 3 +++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb | 3 +++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb | 3 +++ 31 files changed, 93 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb index 8e7a8e3488a..8262e101c7b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb @@ -7,6 +7,9 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb index 1aae2d7107f..1f74bae982e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb @@ -7,6 +7,9 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.8.4'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb index 1474c30ba6c..cf08b1518e0 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb @@ -7,6 +7,9 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb index e83941b54cd..8be25d8c688 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb @@ -7,6 +7,9 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '1.5.16'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb index 9be631f2d33..2fcc4983a9b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb @@ -7,6 +7,9 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb index d1b44dfae90..227c532863a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb @@ -7,6 +7,9 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb index 1c0d99523c7..e92c37446fc 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb @@ -7,6 +7,9 @@ lapackver = '3.6.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb index 475ac86396b..92f00e4dc43 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb @@ -7,6 +7,9 @@ lapackver = '3.6.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.9.4-2.25'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb index 06c39b82613..bba01f87e99 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb @@ -7,6 +7,9 @@ lapackver = '3.6.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb index eaa818e6252..c270c4d3741 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb @@ -7,6 +7,9 @@ lapackver = '3.6.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb index aeade399d4c..d8e7837f8f5 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -7,6 +7,9 @@ lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb index 17a2ecb8289..f6e6cfea7c2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb @@ -7,6 +7,9 @@ lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '2016.07'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb index 61372509b2a..cba0f60271e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb @@ -7,6 +7,9 @@ lapackver = '3.7.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb index d9aed5da097..4f9a0ff4414 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb @@ -7,6 +7,9 @@ lapackver = '3.7.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb index 761f990fdbd..ede03fa45d2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb @@ -7,6 +7,9 @@ lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '2016.09'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb index f4055fe601b..09d77e691a8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb @@ -7,6 +7,9 @@ lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompic', 'version': '2016.10'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb index 0c579f0d962..1ec366a48ad 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb @@ -7,6 +7,9 @@ homepage = 'http://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} large_src = 'large.tgz' timing_src = 'timing.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb index 5b7ec851fcd..791558473da 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb @@ -7,6 +7,9 @@ homepage = 'http://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} large_src = 'large.tgz' timing_src = 'timing.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb index 86b86542660..e07336992ee 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb @@ -7,6 +7,9 @@ homepage = 'http://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '7.2.0-2.29'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} large_src = 'large.tgz' timing_src = 'timing.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb index 1e915a802ff..41033cfc6f8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb @@ -7,6 +7,9 @@ lapackver = '3.4.2' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb index 30835b68780..354b75e5aba 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb @@ -7,6 +7,9 @@ lapackver = '3.4.2' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb index b1e3b0dad6f..b9a8888c138 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb @@ -7,6 +7,9 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '1.5.14'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb index 19c2176d82f..f290e77248b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb @@ -7,6 +7,9 @@ lapackver = '3.4.2' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '1.6.10'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb index d346fc16be0..1e004c5ecd0 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb @@ -7,6 +7,9 @@ lapackver = '3.4.2' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb index 4cb827eecc2..92aaef6a932 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb @@ -7,6 +7,9 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.8.3'} diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb index a7338b7c2ce..4a9cb36e996 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb @@ -7,6 +7,9 @@ homepage = 'http://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} large_src = 'large.tgz' timing_src = 'timing.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb index dff6c7332d6..6fd5cf7e3a0 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb @@ -7,6 +7,9 @@ homepage = 'http://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} large_src = 'large.tgz' timing_src = 'timing.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb index eec4461cf73..fb91851bfd1 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb @@ -7,6 +7,9 @@ homepage = 'http://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} large_src = 'large.tgz' timing_src = 'timing.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb index 201972a8291..94de7863818 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb @@ -7,6 +7,9 @@ homepage = 'http://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} large_src = 'large.tgz' timing_src = 'timing.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb index 46de6704cff..bd0615ae66c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb @@ -7,6 +7,9 @@ homepage = 'http://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} large_src = 'large.tgz' timing_src = 'timing.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb index 531c7ff74bd..ac9dcfbc69e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb @@ -7,6 +7,9 @@ homepage = 'http://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} large_src = 'large.tgz' timing_src = 'timing.tgz' From de8122b15565601ac38fa4215d186cb01e683ed9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 Mar 2019 08:48:33 +0100 Subject: [PATCH 0680/5331] avoid use of .items() in R (bundle) easyconfigs --- ...le-Bioconductor-3.3-intel-2016b-R-3.3.1.eb | 214 ++-- ...le-Bioconductor-3.5-intel-2017a-R-3.4.0.eb | 234 ++--- ...bundle-pbd-20150605-intel-2015a-R-3.1.3.eb | 19 +- .../easyconfigs/r/R/R-3.1.1-intel-2014b.eb | 486 ++++----- .../easyconfigs/r/R/R-3.1.2-foss-2015a.eb | 540 +++++----- .../easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb | 540 +++++----- .../easyconfigs/r/R/R-3.1.2-intel-2015a.eb | 540 +++++----- .../easyconfigs/r/R/R-3.1.3-foss-2015a.eb | 560 +++++----- .../easyconfigs/r/R/R-3.1.3-intel-2015a.eb | 562 +++++----- .../easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb | 602 +++++------ .../easyconfigs/r/R/R-3.2.1-intel-2015a.eb | 718 ++++++------- .../easyconfigs/r/R/R-3.2.1-intel-2015b.eb | 718 ++++++------- .../r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 790 +++++++------- .../easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 790 +++++++------- .../easyconfigs/r/R/R-3.3.1-intel-2016b.eb | 823 +++++++-------- .../r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 860 +++++++-------- .../r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 874 ++++++++-------- .../r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 986 +++++++++--------- .../r/R/R-3.4.1-foss-2016b-X11-20160819.eb | 940 ++++++++--------- 19 files changed, 5959 insertions(+), 5837 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb index c43e3ff869c..759e7716239 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb @@ -23,7 +23,7 @@ ext_options = { ], 'source_tmpl': name_tmpl, } -bioconductor_options = { +exts_default_options = { 'source_urls': [ 'http://bioconductor.org/packages/3.3/bioc/src/contrib/', 'http://bioconductor.org/packages/3.3/data/annotation/src/contrib/', @@ -38,117 +38,119 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! exts_list = [ - ('BiocGenerics', '0.18.0', bioconductor_options), - ('Biobase', '2.32.0', bioconductor_options), - ('S4Vectors', '0.10.3', bioconductor_options), - ('IRanges', '2.6.1', bioconductor_options), - ('GenomeInfoDb', '1.8.3', bioconductor_options), - ('AnnotationDbi', '1.34.4', bioconductor_options), - ('zlibbioc', '1.18.0', bioconductor_options), - ('XVector', '0.12.1', bioconductor_options), - ('Biostrings', '2.40.2', bioconductor_options), - ('GenomicRanges', '1.24.2', bioconductor_options), - ('BiocParallel', '1.6.6', bioconductor_options), - ('Rsamtools', '1.24.0', bioconductor_options), + ('BiocGenerics', '0.18.0'), + ('Biobase', '2.32.0'), + ('S4Vectors', '0.10.3'), + ('IRanges', '2.6.1'), + ('GenomeInfoDb', '1.8.3'), + ('AnnotationDbi', '1.34.4'), + ('zlibbioc', '1.18.0'), + ('XVector', '0.12.1'), + ('Biostrings', '2.40.2'), + ('GenomicRanges', '1.24.2'), + ('BiocParallel', '1.6.6'), + ('Rsamtools', '1.24.0'), ('lambda.r', '1.1.9', ext_options), ('futile.options', '1.0.0', ext_options), ('futile.logger', '1.4.3', ext_options), - ('SummarizedExperiment', '1.2.3', bioconductor_options), - ('GenomicAlignments', '1.8.4', bioconductor_options), - ('ShortRead', '1.30.0', bioconductor_options), - ('graph', '1.50.0', bioconductor_options), - ('affyio', '1.42.0', bioconductor_options), - ('BiocInstaller', '1.22.3', bioconductor_options), - ('preprocessCore', '1.34.0', bioconductor_options), - ('affy', '1.50.0', bioconductor_options), - ('GO.db', '3.3.0', bioconductor_options), - ('limma', '3.28.19', bioconductor_options), - ('RBGL', '1.48.1', bioconductor_options), - ('org.Hs.eg.db', '3.3.0', bioconductor_options), - ('AnnotationForge', '1.14.2', bioconductor_options), - ('KEGG.db', '3.2.3', bioconductor_options), - ('annaffy', '1.44.0', bioconductor_options), - ('gcrma', '2.44.0', bioconductor_options), - ('oligoClasses', '1.34.0', bioconductor_options), - ('edgeR', '3.14.0', bioconductor_options), - ('PFAM.db', '3.3.0', bioconductor_options), + ('SummarizedExperiment', '1.2.3'), + ('GenomicAlignments', '1.8.4'), + ('ShortRead', '1.30.0'), + ('graph', '1.50.0'), + ('affyio', '1.42.0'), + ('BiocInstaller', '1.22.3'), + ('preprocessCore', '1.34.0'), + ('affy', '1.50.0'), + ('GO.db', '3.3.0'), + ('limma', '3.28.19'), + ('RBGL', '1.48.1'), + ('org.Hs.eg.db', '3.3.0'), + ('AnnotationForge', '1.14.2'), + ('KEGG.db', '3.2.3'), + ('annaffy', '1.44.0'), + ('gcrma', '2.44.0'), + ('oligoClasses', '1.34.0'), + ('edgeR', '3.14.0'), + ('PFAM.db', '3.3.0'), ('perm', '1.0-0.0', ext_options), - ('baySeq', '2.6.0', bioconductor_options), - ('qvalue', '2.4.2', bioconductor_options), - ('impute', '1.46.0', bioconductor_options), + ('baySeq', '2.6.0'), + ('qvalue', '2.4.2'), + ('impute', '1.46.0'), ('samr', '2.0', ext_options), - ('DEGseq', '1.26.0', bioconductor_options), - ('hgu133plus2.db', '3.2.3', bioconductor_options), - ('illuminaio', '0.14.0', bioconductor_options), - ('rtracklayer', '1.32.2', bioconductor_options), - ('biomaRt', '2.28.0', bioconductor_options), - ('GenomicFeatures', '1.24.5', bioconductor_options), - ('bumphunter', '1.12.0', bioconductor_options), - ('multtest', '2.28.0', bioconductor_options), - ('siggenes', '1.46.0', bioconductor_options), - ('DynDoc', '1.50.0', bioconductor_options), - ('genoset', '1.28.2', bioconductor_options), - ('NOISeq', '2.16.0', bioconductor_options), - ('Rgraphviz', '2.16.0', bioconductor_options), - ('RNASeqPower', '1.12.0', bioconductor_options), - ('annotate', '1.50.0', bioconductor_options), - ('GSEABase', '1.34.0', bioconductor_options), - ('genefilter', '1.54.2', bioconductor_options), - ('Category', '2.38.0', bioconductor_options), - ('GOstats', '2.38.1', bioconductor_options), - ('BSgenome', '1.40.1', bioconductor_options), - ('VariantAnnotation', '1.18.7', bioconductor_options), - ('interactiveDisplayBase', '1.10.3', bioconductor_options), - ('AnnotationHub', '2.4.2', bioconductor_options), - ('ensembldb', '1.4.7', bioconductor_options), - ('biovizBase', '1.20.0', bioconductor_options), - ('OrganismDbi', '1.14.1', bioconductor_options), - ('ggbio', '1.20.2', bioconductor_options), - ('geneplotter', '1.50.0', bioconductor_options), - ('DESeq2', '1.12.4', bioconductor_options), - ('ReportingTools', '2.12.2', bioconductor_options), - ('affycoretools', '1.44.3', bioconductor_options), - ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', bioconductor_options), - ('Homo.sapiens', '1.3.1', bioconductor_options), - ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), - ('AgiMicroRna', '2.22.0', bioconductor_options), - ('GenomeGraphs', '1.32.0', bioconductor_options), - ('geneLenDataBase', '1.8.0', bioconductor_options), - ('goseq', '1.24.0', bioconductor_options), - ('KEGGREST', '1.12.2', bioconductor_options), - ('KEGGgraph', '1.30.0', bioconductor_options), - ('KEGGprofile', '1.14.0', bioconductor_options), - ('GEOquery', '2.38.4', bioconductor_options), + ('DEGseq', '1.26.0'), + ('hgu133plus2.db', '3.2.3'), + ('illuminaio', '0.14.0'), + ('rtracklayer', '1.32.2'), + ('biomaRt', '2.28.0'), + ('GenomicFeatures', '1.24.5'), + ('bumphunter', '1.12.0'), + ('multtest', '2.28.0'), + ('siggenes', '1.46.0'), + ('DynDoc', '1.50.0'), + ('genoset', '1.28.2'), + ('NOISeq', '2.16.0'), + ('Rgraphviz', '2.16.0'), + ('RNASeqPower', '1.12.0'), + ('annotate', '1.50.0'), + ('GSEABase', '1.34.0'), + ('genefilter', '1.54.2'), + ('Category', '2.38.0'), + ('GOstats', '2.38.1'), + ('BSgenome', '1.40.1'), + ('VariantAnnotation', '1.18.7'), + ('interactiveDisplayBase', '1.10.3'), + ('AnnotationHub', '2.4.2'), + ('ensembldb', '1.4.7'), + ('biovizBase', '1.20.0'), + ('OrganismDbi', '1.14.1'), + ('ggbio', '1.20.2'), + ('geneplotter', '1.50.0'), + ('DESeq2', '1.12.4'), + ('ReportingTools', '2.12.2'), + ('affycoretools', '1.44.3'), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2'), + ('Homo.sapiens', '1.3.1'), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0'), + ('AgiMicroRna', '2.22.0'), + ('GenomeGraphs', '1.32.0'), + ('geneLenDataBase', '1.8.0'), + ('goseq', '1.24.0'), + ('KEGGREST', '1.12.2'), + ('KEGGgraph', '1.30.0'), + ('KEGGprofile', '1.14.0'), + ('GEOquery', '2.38.4'), ('mixOmics', '6.0.0', ext_options), - ('minfi', '1.18.6', bioconductor_options), - ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), - ('methylumi', '2.18.2', bioconductor_options), - ('lumi', '2.24.0', bioconductor_options), - ('widgetTools', '1.50.0', bioconductor_options), - ('tkWidgets', '1.50.0', bioconductor_options), - ('Mfuzz', '2.32.0', bioconductor_options), - ('maSigPro', '1.44.0', bioconductor_options), - ('SPIA', '2.24.0', bioconductor_options), - ('Gviz', '1.16.4', bioconductor_options), - ('cummeRbund', '2.14.0', bioconductor_options), - ('GenomicFiles', '1.8.0', bioconductor_options), - ('derfinderHelper', '1.6.3', bioconductor_options), - ('derfinder', '1.6.4', bioconductor_options), - ('polyester', '1.8.3', bioconductor_options), - ('Rsubread', '1.22.3', bioconductor_options), - ('pcaMethods', '1.64.0', bioconductor_options), - ('marray', '1.50.0', bioconductor_options), - ('CGHbase', '1.32.0', bioconductor_options), - ('sigaR', '1.15.0', bioconductor_options), - ('HCsnip', '1.12.0', bioconductor_options), - ('metagenomeSeq', '1.14.2', bioconductor_options), - ('gdsfmt', '1.8.3', bioconductor_options), - ('SNPRelate', '1.6.5', dict(bioconductor_options.items() + [('patches', ['SNPRelate-1.6.5_no-SSE-intr.patch'])])), - ('rhdf5', '2.16.0', bioconductor_options), - ('biomformat', '1.0.2', bioconductor_options), - ('phyloseq', '1.16.2', bioconductor_options), - ('ALDEx2', '1.4.0', bioconductor_options), - ('dada2', '1.0.3', bioconductor_options), + ('minfi', '1.18.6'), + ('FDb.InfiniumMethylation.hg19', '2.2.0'), + ('methylumi', '2.18.2'), + ('lumi', '2.24.0'), + ('widgetTools', '1.50.0'), + ('tkWidgets', '1.50.0'), + ('Mfuzz', '2.32.0'), + ('maSigPro', '1.44.0'), + ('SPIA', '2.24.0'), + ('Gviz', '1.16.4'), + ('cummeRbund', '2.14.0'), + ('GenomicFiles', '1.8.0'), + ('derfinderHelper', '1.6.3'), + ('derfinder', '1.6.4'), + ('polyester', '1.8.3'), + ('Rsubread', '1.22.3'), + ('pcaMethods', '1.64.0'), + ('marray', '1.50.0'), + ('CGHbase', '1.32.0'), + ('sigaR', '1.15.0'), + ('HCsnip', '1.12.0'), + ('metagenomeSeq', '1.14.2'), + ('gdsfmt', '1.8.3'), + ('SNPRelate', '1.6.5', { + 'patches': ['SNPRelate-1.6.5_no-SSE-intr.patch'], + }), + ('rhdf5', '2.16.0'), + ('biomformat', '1.0.2'), + ('phyloseq', '1.16.2'), + ('ALDEx2', '1.4.0'), + ('dada2', '1.0.3'), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb index 4eb3ffe0f7a..cb97e22cbec 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.5-intel-2017a-R-3.4.0.eb @@ -23,7 +23,7 @@ ext_options = { ], 'source_tmpl': name_tmpl, } -bioconductor_options = { +exts_default_options = { 'source_urls': [ 'http://bioconductor.org/packages/3.5/bioc/src/contrib/', 'http://bioconductor.org/packages/3.5/data/annotation/src/contrib/', @@ -39,129 +39,131 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") # !! order of packages is important !! # packages updated on May 28th 2017 exts_list = [ - ('BiocGenerics', '0.22.0', bioconductor_options), - ('Biobase', '2.36.2', bioconductor_options), - ('S4Vectors', '0.14.2', bioconductor_options), - ('IRanges', '2.10.2', bioconductor_options), - ('GenomeInfoDbData', '0.99.0', bioconductor_options), - ('GenomeInfoDb', '1.12.0', bioconductor_options), - ('AnnotationDbi', '1.38.0', bioconductor_options), - ('zlibbioc', '1.22.0', bioconductor_options), - ('XVector', '0.16.0', bioconductor_options), - ('Biostrings', '2.44.0', bioconductor_options), - ('GenomicRanges', '1.28.3', bioconductor_options), - ('BiocParallel', '1.10.1', bioconductor_options), - ('Rsamtools', '1.28.0', bioconductor_options), + ('BiocGenerics', '0.22.0'), + ('Biobase', '2.36.2'), + ('S4Vectors', '0.14.2'), + ('IRanges', '2.10.2'), + ('GenomeInfoDbData', '0.99.0'), + ('GenomeInfoDb', '1.12.0'), + ('AnnotationDbi', '1.38.0'), + ('zlibbioc', '1.22.0'), + ('XVector', '0.16.0'), + ('Biostrings', '2.44.0'), + ('GenomicRanges', '1.28.3'), + ('BiocParallel', '1.10.1'), + ('Rsamtools', '1.28.0'), ('lambda.r', '1.1.9', ext_options), ('futile.options', '1.0.0', ext_options), ('futile.logger', 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+ ('DelayedArray', '0.2.4'), + ('SummarizedExperiment', '1.6.1'), + ('GenomicAlignments', '1.12.1'), + ('ShortRead', '1.34.0'), + ('graph', '1.54.0'), + ('affyio', '1.46.0'), + ('BiocInstaller', '1.26.0'), + ('preprocessCore', '1.38.1'), + ('affy', '1.54.0'), + ('GO.db', '3.4.1'), + ('limma', '3.32.2'), + ('RBGL', '1.52.0'), + ('org.Hs.eg.db', '3.4.1'), + ('AnnotationForge', '1.18.0'), + ('KEGG.db', '3.2.3'), + ('annaffy', '1.48.0'), + ('gcrma', '2.48.0'), + ('oligoClasses', '1.38.0'), + ('edgeR', '3.18.1'), + ('PFAM.db', '3.4.1'), ('perm', '1.0-0.0', ext_options), - ('baySeq', '2.10.0', bioconductor_options), - ('qvalue', '2.8.0', bioconductor_options), - ('impute', '1.50.1', bioconductor_options), + ('baySeq', '2.10.0'), + ('qvalue', '2.8.0'), + ('impute', '1.50.1'), ('samr', '2.0', ext_options), - ('DEGseq', '1.30.0', bioconductor_options), - ('hgu133plus2.db', '3.2.3', bioconductor_options), - ('illuminaio', '0.18.0', bioconductor_options), - ('rtracklayer', '1.36.3', 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'1.14.0', bioconductor_options), + ('dada2', '1.4.0'), + ('LEA', '1.8.1'), + ('tximport', '1.4.0'), + ('scater', '1.4.0'), + ('scran', '1.4.5'), + ('SC3', '1.4.2'), + ('ComplexHeatmap', '1.14.0'), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb index 95d136f187d..264405cbbb9 100644 --- a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb @@ -19,7 +19,7 @@ dependencies = [ ] name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -30,14 +30,15 @@ ext_options = { # !! order of packages is important !! exts_list = [ - ('pbdMPI', '0.2-5', ext_options), - ('pbdSLAP', '0.2-0', ext_options), - ('pbdBASE', '0.2-3', dict(ext_options.items() + - [('patches', ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'])])), - ('pbdDMAT', '0.2-3', ext_options), - ('pbdDEMO', '0.2-0', ext_options), - ('pmclust', '0.1-6', ext_options), - ('EMCluster', '0.2-4', ext_options), + ('pbdMPI', '0.2-5'), + ('pbdSLAP', '0.2-0'), + ('pbdBASE', '0.2-3', { + 'patches': ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'], + }), + ('pbdDMAT', '0.2-3'), + ('pbdDEMO', '0.2-0'), + ('pmclust', '0.1-6'), + ('EMCluster', '0.2-4'), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb b/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb index 6b5e378b403..3462ebf3f2c 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb @@ -26,7 +26,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.freestatistics.org/src/contrib', # alternative for packages @@ -57,162 +57,164 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', ext_options), - ('abind', '1.4-0', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-4', dict(ext_options.items() + {'patches': ['geometry-0.3-4-icc.patch']}.items())), - ('bit', '1.1-12', ext_options), - ('filehash', '2.2-2', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '3.6', ext_options), - ('bootstrap', '2014.4', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('Defaults', '1.1-1', ext_options), - ('fdrtool', '1.2.12', ext_options), - ('formatR', '0.10', ext_options), - ('gtools', '3.4.1', ext_options), - ('gdata', '2.13.3', 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('R.oo', '1.18.0', ext_options), - ('cgdsr', '1.1.30', ext_options), - ('R.utils', '1.32.4', ext_options), - ('R.matlab', '3.0.1', ext_options), - ('Rniftilib', '0.0-32', ext_options), + ('Rmpi', '0.6-5'), + ('abind', '1.4-0'), + ('magic', '1.5-6'), + ('geometry', '0.3-4', { + 'patches': ['geometry-0.3-4-icc.patch'], + }), + ('bit', '1.1-12'), + ('filehash', '2.2-2'), + ('ff', '2.2-13'), + ('bnlearn', '3.6'), + ('bootstrap', '2014.4'), + ('combinat', '0.0-8'), + ('deal', '1.2-37'), + ('Defaults', '1.1-1'), + ('fdrtool', '1.2.12'), + ('formatR', '0.10'), + ('gtools', '3.4.1'), + ('gdata', '2.13.3'), + ('GSA', '1.03'), + ('highr', '0.3'), + ('infotheo', '1.1.1'), + ('lars', '1.2'), + ('lazy', '1.2-15'), + ('kernlab', '0.9-19'), + ('mime', '0.1.1'), + ('markdown', '0.7'), + ('mlbench', '2.1-1'), + ('NLP', '0.1-3'), + ('mclust', '4.3'), + ('RANN', '2.3.0'), + ('rmeta', '2.16'), + ('segmented', '0.3-1.0'), + ('som', '0.3-5'), + ('SuppDists', '1.1-9.1'), + ('stabledist', '0.6-6'), + ('survivalROC', '1.0.3'), + ('pspline', '1.0-16'), + ('timeDate', '3010.98'), + ('longmemo', '1.0-0'), + ('ADGofTest', '0.3'), + ('ade4', '1.6-2'), + ('AlgDesign', '1.1-7.2'), + ('base64enc', '0.1-2'), + ('BH', '1.54.0-2'), + ('brew', '1.0-6'), + ('Brobdingnag', '1.2-4'), + ('corpcor', '1.6.6'), + ('longitudinal', '1.1.9'), + ('checkmate', '1.1'), + ('cubature', '1.1-2'), + ('DEoptimR', '1.0-1'), + ('digest', '0.6.4'), + ('fastmatch', '1.0-4'), + ('ffbase', '0.11.3'), + ('iterators', '1.0.7'), + ('maps', '2.3-7'), + ('nnls', '1.4'), + ('sendmailR', '1.1-2'), + ('spam', '0.41-0'), + ('subplex', '1.1-3'), + ('stringr', '0.6.2'), + ('evaluate', '0.5.5'), + ('logspline', '2.1.5'), + ('ncbit', '2013.03.29'), + ('permute', '0.8-3'), + ('plotrix', '3.5-7'), + ('randomForest', '4.6-7'), + ('scatterplot3d', '0.3-35'), + ('SparseM', '1.03'), + ('tripack', '1.3-6'), + ('irace', '1.04'), + ('rJava', '0.9-6'), + ('lattice', '0.20-29'), + ('RColorBrewer', '1.0-5'), + ('latticeExtra', '0.6-26'), + ('Matrix', '1.1-4'), + ('png', '0.1-7'), + ('Rcpp', '0.11.2'), + ('RcppArmadillo', '0.4.300.8.0'), + ('plyr', '1.8.1'), + ('pROC', '1.7.3'), + ('quadprog', '1.5-5'), + ('BB', '2014.1-1'), + ('BBmisc', '1.7'), + ('fail', '1.2'), + ('rlecuyer', '0.3-3'), + ('snow', '0.3-13'), + ('MASS', '7.3-33'), + ('tree', '1.0-35'), + ('pls', '2.4-3'), + ('class', '7.3-10'), + ('e1071', '1.6-3'), + ('nnet', '7.3-8'), + ('car', '2.0-20'), + ('colorspace', '1.2-4'), + ('robustbase', '0.91-1'), + ('sp', '1.0-15'), + ('vcd', '1.3-1'), + ('snowfall', '1.84-6'), + ('rpart', '4.1-8'), + ('mice', '2.22'), + ('nlme', '3.1-117'), + ('urca', '1.2-8'), + ('fracdiff', '1.4-2'), + ('mgcv', '1.8-0'), + ('logistf', '1.21'), + ('akima', '0.5-11'), + ('bitops', '1.0-6'), + ('boot', '1.3-11'), + ('mixtools', '1.0.2'), + ('cluster', '1.15.2'), + ('gclus', '1.3.1'), + ('coda', '0.16-1'), + ('codetools', '0.2-8'), + ('foreach', '1.4.2'), + ('doMC', '1.3.3'), + ('DBI', '0.2-7'), + ('foreign', '0.8-61'), + ('survival', '2.37-7'), + ('gam', '1.09.1'), + ('gamlss.data', '4.2-7'), + ('gamlss.dist', '4.3-0'), + ('hwriter', '1.3'), + ('KernSmooth', '2.23-12'), + ('zoo', '1.7-11'), + ('xts', '0.9-7'), + ('TTR', '0.22-0'), + ('quantmod', '0.4-0'), + ('lmtest', '0.9-33'), + ('mnormt', '1.5-1'), + ('mvtnorm', '0.9-99992'), + ('pcaPP', '1.9-49'), + ('numDeriv', '2012.9-1'), + ('lava', '1.2.6'), + ('prodlim', '1.4.3'), + ('pscl', '1.04.4'), + ('RSQLite', '0.11.4'), + ('BatchJobs', '1.2'), + ('sandwich', '2.3-0'), + ('sfsmisc', '1.0-26'), + ('spatial', '7.3-8'), + ('VGAM', '0.9-4'), + ('waveslim', '1.7.3'), + ('xtable', '1.7-3'), + ('profileModel', '0.5-9'), + ('brglm', '0.5-9'), + ('deSolve', '1.10-9'), + ('odesolve', '0.9-9'), + ('tseriesChaos', '0.1-13'), + ('tseries', '0.10-32'), + ('neuRosim', '0.2-10'), + ('fastICA', '1.2-0'), + ('R.methodsS3', '1.6.1'), + ('R.oo', '1.18.0'), + ('cgdsr', '1.1.30'), + ('R.utils', '1.32.4'), + ('R.matlab', '3.0.1'), + ('Rniftilib', '0.0-32'), ('BiocGenerics', '0.10.0', bioconductor_options), ('Biobase', '2.24.0', bioconductor_options), ('IRanges', '1.22.10', bioconductor_options), @@ -228,91 +230,91 @@ exts_list = [ ('GenomicAlignments', '1.0.4', bioconductor_options), ('ShortRead', '1.22.0', bioconductor_options), ('graph', '1.42.0', bioconductor_options), - ('igraph0', '0.5.7', ext_options), - ('gbm', '2.1', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.1-1', ext_options), - ('Hmisc', '3.14-4', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.2', ext_options), - ('scales', '0.2.4', ext_options), - ('fastcluster', '1.1.13', ext_options), - ('reshape2', '1.4', ext_options), - ('data.table', '1.9.2', ext_options), - ('gtable', '0.1.2', ext_options), - ('proto', '0.3-10', ext_options), - ('ggplot2', '1.0.0', ext_options), - ('igraph', '0.7.1', ext_options), - ('GeneNet', '1.2.9', ext_options), - ('ape', '3.1-2', ext_options), - ('htmltools', '0.2.4', ext_options), - ('RJSONIO', '1.2-0.2', ext_options), - ('caTools', '1.17', ext_options), - ('gplots', '2.14.0', ext_options), - ('ROCR', '1.0-5', ext_options), - ('httpuv', '1.3.0', ext_options), - ('shiny', '0.10.0', ext_options), - ('adegenet', '1.4-2', ext_options), - ('phylobase', '0.6.8', ext_options), - ('adephylo', '1.1-6', ext_options), - ('animation', '2.2', ext_options), - ('bigmemory.sri', '0.1.2', ext_options), - ('bigmemory', '4.4.6', ext_options), - ('calibrate', '1.7.2', ext_options), - ('clusterGeneration', '1.3.1', ext_options), - ('raster', '2.2-31', ext_options), - ('dismo', '0.9-3', ext_options), - ('expm', '0.99-1.1', ext_options), - ('extrafontdb', '1.0', ext_options), - ('Rttf2pt1', '1.3', ext_options), - ('extrafont', '0.16', ext_options), - ('fields', '7.1', ext_options), - ('shapefiles', '0.7', ext_options), - ('fossil', '0.3.7', ext_options), - ('geiger', '2.0.3', ext_options), - ('glmnet', '1.9-8', ext_options), - ('gmp', '0.5-11', ext_options), - ('labdsv', '1.6-1', ext_options), - ('MatrixModels', '0.3-1.1', ext_options), - ('mboost', '2.3-0', ext_options), - ('msm', '1.3', ext_options), - ('nor1mix', '1.1-4', ext_options), - ('np', '0.60-2', ext_options), - ('polynom', '1.3-8', ext_options), - ('partitions', '1.9-15', ext_options), - ('phangorn', '1.99-7', ext_options), - ('phytools', '0.4-21', ext_options), - ('vegan', '2.0-10', ext_options), - ('picante', '1.6-2', ext_options), - ('quantreg', '5.05', ext_options), - ('RcppEigen', '0.3.2.1.2', ext_options), - ('rgl', '0.93.996', ext_options), - ('rms', '4.2-0', ext_options), - ('RWekajars', '3.7.11-1', ext_options), - ('RWeka', '0.4-23', ext_options), - ('slam', '0.1-32', ext_options), - ('Snowball', '0.0-11', ext_options), - ('spacodiR', '0.13.0115', ext_options), - ('tm', '0.6', ext_options), - ('TraMineR', '1.8-8', ext_options), - ('untb', '1.7-2', ext_options), - ('chemometrics', '1.3.8', ext_options), - ('FNN', '1.1', ext_options), - ('forecast', '5.4', ext_options), - ('Mcomp', '2.05', ext_options), - ('ipred', '0.9-3', ext_options), - ('knitr', '1.6', ext_options), - ('statmod', '1.4.20', ext_options), - ('miscTools', '0.6-16', ext_options), - ('maxLik', '1.2-0', ext_options), - ('mlogit', '0.2-4', ext_options), - ('gdsfmt', '1.0.4', ext_options), - ('SNPRelate', '0.9.19', ext_options), - ('getopt', '1.20.0', ext_options), - ('gsalib', '2.0', ext_options), - ('reshape', '0.8.5', ext_options), - ('optparse', '1.2.0', ext_options), - ('klaR', '0.6-11', ext_options), + ('igraph0', '0.5.7'), + ('gbm', '2.1'), + ('dichromat', '2.0-0'), + ('Formula', '1.1-1'), + ('Hmisc', '3.14-4'), + ('munsell', '0.4.2'), + ('labeling', '0.2'), + ('scales', '0.2.4'), + ('fastcluster', '1.1.13'), + ('reshape2', '1.4'), + ('data.table', '1.9.2'), + ('gtable', '0.1.2'), + ('proto', '0.3-10'), + ('ggplot2', '1.0.0'), + ('igraph', '0.7.1'), + ('GeneNet', '1.2.9'), + ('ape', '3.1-2'), + ('htmltools', '0.2.4'), + ('RJSONIO', '1.2-0.2'), + ('caTools', '1.17'), + ('gplots', '2.14.0'), + ('ROCR', '1.0-5'), + ('httpuv', '1.3.0'), + ('shiny', '0.10.0'), + ('adegenet', '1.4-2'), + ('phylobase', '0.6.8'), + ('adephylo', '1.1-6'), + ('animation', '2.2'), + ('bigmemory.sri', '0.1.2'), + ('bigmemory', '4.4.6'), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.1'), + ('raster', '2.2-31'), + ('dismo', '0.9-3'), + ('expm', '0.99-1.1'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3'), + ('extrafont', '0.16'), + ('fields', '7.1'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.3'), + ('glmnet', '1.9-8'), + ('gmp', '0.5-11'), + ('labdsv', '1.6-1'), + ('MatrixModels', '0.3-1.1'), + ('mboost', '2.3-0'), + ('msm', '1.3'), + ('nor1mix', '1.1-4'), + ('np', '0.60-2'), + ('polynom', '1.3-8'), + ('partitions', '1.9-15'), + ('phangorn', '1.99-7'), + ('phytools', '0.4-21'), + ('vegan', '2.0-10'), + ('picante', '1.6-2'), + ('quantreg', '5.05'), + ('RcppEigen', '0.3.2.1.2'), + ('rgl', '0.93.996'), + ('rms', '4.2-0'), + ('RWekajars', '3.7.11-1'), + ('RWeka', '0.4-23'), + ('slam', '0.1-32'), + ('Snowball', '0.0-11'), + ('spacodiR', '0.13.0115'), + ('tm', '0.6'), + ('TraMineR', '1.8-8'), + ('untb', '1.7-2'), + ('chemometrics', '1.3.8'), + ('FNN', '1.1'), + ('forecast', '5.4'), + ('Mcomp', '2.05'), + ('ipred', '0.9-3'), + ('knitr', '1.6'), + ('statmod', '1.4.20'), + ('miscTools', '0.6-16'), + ('maxLik', '1.2-0'), + ('mlogit', '0.2-4'), + ('gdsfmt', '1.0.4'), + ('SNPRelate', '0.9.19'), + ('getopt', '1.20.0'), + ('gsalib', '2.0'), + ('reshape', '0.8.5'), + ('optparse', '1.2.0'), + ('klaR', '0.6-11'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index 8458339b7d6..32f9e3876e9 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -26,7 +26,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -63,158 +63,162 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-0', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-4', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.2-2', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '3.6', ext_options), - ('bootstrap', '2014.4', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.13', ext_options), - ('formatR', '1.0', ext_options), - ('gtools', '3.4.1', ext_options), - ('gdata', '2.13.3', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.4', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-19', ext_options), - ('mime', '0.2', ext_options), - ('markdown', '0.7.4', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-5', ext_options), - ('mclust', '4.4', ext_options), - ('RANN', '2.4.1', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.0', ext_options), - ('som', '0.3-5', ext_options), - ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.6-6', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-16', ext_options), - ('timeDate', '3011.99', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.6-2', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-2', ext_options), - ('BH', '1.55.0-3', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.7', ext_options), - ('longitudinal', '1.1.10', ext_options), - ('checkmate', '1.5.1', ext_options), - ('cubature', '1.1-2', ext_options), - ('DEoptimR', '1.0-2', ext_options), - ('digest', '0.6.8', ext_options), - ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.11.3', ext_options), - ('iterators', '1.0.7', ext_options), - ('maps', '2.3-9', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.0-1', ext_options), - ('subplex', '1.1-4', ext_options), - ('stringr', '0.6.2', ext_options), - ('evaluate', '0.5.5', ext_options), - ('logspline', '2.1.5', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.8-3', ext_options), - ('plotrix', '3.5-10', ext_options), - ('randomForest', '4.6-10', ext_options), - ('scatterplot3d', '0.3-35', ext_options), - ('SparseM', '1.6', ext_options), - ('tripack', '1.3-6', ext_options), - ('irace', '1.06', ext_options), - ('rJava', '0.9-6', ext_options), - ('lattice', '0.20-29', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.1-4', ext_options), - ('png', '0.1-7', ext_options), - ('Rcpp', '0.11.3', ext_options), - ('RcppArmadillo', '0.4.600.0', ext_options), - ('plyr', '1.8.1', ext_options), - ('pROC', '1.7.3', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.8', ext_options), - ('fail', '1.2', ext_options), - ('rlecuyer', '0.3-3', ext_options), - ('snow', '0.3-13', ext_options), - ('MASS', '7.3-35', ext_options), - ('tree', '1.0-35', ext_options), - ('pls', '2.4-3', ext_options), - ('class', '7.3-11', ext_options), - ('e1071', '1.6-4', ext_options), - ('nnet', '7.3-8', ext_options), - ('car', '2.0-22', ext_options), - ('colorspace', '1.2-4', ext_options), - ('robustbase', '0.92-2', ext_options), - ('sp', '1.0-17', ext_options), - ('vcd', '1.3-2', ext_options), - ('snowfall', '1.84-6', ext_options), - ('rpart', '4.1-8', ext_options), - ('mice', '2.22', ext_options), - ('nlme', '3.1-118', ext_options), - ('urca', '1.2-8', ext_options), - ('fracdiff', '1.4-2', ext_options), - ('mgcv', '1.8-4', ext_options), - ('logistf', '1.21', ext_options), - ('akima', '0.5-11', ext_options), - ('bitops', '1.0-6', ext_options), - ('boot', '1.3-13', ext_options), - ('mixtools', '1.0.2', ext_options), - ('cluster', '1.15.3', ext_options), - ('gclus', '1.3.1', ext_options), - ('coda', '0.16-1', ext_options), - ('codetools', '0.2-9', ext_options), - ('foreach', '1.4.2', ext_options), - ('doMC', '1.3.3', ext_options), - ('DBI', '0.3.1', ext_options), - ('foreign', '0.8-62', ext_options), - ('survival', '2.37-7', ext_options), - ('gam', '1.09.1', ext_options), - ('gamlss.data', '4.2-7', ext_options), - ('gamlss.dist', '4.3-1', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-13', ext_options), - ('zoo', '1.7-11', ext_options), - ('xts', '0.9-7', ext_options), - ('TTR', '0.22-0', ext_options), - ('quantmod', '0.4-3', ext_options), - ('lmtest', '0.9-33', ext_options), - ('mnormt', '1.5-1', ext_options), - ('mvtnorm', '1.0-2', ext_options), - ('pcaPP', '1.9-60', ext_options), - ('numDeriv', '2012.9-1', ext_options), - ('lava', '1.3', ext_options), - ('prodlim', '1.5.1', ext_options), - ('pscl', '1.4.6', ext_options), - ('RSQLite', '1.0.0', ext_options), - ('BatchJobs', '1.5', ext_options), - ('sandwich', '2.3-2', ext_options), - ('sfsmisc', '1.0-27', ext_options), - ('spatial', '7.3-8', ext_options), - ('VGAM', '0.9-6', ext_options), - ('waveslim', '1.7.3', ext_options), - ('xtable', '1.7-4', ext_options), - ('profileModel', '0.5-9', ext_options), - ('brglm', '0.5-9', ext_options), - ('deSolve', '1.11', ext_options), - ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-32', ext_options), - ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.6.1', ext_options), - ('R.oo', '1.18.0', ext_options), - ('cgdsr', '1.1.33', ext_options), - ('R.utils', '1.34.0', ext_options), - ('R.matlab', '3.1.1', ext_options), + ('Rmpi', '0.6-5', { + 'patches': ['Rmpi-0.6-5_impi5.patch'], + }), + ('abind', '1.4-0'), + ('magic', '1.5-6'), + ('geometry', '0.3-4', { + 'patches': ['geometry-0.3-4-icc.patch'], + }), + ('bit', '1.1-12'), + ('filehash', '2.2-2'), + ('ff', '2.2-13'), + ('bnlearn', '3.6'), + ('bootstrap', '2014.4'), + ('combinat', '0.0-8'), + ('deal', '1.2-37'), + ('fdrtool', '1.2.13'), + ('formatR', '1.0'), + ('gtools', '3.4.1'), + ('gdata', '2.13.3'), + ('GSA', '1.03'), + ('highr', '0.4'), + ('infotheo', '1.2.0'), + ('lars', '1.2'), + ('lazy', '1.2-15'), + ('kernlab', '0.9-19'), + ('mime', '0.2'), + ('markdown', '0.7.4'), + ('mlbench', '2.1-1'), + ('NLP', '0.1-5'), + ('mclust', '4.4'), + ('RANN', '2.4.1'), + ('rmeta', '2.16'), + ('segmented', '0.5-1.0'), + ('som', '0.3-5'), + ('SuppDists', '1.1-9.1'), + ('stabledist', '0.6-6'), + ('survivalROC', '1.0.3'), + ('pspline', '1.0-16'), + ('timeDate', '3011.99'), + ('longmemo', '1.0-0'), + ('ADGofTest', '0.3'), + ('ade4', '1.6-2'), + ('AlgDesign', '1.1-7.3'), + ('base64enc', '0.1-2'), + ('BH', '1.55.0-3'), + ('brew', '1.0-6'), + ('Brobdingnag', '1.2-4'), + ('corpcor', '1.6.7'), + ('longitudinal', '1.1.10'), + ('checkmate', '1.5.1'), + ('cubature', '1.1-2'), + ('DEoptimR', '1.0-2'), + ('digest', '0.6.8'), + ('fastmatch', '1.0-4'), + ('ffbase', '0.11.3'), + ('iterators', '1.0.7'), + ('maps', '2.3-9'), + ('nnls', '1.4'), + ('sendmailR', '1.2-1'), + ('spam', '1.0-1'), + ('subplex', '1.1-4'), + ('stringr', '0.6.2'), + ('evaluate', '0.5.5'), + ('logspline', '2.1.5'), + ('ncbit', '2013.03.29'), + ('permute', '0.8-3'), + ('plotrix', '3.5-10'), + ('randomForest', '4.6-10'), + ('scatterplot3d', '0.3-35'), + ('SparseM', '1.6'), + ('tripack', '1.3-6'), + ('irace', '1.06'), + ('rJava', '0.9-6'), + ('lattice', '0.20-29'), + ('RColorBrewer', '1.1-2'), + ('latticeExtra', '0.6-26'), + ('Matrix', '1.1-4'), + ('png', '0.1-7'), + ('Rcpp', '0.11.3'), + ('RcppArmadillo', '0.4.600.0'), + ('plyr', '1.8.1'), + ('pROC', '1.7.3'), + ('quadprog', '1.5-5'), + ('BB', '2014.10-1'), + ('BBmisc', '1.8'), + ('fail', '1.2'), + ('rlecuyer', '0.3-3'), + ('snow', '0.3-13'), + ('MASS', '7.3-35'), + ('tree', '1.0-35'), + ('pls', '2.4-3'), + ('class', '7.3-11'), + ('e1071', '1.6-4'), + ('nnet', '7.3-8'), + ('car', '2.0-22'), + ('colorspace', '1.2-4'), + ('robustbase', '0.92-2'), + ('sp', '1.0-17'), + ('vcd', '1.3-2'), + ('snowfall', '1.84-6'), + ('rpart', '4.1-8'), + ('mice', '2.22'), + ('nlme', '3.1-118'), + ('urca', '1.2-8'), + ('fracdiff', '1.4-2'), + ('mgcv', '1.8-4'), + ('logistf', '1.21'), + ('akima', '0.5-11'), + ('bitops', '1.0-6'), + ('boot', '1.3-13'), + ('mixtools', '1.0.2'), + ('cluster', '1.15.3'), + ('gclus', '1.3.1'), + ('coda', '0.16-1'), + ('codetools', '0.2-9'), + ('foreach', '1.4.2'), + ('doMC', '1.3.3'), + ('DBI', '0.3.1'), + ('foreign', '0.8-62'), + ('survival', '2.37-7'), + ('gam', '1.09.1'), + ('gamlss.data', '4.2-7'), + ('gamlss.dist', '4.3-1'), + ('hwriter', '1.3.2'), + ('KernSmooth', '2.23-13'), + ('zoo', '1.7-11'), + ('xts', '0.9-7'), + ('TTR', '0.22-0'), + ('quantmod', '0.4-3'), + ('lmtest', '0.9-33'), + ('mnormt', '1.5-1'), + ('mvtnorm', '1.0-2'), + ('pcaPP', '1.9-60'), + ('numDeriv', '2012.9-1'), + ('lava', '1.3'), + ('prodlim', '1.5.1'), + ('pscl', '1.4.6'), + ('RSQLite', '1.0.0'), + ('BatchJobs', '1.5'), + ('sandwich', '2.3-2'), + ('sfsmisc', '1.0-27'), + ('spatial', '7.3-8'), + ('VGAM', '0.9-6'), + ('waveslim', '1.7.3'), + ('xtable', '1.7-4'), + ('profileModel', '0.5-9'), + ('brglm', '0.5-9'), + ('deSolve', '1.11'), + ('tseriesChaos', '0.1-13'), + ('tseries', '0.10-32'), + ('fastICA', '1.2-0'), + ('R.methodsS3', '1.6.1'), + ('R.oo', '1.18.0'), + ('cgdsr', '1.1.33'), + ('R.utils', '1.34.0'), + ('R.matlab', '3.1.1'), ('BiocGenerics', '0.12.1', bioconductor_options), ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), @@ -230,84 +234,84 @@ exts_list = [ ('GenomicAlignments', '1.2.1', bioconductor_options), ('ShortRead', '1.24.0', bioconductor_options), ('graph', '1.44.1', bioconductor_options), - ('gbm', '2.1', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.1-2', ext_options), - ('acepack', '1.3-3.3', ext_options), - ('Hmisc', '3.14-6', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), - ('scales', '0.2.4', ext_options), - ('fastcluster', '1.1.15', ext_options), - ('reshape2', '1.4.1', ext_options), - ('chron', '2.3-45', ext_options), - ('data.table', '1.9.4', ext_options), - ('gtable', '0.1.2', ext_options), - ('proto', '0.3-10', ext_options), - ('ggplot2', '1.0.0', ext_options), - ('igraph', '0.7.1', ext_options), - ('GeneNet', '1.2.11', ext_options), - ('ape', '3.2', ext_options), - ('htmltools', '0.2.6', ext_options), - ('RJSONIO', '1.3-0', ext_options), - ('caTools', '1.17.1', ext_options), - ('gplots', '2.16.0', ext_options), - ('ROCR', '1.0-5', ext_options), - ('httpuv', '1.3.2', ext_options), - ('R6', '2.0.1', ext_options), - ('shiny', '0.10.2.2', ext_options), - ('adegenet', '1.4-2', ext_options), - ('phylobase', '0.6.8', ext_options), - ('adephylo', '1.1-6', ext_options), - ('animation', '2.3', ext_options), - ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.4.6', ext_options), - ('calibrate', '1.7.2', ext_options), - ('clusterGeneration', '1.3.1', ext_options), - ('raster', '2.3-12', ext_options), - ('dismo', '1.0-5', ext_options), - ('expm', '0.99-1.1', ext_options), - ('extrafontdb', '1.0', ext_options), - ('Rttf2pt1', '1.3.2', ext_options), - ('extrafont', '0.17', ext_options), - ('fields', '7.1', ext_options), - ('shapefiles', '0.7', ext_options), - ('fossil', '0.3.7', ext_options), - ('geiger', '2.0.3', ext_options), - ('glmnet', '1.9-8', ext_options), - ('labdsv', '1.6-1', ext_options), - ('MatrixModels', '0.3-1.1', ext_options), - ('stabs', '0.5-0', ext_options), - ('mboost', '2.4-1', ext_options), - ('msm', '1.5', ext_options), - ('nor1mix', '1.2-0', ext_options), - ('np', '0.60-2', ext_options), - ('polynom', '1.3-8', ext_options), - ('quantreg', '5.05', ext_options), - ('RcppEigen', '0.3.2.3.0', ext_options), - ('polspline', '1.1.9', ext_options), - ('TH.data', '1.0-6', ext_options), - ('multcomp', '1.3-8', ext_options), - ('rms', '4.2-1', ext_options), - ('RWekajars', '3.7.11-1', ext_options), - ('RWeka', '0.4-23', ext_options), - ('slam', '0.1-32', ext_options), - ('tm', '0.6', ext_options), - ('TraMineR', '1.8-8', ext_options), - ('chemometrics', '1.3.8', ext_options), - ('FNN', '1.1', ext_options), - ('ipred', '0.9-3', ext_options), - ('knitr', '1.8', ext_options), - ('statmod', '1.4.20', ext_options), - ('miscTools', '0.6-16', ext_options), - ('maxLik', '1.2-4', ext_options), - ('mlogit', '0.2-4', ext_options), - ('getopt', '1.20.0', ext_options), - ('gsalib', '2.1', ext_options), - ('reshape', '0.8.5', ext_options), - ('optparse', '1.3.0', ext_options), - ('klaR', '0.6-12', ext_options), - ('neuRosim', '0.2-12', ext_options), + ('gbm', '2.1'), + ('dichromat', '2.0-0'), + ('Formula', '1.1-2'), + ('acepack', '1.3-3.3'), + ('Hmisc', '3.14-6'), + ('munsell', '0.4.2'), + ('labeling', '0.3'), + ('scales', '0.2.4'), + ('fastcluster', '1.1.15'), + ('reshape2', '1.4.1'), + ('chron', '2.3-45'), + ('data.table', '1.9.4'), + ('gtable', '0.1.2'), + ('proto', '0.3-10'), + ('ggplot2', '1.0.0'), + ('igraph', '0.7.1'), + ('GeneNet', '1.2.11'), + ('ape', '3.2'), + ('htmltools', '0.2.6'), + ('RJSONIO', '1.3-0'), + ('caTools', '1.17.1'), + ('gplots', '2.16.0'), + ('ROCR', '1.0-5'), + ('httpuv', '1.3.2'), + ('R6', '2.0.1'), + ('shiny', '0.10.2.2'), + ('adegenet', '1.4-2'), + ('phylobase', '0.6.8'), + ('adephylo', '1.1-6'), + ('animation', '2.3'), + ('bigmemory.sri', '0.1.3'), + ('bigmemory', '4.4.6'), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.1'), + ('raster', '2.3-12'), + ('dismo', '1.0-5'), + ('expm', '0.99-1.1'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3.2'), + ('extrafont', '0.17'), + ('fields', '7.1'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.3'), + ('glmnet', '1.9-8'), + ('labdsv', '1.6-1'), + ('MatrixModels', '0.3-1.1'), + ('stabs', '0.5-0'), + ('mboost', '2.4-1'), + ('msm', '1.5'), + ('nor1mix', '1.2-0'), + ('np', '0.60-2'), + ('polynom', '1.3-8'), + ('quantreg', '5.05'), + ('RcppEigen', '0.3.2.3.0'), + ('polspline', '1.1.9'), + ('TH.data', '1.0-6'), + ('multcomp', '1.3-8'), + ('rms', '4.2-1'), + ('RWekajars', '3.7.11-1'), + ('RWeka', '0.4-23'), + ('slam', '0.1-32'), + ('tm', '0.6'), + ('TraMineR', '1.8-8'), + ('chemometrics', '1.3.8'), + ('FNN', '1.1'), + ('ipred', '0.9-3'), + ('knitr', '1.8'), + ('statmod', '1.4.20'), + ('miscTools', '0.6-16'), + ('maxLik', '1.2-4'), + ('mlogit', '0.2-4'), + ('getopt', '1.20.0'), + ('gsalib', '2.1'), + ('reshape', '0.8.5'), + ('optparse', '1.3.0'), + ('klaR', '0.6-12'), + ('neuRosim', '0.2-12'), ('affyio', '1.34.0', bioconductor_options), ('BiocInstaller', '1.16.1', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), @@ -323,58 +327,58 @@ exts_list = [ ('oligoClasses', '1.28.0', bioconductor_options), ('edgeR', '3.8.5', bioconductor_options), ('PFAM.db', '3.0.0', bioconductor_options), - ('locfit', '1.5-9.1', ext_options), - ('gridExtra', '0.9.1', ext_options), - ('GGally', '0.5.0', ext_options), + ('locfit', '1.5-9.1'), + ('gridExtra', '0.9.1'), + ('GGally', '0.5.0'), ('baySeq', '2.0.50', bioconductor_options), - ('beanplot', '1.2', ext_options), - ('clValid', '0.6-6', ext_options), + ('beanplot', '1.2'), + ('clValid', '0.6-6'), ('qvalue', '1.40.0', bioconductor_options), ('impute', '1.40.0', bioconductor_options), - ('matrixStats', '0.12.2', ext_options), - ('samr', '2.0', ext_options), + ('matrixStats', '0.12.2'), + ('samr', '2.0'), ('DEGseq', '1.20.0', bioconductor_options), - ('DiscriMiner', '0.1-29', ext_options), - ('ellipse', '0.3-8', ext_options), - ('leaps', '2.9', ext_options), - ('FactoMineR', '1.28', ext_options), - ('modeltools', '0.2-21', ext_options), - ('flexclust', '1.3-4', ext_options), - ('flexmix', '2.3-12', ext_options), - ('prabclus', '2.2-6', ext_options), - ('diptest', '0.75-6', ext_options), - ('trimcluster', '0.1-2', ext_options), - ('fpc', '2.1-9', ext_options), - ('BiasedUrn', '1.06.1', ext_options), + ('DiscriMiner', '0.1-29'), + ('ellipse', '0.3-8'), + ('leaps', '2.9'), + ('FactoMineR', '1.28'), + ('modeltools', '0.2-21'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-12'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-6'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-9'), + ('BiasedUrn', '1.06.1'), ('hgu133plus2.db', '3.0.0', bioconductor_options), - ('TeachingDemos', '2.9', ext_options), - ('jsonlite', '0.9.14', ext_options), - ('kohonen', '2.0.15', ext_options), - ('base64', '1.1', ext_options), + ('TeachingDemos', '2.9'), + ('jsonlite', '0.9.14'), + ('kohonen', '2.0.15'), + ('base64', '1.1'), ('illuminaio', '0.8.0', bioconductor_options), - ('registry', '0.2', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), - ('doRNG', '1.6', ext_options), + ('registry', '0.2'), + ('pkgmaker', '0.22'), + ('rngtools', '1.2.4'), + ('doRNG', '1.6'), ('bumphunter', '1.6.0', bioconductor_options), ('multtest', '2.22.0', bioconductor_options), ('siggenes', '1.40.0', bioconductor_options), - ('nleqslv', '2.5', ext_options), + ('nleqslv', '2.5'), ('DynDoc', '1.44.0', bioconductor_options), ('genoset', '1.20.0', bioconductor_options), - ('RGCCA', '2.0', ext_options), - ('pheatmap', '0.7.7', ext_options), + ('RGCCA', '2.0'), + ('pheatmap', '0.7.7'), ('multtest', '2.22.0', bioconductor_options), ('NOISeq', '2.8.0', bioconductor_options), - ('openxlsx', '2.2.1', ext_options), + ('openxlsx', '2.2.1'), ('Rgraphviz', '2.10.0', bioconductor_options), - ('pvclust', '1.3-2', ext_options), - ('RCircos', '1.1.2', ext_options), - ('reshape', '0.8.5', ext_options), + ('pvclust', '1.3-2'), + ('RCircos', '1.1.2'), + ('reshape', '0.8.5'), ('RNASeqPower', '1.6.0', bioconductor_options), - ('VennDiagram', '1.6.9', ext_options), - ('xlsxjars', '0.6.1', ext_options), - ('xlsx', '0.5.7', ext_options), + ('VennDiagram', '1.6.9'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb index e81562bee3d..8dfe1121a12 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb @@ -26,7 +26,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -63,158 +63,162 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-0', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-4', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.2-2', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '3.6', ext_options), - ('bootstrap', '2014.4', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.13', ext_options), - ('formatR', '1.0', ext_options), - ('gtools', '3.4.1', ext_options), - ('gdata', '2.13.3', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.4', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-19', ext_options), - ('mime', '0.2', ext_options), - ('markdown', '0.7.4', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-5', ext_options), - ('mclust', '4.4', ext_options), - ('RANN', '2.4.1', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.0', ext_options), - ('som', '0.3-5', ext_options), - ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.6-6', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-16', ext_options), - ('timeDate', '3011.99', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.6-2', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-2', ext_options), - ('BH', '1.55.0-3', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.7', ext_options), - ('longitudinal', '1.1.10', ext_options), - ('checkmate', '1.5.1', ext_options), - ('cubature', '1.1-2', ext_options), - ('DEoptimR', '1.0-2', ext_options), - ('digest', '0.6.8', ext_options), - ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.11.3', ext_options), - ('iterators', '1.0.7', ext_options), - ('maps', '2.3-9', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', 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'2.3-12'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-6'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-9'), + ('BiasedUrn', '1.06.1'), ('hgu133plus2.db', '3.0.0', bioconductor_options), - ('TeachingDemos', '2.9', ext_options), - ('jsonlite', '0.9.14', ext_options), - ('kohonen', '2.0.15', ext_options), - ('base64', '1.1', ext_options), + ('TeachingDemos', '2.9'), + ('jsonlite', '0.9.14'), + ('kohonen', '2.0.15'), + ('base64', '1.1'), ('illuminaio', '0.8.0', bioconductor_options), - ('registry', '0.2', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), - ('doRNG', '1.6', ext_options), + ('registry', '0.2'), + ('pkgmaker', '0.22'), + ('rngtools', '1.2.4'), + ('doRNG', '1.6'), ('bumphunter', '1.6.0', bioconductor_options), ('multtest', '2.22.0', bioconductor_options), ('siggenes', '1.40.0', bioconductor_options), - ('nleqslv', '2.5', ext_options), + ('nleqslv', '2.5'), ('DynDoc', '1.44.0', bioconductor_options), ('genoset', '1.20.0', bioconductor_options), - ('RGCCA', '2.0', ext_options), - ('pheatmap', '0.7.7', ext_options), + ('RGCCA', '2.0'), + ('pheatmap', '0.7.7'), ('multtest', '2.22.0', bioconductor_options), ('NOISeq', '2.8.0', bioconductor_options), - ('openxlsx', '2.2.1', ext_options), + ('openxlsx', '2.2.1'), ('Rgraphviz', '2.10.0', bioconductor_options), - ('pvclust', '1.3-2', ext_options), - ('RCircos', '1.1.2', ext_options), - ('reshape', '0.8.5', ext_options), + ('pvclust', '1.3-2'), + ('RCircos', '1.1.2'), + ('reshape', '0.8.5'), ('RNASeqPower', '1.6.0', bioconductor_options), - ('VennDiagram', '1.6.9', ext_options), - ('xlsxjars', '0.6.1', ext_options), - ('xlsx', '0.5.7', ext_options), + ('VennDiagram', '1.6.9'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb index aa4b8513105..20b83d30bca 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb @@ -26,7 +26,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -63,158 +63,162 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-0', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-4', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.2-2', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '3.6', ext_options), - ('bootstrap', '2014.4', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.13', ext_options), - ('formatR', '1.0', ext_options), - ('gtools', '3.4.1', ext_options), - ('gdata', '2.13.3', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.4', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-19', ext_options), - ('mime', '0.2', ext_options), - ('markdown', '0.7.4', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-5', ext_options), - ('mclust', '4.4', ext_options), - ('RANN', '2.4.1', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.0', ext_options), - ('som', '0.3-5', ext_options), - ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.6-6', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-16', ext_options), - ('timeDate', '3011.99', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.6-2', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-2', ext_options), - ('BH', '1.55.0-3', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.7', ext_options), - ('longitudinal', '1.1.10', ext_options), - ('checkmate', '1.5.1', ext_options), - ('cubature', '1.1-2', ext_options), - ('DEoptimR', '1.0-2', ext_options), - ('digest', '0.6.8', ext_options), - ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.11.3', ext_options), - ('iterators', '1.0.7', ext_options), - ('maps', '2.3-9', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.0-1', ext_options), - ('subplex', '1.1-4', ext_options), - ('stringr', '0.6.2', ext_options), - ('evaluate', '0.5.5', ext_options), - ('logspline', '2.1.5', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.8-3', ext_options), - ('plotrix', '3.5-10', ext_options), - ('randomForest', '4.6-10', ext_options), - ('scatterplot3d', '0.3-35', ext_options), - ('SparseM', '1.6', ext_options), - ('tripack', '1.3-6', ext_options), - ('irace', '1.06', ext_options), - ('rJava', '0.9-6', ext_options), - ('lattice', '0.20-29', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.1-4', ext_options), - ('png', '0.1-7', ext_options), - ('Rcpp', '0.11.3', ext_options), - ('RcppArmadillo', '0.4.600.0', ext_options), - ('plyr', '1.8.1', ext_options), - ('pROC', '1.7.3', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.8', ext_options), - ('fail', '1.2', ext_options), - ('rlecuyer', '0.3-3', ext_options), - ('snow', '0.3-13', ext_options), - ('MASS', '7.3-35', ext_options), - ('tree', '1.0-35', ext_options), - ('pls', '2.4-3', ext_options), - ('class', '7.3-11', ext_options), - ('e1071', '1.6-4', ext_options), - ('nnet', '7.3-8', ext_options), - ('car', '2.0-22', ext_options), - ('colorspace', '1.2-4', ext_options), - ('robustbase', '0.92-2', ext_options), - ('sp', '1.0-17', ext_options), - ('vcd', '1.3-2', ext_options), - ('snowfall', '1.84-6', ext_options), - ('rpart', '4.1-8', ext_options), - ('mice', '2.22', ext_options), - ('nlme', '3.1-118', ext_options), - ('urca', '1.2-8', ext_options), - ('fracdiff', '1.4-2', ext_options), - ('mgcv', '1.8-4', ext_options), - ('logistf', '1.21', ext_options), - ('akima', '0.5-11', ext_options), - ('bitops', '1.0-6', ext_options), - ('boot', '1.3-13', ext_options), - ('mixtools', '1.0.2', ext_options), - ('cluster', '1.15.3', ext_options), - ('gclus', '1.3.1', ext_options), - ('coda', '0.16-1', ext_options), - ('codetools', '0.2-9', ext_options), - ('foreach', '1.4.2', ext_options), - ('doMC', '1.3.3', ext_options), - ('DBI', '0.3.1', ext_options), - ('foreign', '0.8-62', ext_options), - ('survival', '2.37-7', ext_options), - ('gam', '1.09.1', ext_options), - ('gamlss.data', '4.2-7', ext_options), - ('gamlss.dist', '4.3-1', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-13', ext_options), - ('zoo', '1.7-11', ext_options), - ('xts', '0.9-7', ext_options), - ('TTR', '0.22-0', ext_options), - ('quantmod', '0.4-3', ext_options), - ('lmtest', '0.9-33', ext_options), - ('mnormt', '1.5-1', ext_options), - ('mvtnorm', '1.0-2', ext_options), - ('pcaPP', '1.9-60', ext_options), - ('numDeriv', '2012.9-1', ext_options), - ('lava', '1.3', ext_options), - ('prodlim', '1.5.1', ext_options), - ('pscl', '1.4.6', ext_options), - ('RSQLite', '1.0.0', ext_options), - ('BatchJobs', '1.5', ext_options), - ('sandwich', '2.3-2', ext_options), - ('sfsmisc', '1.0-27', ext_options), - ('spatial', '7.3-8', ext_options), - ('VGAM', '0.9-6', ext_options), - ('waveslim', '1.7.3', ext_options), - ('xtable', '1.7-4', ext_options), - ('profileModel', '0.5-9', ext_options), - ('brglm', '0.5-9', ext_options), - ('deSolve', '1.11', ext_options), - ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-32', ext_options), - ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.6.1', ext_options), - ('R.oo', '1.18.0', ext_options), - ('cgdsr', '1.1.33', ext_options), - ('R.utils', '1.34.0', ext_options), - ('R.matlab', '3.1.1', ext_options), + ('Rmpi', '0.6-5', { + 'patches': ['Rmpi-0.6-5_impi5.patch'], + }), + ('abind', '1.4-0'), + ('magic', '1.5-6'), + ('geometry', '0.3-4', { + 'patches': ['geometry-0.3-4-icc.patch'], + }), + ('bit', '1.1-12'), + ('filehash', '2.2-2'), + ('ff', '2.2-13'), + ('bnlearn', '3.6'), + ('bootstrap', '2014.4'), + ('combinat', '0.0-8'), + ('deal', '1.2-37'), + ('fdrtool', '1.2.13'), + ('formatR', '1.0'), + ('gtools', '3.4.1'), + ('gdata', '2.13.3'), + ('GSA', '1.03'), + ('highr', '0.4'), + ('infotheo', '1.2.0'), + ('lars', '1.2'), + ('lazy', '1.2-15'), + ('kernlab', '0.9-19'), + ('mime', '0.2'), + ('markdown', '0.7.4'), + ('mlbench', '2.1-1'), + ('NLP', '0.1-5'), + ('mclust', '4.4'), + ('RANN', '2.4.1'), + ('rmeta', '2.16'), + ('segmented', '0.5-1.0'), + ('som', '0.3-5'), + ('SuppDists', '1.1-9.1'), + ('stabledist', '0.6-6'), + ('survivalROC', '1.0.3'), + ('pspline', '1.0-16'), + ('timeDate', '3011.99'), + ('longmemo', '1.0-0'), + ('ADGofTest', '0.3'), + ('ade4', '1.6-2'), + ('AlgDesign', '1.1-7.3'), + ('base64enc', '0.1-2'), + ('BH', '1.55.0-3'), + ('brew', '1.0-6'), + ('Brobdingnag', '1.2-4'), + ('corpcor', '1.6.7'), + ('longitudinal', '1.1.10'), + ('checkmate', '1.5.1'), + ('cubature', '1.1-2'), + ('DEoptimR', '1.0-2'), + ('digest', '0.6.8'), + ('fastmatch', '1.0-4'), + ('ffbase', '0.11.3'), + ('iterators', '1.0.7'), + ('maps', '2.3-9'), + ('nnls', '1.4'), + ('sendmailR', '1.2-1'), + ('spam', '1.0-1'), + ('subplex', '1.1-4'), + ('stringr', '0.6.2'), + ('evaluate', '0.5.5'), + ('logspline', '2.1.5'), + ('ncbit', '2013.03.29'), + ('permute', '0.8-3'), + ('plotrix', '3.5-10'), + ('randomForest', '4.6-10'), + ('scatterplot3d', '0.3-35'), + ('SparseM', '1.6'), + ('tripack', '1.3-6'), + ('irace', '1.06'), + ('rJava', '0.9-6'), + ('lattice', '0.20-29'), + ('RColorBrewer', '1.1-2'), + ('latticeExtra', '0.6-26'), + ('Matrix', '1.1-4'), + ('png', '0.1-7'), + ('Rcpp', '0.11.3'), + ('RcppArmadillo', '0.4.600.0'), + ('plyr', '1.8.1'), + ('pROC', '1.7.3'), + ('quadprog', '1.5-5'), + ('BB', '2014.10-1'), + ('BBmisc', '1.8'), + ('fail', '1.2'), + ('rlecuyer', '0.3-3'), + ('snow', '0.3-13'), + ('MASS', '7.3-35'), + ('tree', '1.0-35'), + ('pls', '2.4-3'), + ('class', '7.3-11'), + ('e1071', '1.6-4'), + ('nnet', '7.3-8'), + ('car', '2.0-22'), + ('colorspace', '1.2-4'), + ('robustbase', '0.92-2'), + ('sp', '1.0-17'), + ('vcd', '1.3-2'), + ('snowfall', '1.84-6'), + ('rpart', '4.1-8'), + ('mice', '2.22'), + ('nlme', '3.1-118'), + ('urca', '1.2-8'), + ('fracdiff', '1.4-2'), + ('mgcv', '1.8-4'), + ('logistf', '1.21'), + ('akima', '0.5-11'), + ('bitops', '1.0-6'), + ('boot', '1.3-13'), + ('mixtools', '1.0.2'), + ('cluster', '1.15.3'), + ('gclus', '1.3.1'), + ('coda', '0.16-1'), + ('codetools', '0.2-9'), + ('foreach', '1.4.2'), + ('doMC', '1.3.3'), + ('DBI', '0.3.1'), + ('foreign', '0.8-62'), + ('survival', '2.37-7'), + ('gam', '1.09.1'), + ('gamlss.data', '4.2-7'), + ('gamlss.dist', '4.3-1'), + ('hwriter', '1.3.2'), + ('KernSmooth', '2.23-13'), + ('zoo', '1.7-11'), + ('xts', '0.9-7'), + ('TTR', '0.22-0'), + ('quantmod', '0.4-3'), + ('lmtest', '0.9-33'), + ('mnormt', '1.5-1'), + ('mvtnorm', '1.0-2'), + ('pcaPP', '1.9-60'), + ('numDeriv', '2012.9-1'), + ('lava', '1.3'), + ('prodlim', '1.5.1'), + ('pscl', '1.4.6'), + ('RSQLite', '1.0.0'), + ('BatchJobs', '1.5'), + ('sandwich', '2.3-2'), + ('sfsmisc', '1.0-27'), + ('spatial', '7.3-8'), + ('VGAM', '0.9-6'), + ('waveslim', '1.7.3'), + ('xtable', '1.7-4'), + ('profileModel', '0.5-9'), + ('brglm', '0.5-9'), + ('deSolve', '1.11'), + ('tseriesChaos', '0.1-13'), + ('tseries', '0.10-32'), + ('fastICA', '1.2-0'), + ('R.methodsS3', '1.6.1'), + ('R.oo', '1.18.0'), + ('cgdsr', '1.1.33'), + ('R.utils', '1.34.0'), + ('R.matlab', '3.1.1'), ('BiocGenerics', '0.12.1', bioconductor_options), ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), @@ -230,84 +234,84 @@ exts_list = [ ('GenomicAlignments', '1.2.1', bioconductor_options), ('ShortRead', '1.24.0', bioconductor_options), ('graph', '1.44.1', bioconductor_options), - ('gbm', '2.1', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.1-2', ext_options), - ('acepack', '1.3-3.3', ext_options), - ('Hmisc', '3.14-6', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), - ('scales', '0.2.4', ext_options), - ('fastcluster', '1.1.15', ext_options), - ('reshape2', '1.4.1', ext_options), - ('chron', '2.3-45', ext_options), - ('data.table', '1.9.4', ext_options), - ('gtable', '0.1.2', ext_options), - ('proto', '0.3-10', ext_options), - ('ggplot2', '1.0.0', ext_options), - ('igraph', '0.7.1', ext_options), - ('GeneNet', '1.2.11', ext_options), - ('ape', '3.2', ext_options), - ('htmltools', '0.2.6', ext_options), - ('RJSONIO', '1.3-0', ext_options), - ('caTools', '1.17.1', ext_options), - ('gplots', '2.16.0', ext_options), - ('ROCR', '1.0-5', ext_options), - ('httpuv', '1.3.2', ext_options), - ('R6', '2.0.1', ext_options), - ('shiny', '0.10.2.2', ext_options), - ('adegenet', '1.4-2', ext_options), - ('phylobase', '0.6.8', ext_options), - ('adephylo', '1.1-6', ext_options), - ('animation', '2.3', ext_options), - ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.4.6', ext_options), - ('calibrate', '1.7.2', ext_options), - ('clusterGeneration', '1.3.1', ext_options), - ('raster', '2.3-12', ext_options), - ('dismo', '1.0-5', ext_options), - ('expm', '0.99-1.1', ext_options), - ('extrafontdb', '1.0', ext_options), - ('Rttf2pt1', '1.3.2', ext_options), - ('extrafont', '0.17', ext_options), - ('fields', '7.1', ext_options), - ('shapefiles', '0.7', ext_options), - ('fossil', '0.3.7', ext_options), - ('geiger', '2.0.3', ext_options), - ('glmnet', '1.9-8', ext_options), - ('labdsv', '1.6-1', ext_options), - ('MatrixModels', '0.3-1.1', ext_options), - ('stabs', '0.5-0', ext_options), - ('mboost', '2.4-1', ext_options), - ('msm', '1.5', ext_options), - ('nor1mix', '1.2-0', ext_options), - ('np', '0.60-2', ext_options), - ('polynom', '1.3-8', ext_options), - ('quantreg', '5.05', ext_options), - ('RcppEigen', '0.3.2.3.0', ext_options), - ('polspline', '1.1.9', ext_options), - ('TH.data', '1.0-6', ext_options), - ('multcomp', '1.3-8', ext_options), - ('rms', '4.2-1', ext_options), - ('RWekajars', '3.7.11-1', ext_options), - ('RWeka', '0.4-23', ext_options), - ('slam', '0.1-32', ext_options), - ('tm', '0.6', ext_options), - ('TraMineR', '1.8-8', ext_options), - ('chemometrics', '1.3.8', ext_options), - ('FNN', '1.1', ext_options), - ('ipred', '0.9-3', ext_options), - ('knitr', '1.8', ext_options), - ('statmod', '1.4.20', ext_options), - ('miscTools', '0.6-16', ext_options), - ('maxLik', '1.2-4', ext_options), - ('mlogit', '0.2-4', ext_options), - ('getopt', '1.20.0', ext_options), - ('gsalib', '2.1', ext_options), - ('reshape', '0.8.5', ext_options), - ('optparse', '1.3.0', ext_options), - ('klaR', '0.6-12', ext_options), - ('neuRosim', '0.2-12', ext_options), + ('gbm', '2.1'), + ('dichromat', '2.0-0'), + ('Formula', '1.1-2'), + ('acepack', '1.3-3.3'), + ('Hmisc', '3.14-6'), + ('munsell', '0.4.2'), + ('labeling', '0.3'), + ('scales', '0.2.4'), + ('fastcluster', '1.1.15'), + ('reshape2', '1.4.1'), + ('chron', '2.3-45'), + ('data.table', '1.9.4'), + ('gtable', '0.1.2'), + ('proto', '0.3-10'), + ('ggplot2', '1.0.0'), + ('igraph', '0.7.1'), + ('GeneNet', '1.2.11'), + ('ape', '3.2'), + ('htmltools', '0.2.6'), + ('RJSONIO', '1.3-0'), + ('caTools', '1.17.1'), + ('gplots', '2.16.0'), + ('ROCR', '1.0-5'), + ('httpuv', '1.3.2'), + ('R6', '2.0.1'), + ('shiny', '0.10.2.2'), + ('adegenet', '1.4-2'), + ('phylobase', '0.6.8'), + ('adephylo', '1.1-6'), + ('animation', '2.3'), + ('bigmemory.sri', '0.1.3'), + ('bigmemory', '4.4.6'), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.1'), + ('raster', '2.3-12'), + ('dismo', '1.0-5'), + ('expm', '0.99-1.1'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3.2'), + ('extrafont', '0.17'), + ('fields', '7.1'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.3'), + ('glmnet', '1.9-8'), + ('labdsv', '1.6-1'), + ('MatrixModels', '0.3-1.1'), + ('stabs', '0.5-0'), + ('mboost', '2.4-1'), + ('msm', '1.5'), + ('nor1mix', '1.2-0'), + ('np', '0.60-2'), + ('polynom', '1.3-8'), + ('quantreg', '5.05'), + ('RcppEigen', '0.3.2.3.0'), + ('polspline', '1.1.9'), + ('TH.data', '1.0-6'), + ('multcomp', '1.3-8'), + ('rms', '4.2-1'), + ('RWekajars', '3.7.11-1'), + ('RWeka', '0.4-23'), + ('slam', '0.1-32'), + ('tm', '0.6'), + ('TraMineR', '1.8-8'), + ('chemometrics', '1.3.8'), + ('FNN', '1.1'), + ('ipred', '0.9-3'), + ('knitr', '1.8'), + ('statmod', '1.4.20'), + ('miscTools', '0.6-16'), + ('maxLik', '1.2-4'), + ('mlogit', '0.2-4'), + ('getopt', '1.20.0'), + ('gsalib', '2.1'), + ('reshape', '0.8.5'), + ('optparse', '1.3.0'), + ('klaR', '0.6-12'), + ('neuRosim', '0.2-12'), ('affyio', '1.34.0', bioconductor_options), ('BiocInstaller', '1.16.1', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), @@ -323,58 +327,58 @@ exts_list = [ ('oligoClasses', '1.28.0', bioconductor_options), ('edgeR', '3.8.5', bioconductor_options), ('PFAM.db', '3.0.0', bioconductor_options), - ('locfit', '1.5-9.1', ext_options), - ('gridExtra', '0.9.1', ext_options), - ('GGally', '0.5.0', ext_options), + ('locfit', '1.5-9.1'), + ('gridExtra', '0.9.1'), + ('GGally', '0.5.0'), ('baySeq', '2.0.50', bioconductor_options), - ('beanplot', '1.2', ext_options), - ('clValid', '0.6-6', ext_options), + ('beanplot', '1.2'), + ('clValid', '0.6-6'), ('qvalue', '1.40.0', bioconductor_options), ('impute', '1.40.0', bioconductor_options), - ('matrixStats', '0.12.2', ext_options), - ('samr', '2.0', ext_options), + ('matrixStats', '0.12.2'), + ('samr', '2.0'), ('DEGseq', '1.20.0', bioconductor_options), - ('DiscriMiner', '0.1-29', ext_options), - ('ellipse', '0.3-8', ext_options), - ('leaps', '2.9', ext_options), - ('FactoMineR', '1.28', ext_options), - ('modeltools', '0.2-21', ext_options), - ('flexclust', '1.3-4', ext_options), - ('flexmix', '2.3-12', ext_options), - ('prabclus', '2.2-6', ext_options), - ('diptest', '0.75-6', ext_options), - ('trimcluster', '0.1-2', ext_options), - ('fpc', '2.1-9', ext_options), - ('BiasedUrn', '1.06.1', ext_options), + ('DiscriMiner', '0.1-29'), + ('ellipse', '0.3-8'), + ('leaps', '2.9'), + ('FactoMineR', '1.28'), + ('modeltools', '0.2-21'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-12'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-6'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-9'), + ('BiasedUrn', '1.06.1'), ('hgu133plus2.db', '3.0.0', bioconductor_options), - ('TeachingDemos', '2.9', ext_options), - ('jsonlite', '0.9.14', ext_options), - ('kohonen', '2.0.15', ext_options), - ('base64', '1.1', ext_options), + ('TeachingDemos', '2.9'), + ('jsonlite', '0.9.14'), + ('kohonen', '2.0.15'), + ('base64', '1.1'), ('illuminaio', '0.8.0', bioconductor_options), - ('registry', '0.2', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), - ('doRNG', '1.6', ext_options), + ('registry', '0.2'), + ('pkgmaker', '0.22'), + ('rngtools', '1.2.4'), + ('doRNG', '1.6'), ('bumphunter', '1.6.0', bioconductor_options), ('multtest', '2.22.0', bioconductor_options), ('siggenes', '1.40.0', bioconductor_options), - ('nleqslv', '2.5', ext_options), + ('nleqslv', '2.5'), ('DynDoc', '1.44.0', bioconductor_options), ('genoset', '1.20.0', bioconductor_options), - ('RGCCA', '2.0', ext_options), - ('pheatmap', '0.7.7', ext_options), + ('RGCCA', '2.0'), + ('pheatmap', '0.7.7'), ('multtest', '2.22.0', bioconductor_options), ('NOISeq', '2.8.0', bioconductor_options), - ('openxlsx', '2.2.1', ext_options), + ('openxlsx', '2.2.1'), ('Rgraphviz', '2.10.0', bioconductor_options), - ('pvclust', '1.3-2', ext_options), - ('RCircos', '1.1.2', ext_options), - ('reshape', '0.8.5', ext_options), + ('pvclust', '1.3-2'), + ('RCircos', '1.1.2'), + ('reshape', '0.8.5'), ('RNASeqPower', '1.6.0', bioconductor_options), - ('VennDiagram', '1.6.9', ext_options), - ('xlsxjars', '0.6.1', ext_options), - ('xlsx', '0.5.7', ext_options), + ('VennDiagram', '1.6.9'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index c57b76da2d7..2b252579399 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -29,7 +29,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -66,164 +66,168 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-3', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.2-2', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '3.7.1', ext_options), - ('bootstrap', '2015.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.14', ext_options), - ('formatR', '1.0', ext_options), - ('gtools', '3.4.1', ext_options), - ('gdata', '2.13.3', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.4', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-20', ext_options), - ('mime', '0.2', ext_options), - ('markdown', '0.7.4', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-6', ext_options), - ('mclust', '4.4', ext_options), - ('RANN', '2.4.1', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.1', ext_options), - ('som', '0.3-5', ext_options), - ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.6-6', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-16', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.6-2', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-2', ext_options), - ('BH', '1.55.0-3', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.7', ext_options), - ('longitudinal', '1.1.11', ext_options), - ('checkmate', '1.5.2', ext_options), - ('cubature', '1.1-2', ext_options), - ('DEoptimR', '1.0-2', ext_options), - ('digest', '0.6.8', ext_options), - ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.11.3', ext_options), - ('iterators', '1.0.7', ext_options), - ('maps', '2.3-9', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.0-1', ext_options), - ('subplex', '1.1-4', ext_options), - ('stringr', '0.6.2', ext_options), - ('evaluate', '0.5.5', ext_options), - ('logspline', '2.1.5', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.8-3', ext_options), - ('plotrix', '3.5-11', ext_options), - ('randomForest', '4.6-10', ext_options), - ('scatterplot3d', '0.3-35', ext_options), - ('SparseM', '1.6', ext_options), - ('tripack', '1.3-6', ext_options), - ('irace', '1.06', ext_options), - ('rJava', '0.9-6', ext_options), - ('lattice', '0.20-30', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.1-5', ext_options), - ('png', '0.1-7', ext_options), - ('Rcpp', '0.11.5', ext_options), - ('RcppArmadillo', '0.4.650.1.1', ext_options), - ('plyr', '1.8.1', ext_options), - ('pROC', '1.7.3', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.9', ext_options), - ('fail', '1.2', ext_options), - ('rlecuyer', '0.3-3', ext_options), - ('snow', '0.3-13', ext_options), - ('MASS', '7.3-40', ext_options), - ('tree', '1.0-35', ext_options), - ('pls', '2.4-3', ext_options), - ('class', '7.3-12', ext_options), - ('e1071', '1.6-4', ext_options), - ('nnet', '7.3-9', ext_options), - ('nlme', '3.1-120', ext_options), - ('mgcv', '1.8-5', ext_options), - ('minqa', '1.2.4', ext_options), - ('nloptr', '1.0.4', ext_options), - ('RcppEigen', '0.3.2.4.0', ext_options), - ('lme4', '1.1-7', ext_options), - ('pbkrtest', '0.4-2', ext_options), - ('quantreg', '5.11', ext_options), - ('car', '2.0-25', ext_options), - ('colorspace', '1.2-6', ext_options), - ('robustbase', '0.92-3', ext_options), - ('sp', '1.0-17', ext_options), - ('vcd', '1.3-2', ext_options), - ('snowfall', '1.84-6', ext_options), - ('rpart', '4.1-9', ext_options), - ('mice', '2.22', ext_options), - ('urca', '1.2-8', ext_options), - ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), - ('akima', '0.5-11', ext_options), - ('bitops', '1.0-6', ext_options), - ('boot', '1.3-15', ext_options), - ('mixtools', '1.0.2', ext_options), - ('cluster', '2.0.1', ext_options), - ('gclus', '1.3.1', ext_options), - ('coda', '0.17-1', ext_options), - ('codetools', '0.2-11', ext_options), - ('foreach', '1.4.2', ext_options), - ('doMC', '1.3.3', ext_options), - ('DBI', '0.3.1', ext_options), - ('foreign', '0.8-63', ext_options), - ('survival', '2.38-1', ext_options), - ('gam', '1.09.1', ext_options), - ('gamlss.data', '4.2-7', ext_options), - ('gamlss.dist', '4.3-4', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-14', ext_options), - ('zoo', '1.7-12', ext_options), - ('xts', '0.9-7', ext_options), - ('TTR', '0.22-0', ext_options), - ('quantmod', '0.4-4', ext_options), - ('lmtest', '0.9-33', ext_options), - ('mnormt', '1.5-1', ext_options), - ('mvtnorm', '1.0-2', ext_options), - ('pcaPP', '1.9-60', ext_options), - ('numDeriv', '2012.9-1', ext_options), - ('lava', '1.4.0', ext_options), - ('prodlim', '1.5.1', ext_options), - ('pscl', '1.4.8', ext_options), - ('RSQLite', '1.0.0', ext_options), - ('BatchJobs', '1.6', ext_options), - ('sandwich', '2.3-2', ext_options), - ('sfsmisc', '1.0-27', ext_options), - ('spatial', '7.3-9', ext_options), - ('VGAM', '0.9-7', ext_options), - ('waveslim', '1.7.5', ext_options), - ('xtable', '1.7-4', ext_options), - ('profileModel', '0.5-9', ext_options), - ('brglm', '0.5-9', ext_options), - ('deSolve', '1.11', ext_options), - ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-34', ext_options), - ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.7.0', ext_options), - ('R.oo', '1.19.0', ext_options), - ('cgdsr', '1.1.33', ext_options), - ('R.utils', '2.0.0', ext_options), - ('R.matlab', '3.2.0', ext_options), + ('Rmpi', '0.6-5', { + 'patches': ['Rmpi-0.6-5_impi5.patch'], + }), + ('abind', '1.4-3'), + ('magic', '1.5-6'), + ('geometry', '0.3-5', { + 'patches': ['geometry-0.3-4-icc.patch'], + }), + ('bit', '1.1-12'), + ('filehash', '2.2-2'), + ('ff', '2.2-13'), + ('bnlearn', '3.7.1'), + ('bootstrap', '2015.2'), + ('combinat', '0.0-8'), + ('deal', '1.2-37'), + ('fdrtool', '1.2.14'), + ('formatR', '1.0'), + ('gtools', '3.4.1'), + ('gdata', '2.13.3'), + ('GSA', '1.03'), + ('highr', '0.4'), + ('infotheo', '1.2.0'), + ('lars', '1.2'), + ('lazy', '1.2-15'), + ('kernlab', '0.9-20'), + ('mime', '0.2'), + ('markdown', '0.7.4'), + ('mlbench', '2.1-1'), + ('NLP', '0.1-6'), + ('mclust', '4.4'), + ('RANN', '2.4.1'), + ('rmeta', '2.16'), + ('segmented', '0.5-1.1'), + ('som', '0.3-5'), + ('SuppDists', '1.1-9.1'), + ('stabledist', '0.6-6'), + ('survivalROC', '1.0.3'), + ('pspline', '1.0-16'), + ('timeDate', '3012.100'), + ('longmemo', '1.0-0'), + ('ADGofTest', '0.3'), + ('ade4', '1.6-2'), + ('AlgDesign', '1.1-7.3'), + ('base64enc', '0.1-2'), + ('BH', '1.55.0-3'), + ('brew', '1.0-6'), + ('Brobdingnag', '1.2-4'), + ('corpcor', '1.6.7'), + ('longitudinal', '1.1.11'), + ('checkmate', '1.5.2'), + ('cubature', '1.1-2'), + ('DEoptimR', '1.0-2'), + ('digest', '0.6.8'), + ('fastmatch', '1.0-4'), + ('ffbase', '0.11.3'), + ('iterators', '1.0.7'), + ('maps', '2.3-9'), + ('nnls', '1.4'), + ('sendmailR', '1.2-1'), + ('spam', '1.0-1'), + ('subplex', '1.1-4'), + ('stringr', '0.6.2'), + ('evaluate', '0.5.5'), + ('logspline', '2.1.5'), + ('ncbit', '2013.03.29'), + ('permute', '0.8-3'), + ('plotrix', '3.5-11'), + ('randomForest', '4.6-10'), + ('scatterplot3d', '0.3-35'), + ('SparseM', '1.6'), + ('tripack', '1.3-6'), + ('irace', '1.06'), + ('rJava', '0.9-6'), + ('lattice', '0.20-30'), + ('RColorBrewer', '1.1-2'), + ('latticeExtra', '0.6-26'), + ('Matrix', '1.1-5'), + ('png', '0.1-7'), + ('Rcpp', '0.11.5'), + ('RcppArmadillo', '0.4.650.1.1'), + ('plyr', '1.8.1'), + ('pROC', '1.7.3'), + ('quadprog', '1.5-5'), + ('BB', '2014.10-1'), + ('BBmisc', '1.9'), + ('fail', '1.2'), + ('rlecuyer', '0.3-3'), + ('snow', '0.3-13'), + ('MASS', '7.3-40'), + ('tree', '1.0-35'), + ('pls', '2.4-3'), + ('class', '7.3-12'), + ('e1071', '1.6-4'), + ('nnet', '7.3-9'), + ('nlme', '3.1-120'), + ('mgcv', '1.8-5'), + ('minqa', '1.2.4'), + ('nloptr', '1.0.4'), + ('RcppEigen', '0.3.2.4.0'), + ('lme4', '1.1-7'), + ('pbkrtest', '0.4-2'), + ('quantreg', '5.11'), + ('car', '2.0-25'), + ('colorspace', '1.2-6'), + ('robustbase', '0.92-3'), + ('sp', '1.0-17'), + ('vcd', '1.3-2'), + ('snowfall', '1.84-6'), + ('rpart', '4.1-9'), + ('mice', '2.22'), + ('urca', '1.2-8'), + ('fracdiff', '1.4-2'), + ('logistf', '1.21'), + ('akima', '0.5-11'), + ('bitops', '1.0-6'), + ('boot', '1.3-15'), + ('mixtools', '1.0.2'), + ('cluster', '2.0.1'), + ('gclus', '1.3.1'), + ('coda', '0.17-1'), + ('codetools', '0.2-11'), + ('foreach', '1.4.2'), + ('doMC', '1.3.3'), + ('DBI', '0.3.1'), + ('foreign', '0.8-63'), + ('survival', '2.38-1'), + ('gam', '1.09.1'), + ('gamlss.data', '4.2-7'), + ('gamlss.dist', '4.3-4'), + ('hwriter', '1.3.2'), + ('KernSmooth', '2.23-14'), + ('zoo', '1.7-12'), + ('xts', '0.9-7'), + ('TTR', '0.22-0'), + ('quantmod', '0.4-4'), + ('lmtest', '0.9-33'), + ('mnormt', '1.5-1'), + ('mvtnorm', '1.0-2'), + ('pcaPP', '1.9-60'), + ('numDeriv', '2012.9-1'), + ('lava', '1.4.0'), + ('prodlim', '1.5.1'), + ('pscl', '1.4.8'), + ('RSQLite', '1.0.0'), + ('BatchJobs', '1.6'), + ('sandwich', '2.3-2'), + ('sfsmisc', '1.0-27'), + ('spatial', '7.3-9'), + ('VGAM', '0.9-7'), + ('waveslim', '1.7.5'), + ('xtable', '1.7-4'), + ('profileModel', '0.5-9'), + ('brglm', '0.5-9'), + ('deSolve', '1.11'), + ('tseriesChaos', '0.1-13'), + ('tseries', '0.10-34'), + ('fastICA', '1.2-0'), + ('R.methodsS3', '1.7.0'), + ('R.oo', '1.19.0'), + ('cgdsr', '1.1.33'), + ('R.utils', '2.0.0'), + ('R.matlab', '3.2.0'), ('BiocGenerics', '0.12.1', bioconductor_options), ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), @@ -239,83 +243,83 @@ exts_list = [ ('GenomicAlignments', '1.2.2', bioconductor_options), ('ShortRead', '1.24.0', bioconductor_options), ('graph', '1.44.1', bioconductor_options), - ('gbm', '2.1.1', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.2-0', ext_options), - ('acepack', '1.3-3.3', ext_options), - ('gtable', '0.1.2', ext_options), - ('reshape2', '1.4.1', ext_options), - ('proto', '0.3-10', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), - ('scales', '0.2.4', ext_options), - ('ggplot2', '1.0.1', ext_options), - ('Hmisc', '3.15-0', ext_options), - ('fastcluster', '1.1.16', ext_options), - ('chron', '2.3-45', ext_options), - ('data.table', '1.9.4', ext_options), - ('igraph', '0.7.1', ext_options), - ('GeneNet', '1.2.12', ext_options), - ('ape', '3.2', ext_options), - ('htmltools', '0.2.6', ext_options), - ('RJSONIO', '1.3-0', ext_options), - ('caTools', '1.17.1', ext_options), - ('gplots', '2.16.0', ext_options), - ('ROCR', '1.0-5', ext_options), - ('httpuv', '1.3.2', ext_options), - ('R6', '2.0.1', ext_options), - ('shiny', '0.11.1', ext_options), - ('adegenet', '1.4-2', ext_options), - ('phylobase', '0.6.8', ext_options), - ('adephylo', '1.1-6', ext_options), - ('animation', '2.3', ext_options), - ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.4.6', ext_options), - ('calibrate', '1.7.2', ext_options), - ('clusterGeneration', '1.3.4', ext_options), - ('raster', '2.3-33', ext_options), - ('dismo', '1.0-12', ext_options), - ('expm', '0.99-1.1', ext_options), - ('extrafontdb', '1.0', ext_options), - ('Rttf2pt1', '1.3.3', ext_options), - ('extrafont', '0.17', ext_options), - ('fields', '8.2-1', ext_options), - ('shapefiles', '0.7', ext_options), - ('fossil', '0.3.7', ext_options), - ('geiger', '2.0.3', ext_options), - ('glmnet', '1.9-8', ext_options), - ('labdsv', '1.6-1', ext_options), - ('MatrixModels', '0.4-0', ext_options), - ('stabs', '0.5-1', ext_options), - ('mboost', '2.4-2', ext_options), - ('msm', '1.5', ext_options), - ('nor1mix', '1.2-0', ext_options), - ('np', '0.60-2', ext_options), - ('polynom', '1.3-8', ext_options), - ('polspline', '1.1.9', ext_options), - ('TH.data', '1.0-6', ext_options), - ('multcomp', '1.4-0', ext_options), - ('gridExtra', '0.9.1', ext_options), - ('rms', '4.3-0', ext_options), - ('RWekajars', '3.7.12-1', ext_options), - ('RWeka', '0.4-24', ext_options), - ('slam', '0.1-32', ext_options), - ('tm', '0.6', ext_options), - ('TraMineR', '1.8-9', ext_options), - ('chemometrics', '1.3.9', ext_options), - ('FNN', '1.1', ext_options), - ('ipred', '0.9-4', ext_options), - ('knitr', '1.9', ext_options), - ('statmod', '1.4.20', ext_options), - ('miscTools', '0.6-16', ext_options), - ('maxLik', '1.2-4', ext_options), - ('mlogit', '0.2-4', ext_options), - ('getopt', '1.20.0', ext_options), - ('gsalib', '2.1', ext_options), - ('reshape', '0.8.5', ext_options), - ('optparse', '1.3.0', ext_options), - ('klaR', '0.6-12', ext_options), - ('neuRosim', '0.2-12', ext_options), + ('gbm', '2.1.1'), + ('dichromat', '2.0-0'), + ('Formula', '1.2-0'), + ('acepack', '1.3-3.3'), + ('gtable', '0.1.2'), + ('reshape2', '1.4.1'), + ('proto', '0.3-10'), + ('munsell', '0.4.2'), + ('labeling', '0.3'), + ('scales', '0.2.4'), + ('ggplot2', '1.0.1'), + ('Hmisc', '3.15-0'), + ('fastcluster', '1.1.16'), + ('chron', '2.3-45'), + ('data.table', '1.9.4'), + ('igraph', '0.7.1'), + ('GeneNet', '1.2.12'), + ('ape', '3.2'), + ('htmltools', '0.2.6'), + ('RJSONIO', '1.3-0'), + ('caTools', '1.17.1'), + ('gplots', '2.16.0'), + ('ROCR', '1.0-5'), + ('httpuv', '1.3.2'), + ('R6', '2.0.1'), + ('shiny', '0.11.1'), + ('adegenet', '1.4-2'), + ('phylobase', '0.6.8'), + ('adephylo', '1.1-6'), + ('animation', '2.3'), + ('bigmemory.sri', '0.1.3'), + ('bigmemory', '4.4.6'), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.4'), + ('raster', '2.3-33'), + ('dismo', '1.0-12'), + ('expm', '0.99-1.1'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3.3'), + ('extrafont', '0.17'), + ('fields', '8.2-1'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.3'), + ('glmnet', '1.9-8'), + ('labdsv', '1.6-1'), + ('MatrixModels', '0.4-0'), + ('stabs', '0.5-1'), + ('mboost', '2.4-2'), + ('msm', '1.5'), + ('nor1mix', '1.2-0'), + ('np', '0.60-2'), + ('polynom', '1.3-8'), + ('polspline', '1.1.9'), + ('TH.data', '1.0-6'), + ('multcomp', '1.4-0'), + ('gridExtra', '0.9.1'), + ('rms', '4.3-0'), + ('RWekajars', '3.7.12-1'), + ('RWeka', '0.4-24'), + ('slam', '0.1-32'), + ('tm', '0.6'), + ('TraMineR', '1.8-9'), + ('chemometrics', '1.3.9'), + ('FNN', '1.1'), + ('ipred', '0.9-4'), + ('knitr', '1.9'), + ('statmod', '1.4.20'), + ('miscTools', '0.6-16'), + ('maxLik', '1.2-4'), + ('mlogit', '0.2-4'), + ('getopt', '1.20.0'), + ('gsalib', '2.1'), + ('reshape', '0.8.5'), + ('optparse', '1.3.0'), + ('klaR', '0.6-12'), + ('neuRosim', '0.2-12'), ('affyio', '1.34.0', bioconductor_options), ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), @@ -331,65 +335,65 @@ exts_list = [ ('oligoClasses', '1.28.0', bioconductor_options), ('edgeR', '3.8.6', bioconductor_options), ('PFAM.db', '3.0.0', bioconductor_options), - ('locfit', '1.5-9.1', ext_options), - ('GGally', '0.5.0', ext_options), + ('locfit', '1.5-9.1'), + ('GGally', '0.5.0'), ('baySeq', '2.0.50', bioconductor_options), - ('beanplot', '1.2', ext_options), - ('clValid', '0.6-6', ext_options), + ('beanplot', '1.2'), + ('clValid', '0.6-6'), ('qvalue', '1.43.0', bioconductor_options), ('impute', '1.40.0', bioconductor_options), - ('matrixStats', '0.14.0', ext_options), - ('samr', '2.0', ext_options), + ('matrixStats', '0.14.0'), + ('samr', '2.0'), ('DEGseq', '1.20.0', bioconductor_options), - ('DiscriMiner', '0.1-29', ext_options), - ('ellipse', '0.3-8', ext_options), - ('leaps', '2.9', ext_options), - ('flashClust', '1.01-2', ext_options), - ('FactoMineR', '1.29', ext_options), - ('modeltools', '0.2-21', ext_options), - ('flexclust', '1.3-4', ext_options), - ('flexmix', '2.3-13', ext_options), - ('prabclus', '2.2-6', ext_options), - ('diptest', '0.75-6', ext_options), - ('trimcluster', '0.1-2', ext_options), - ('fpc', '2.1-9', ext_options), - ('BiasedUrn', '1.06.1', ext_options), + ('DiscriMiner', '0.1-29'), + ('ellipse', '0.3-8'), + ('leaps', '2.9'), + ('flashClust', '1.01-2'), + ('FactoMineR', '1.29'), + ('modeltools', '0.2-21'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-13'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-6'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-9'), + ('BiasedUrn', '1.06.1'), ('hgu133plus2.db', '3.0.0', bioconductor_options), - ('TeachingDemos', '2.9', ext_options), - ('jsonlite', '0.9.14', ext_options), - ('kohonen', '2.0.15', ext_options), - ('base64', '1.1', ext_options), + ('TeachingDemos', '2.9'), + ('jsonlite', '0.9.14'), + ('kohonen', '2.0.15'), + ('base64', '1.1'), ('illuminaio', '0.8.0', bioconductor_options), - ('registry', '0.2', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), - ('doRNG', '1.6', ext_options), + ('registry', '0.2'), + ('pkgmaker', '0.22'), + ('rngtools', '1.2.4'), + ('doRNG', '1.6'), ('bumphunter', '1.6.0', bioconductor_options), ('multtest', '2.22.0', bioconductor_options), ('siggenes', '1.40.0', bioconductor_options), - ('nleqslv', '2.6', ext_options), + ('nleqslv', '2.6'), ('DynDoc', '1.44.0', bioconductor_options), ('genoset', '1.20.0', bioconductor_options), - ('RGCCA', '2.0', ext_options), - ('pheatmap', '1.0.2', ext_options), + ('RGCCA', '2.0'), + ('pheatmap', '1.0.2'), ('multtest', '2.22.0', bioconductor_options), ('NOISeq', '2.8.0', bioconductor_options), - ('openxlsx', '2.4.0', ext_options), + ('openxlsx', '2.4.0'), ('Rgraphviz', '2.10.0', bioconductor_options), - ('pvclust', '1.3-2', ext_options), - ('RCircos', '1.1.2', ext_options), - ('reshape', '0.8.5', ext_options), + ('pvclust', '1.3-2'), + ('RCircos', '1.1.2'), + ('reshape', '0.8.5'), ('RNASeqPower', '1.6.0', bioconductor_options), - ('VennDiagram', '1.6.9', ext_options), - ('xlsxjars', '0.6.1', ext_options), - ('xlsx', '0.5.7', ext_options), + ('VennDiagram', '1.6.9'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), ('Rsubread', '1.16.1', bioconductor_options), - ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('vegan', '2.2-1'), # requires Tcl/Tk ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk - ('forecast', '6.1', ext_options), - ('fma', '2.01', ext_options), - ('expsmooth', '2.3', ext_options), - ('fpp', '0.5', ext_options), + ('forecast', '6.1'), + ('fma', '2.01'), + ('expsmooth', '2.3'), + ('fpp', '0.5'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 5c24e4f5982..1992cbe8043 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -29,7 +29,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -66,164 +66,168 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-3', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.2-2', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '3.7.1', ext_options), - ('bootstrap', '2015.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.14', ext_options), - ('formatR', '1.0', ext_options), - ('gtools', '3.4.1', ext_options), - ('gdata', '2.13.3', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.4', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-20', ext_options), - ('mime', '0.2', ext_options), - ('markdown', '0.7.4', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-6', ext_options), - ('mclust', '4.4', ext_options), - ('RANN', '2.4.1', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.1', ext_options), - ('som', '0.3-5', ext_options), - ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.6-6', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-16', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.6-2', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-2', ext_options), - ('BH', '1.55.0-3', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.7', ext_options), - ('longitudinal', '1.1.11', ext_options), - ('checkmate', '1.5.2', ext_options), - ('cubature', '1.1-2', ext_options), - ('DEoptimR', '1.0-2', ext_options), - ('digest', '0.6.8', ext_options), - ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.11.3', ext_options), - ('iterators', '1.0.7', ext_options), - ('maps', '2.3-9', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.0-1', ext_options), - ('subplex', '1.1-4', ext_options), - ('stringr', '0.6.2', ext_options), - ('evaluate', '0.5.5', ext_options), - ('logspline', '2.1.5', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.8-3', ext_options), - ('plotrix', '3.5-11', ext_options), - ('randomForest', '4.6-10', ext_options), - ('scatterplot3d', '0.3-35', ext_options), - ('SparseM', '1.6', ext_options), - ('tripack', '1.3-6', ext_options), - ('irace', '1.06', ext_options), - ('rJava', '0.9-6', ext_options), - ('lattice', '0.20-30', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.1-5', ext_options), - ('png', '0.1-7', ext_options), - ('Rcpp', '0.11.5', ext_options), - ('RcppArmadillo', '0.4.650.1.1', ext_options), - ('plyr', '1.8.1', ext_options), - ('pROC', '1.7.3', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.9', ext_options), - ('fail', '1.2', ext_options), - ('rlecuyer', '0.3-3', ext_options), - ('snow', '0.3-13', ext_options), - ('MASS', '7.3-40', ext_options), - ('tree', '1.0-35', ext_options), - ('pls', '2.4-3', ext_options), - ('class', '7.3-12', ext_options), - ('e1071', '1.6-4', ext_options), - ('nnet', '7.3-9', ext_options), - ('nlme', '3.1-120', ext_options), - ('mgcv', '1.8-5', ext_options), - ('minqa', '1.2.4', ext_options), - ('nloptr', '1.0.4', ext_options), - ('RcppEigen', '0.3.2.4.0', ext_options), - ('lme4', '1.1-7', ext_options), - ('pbkrtest', '0.4-2', ext_options), - ('quantreg', '5.11', ext_options), - ('car', '2.0-25', ext_options), - ('colorspace', '1.2-6', ext_options), - ('robustbase', '0.92-3', ext_options), - ('sp', '1.0-17', ext_options), - ('vcd', '1.3-2', ext_options), - ('snowfall', '1.84-6', ext_options), - ('rpart', '4.1-9', ext_options), - ('mice', '2.22', ext_options), - ('urca', '1.2-8', ext_options), - ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), - ('akima', '0.5-11', ext_options), - ('bitops', '1.0-6', ext_options), - ('boot', '1.3-15', ext_options), - ('mixtools', '1.0.2', ext_options), - ('cluster', '2.0.1', ext_options), - ('gclus', '1.3.1', ext_options), - ('coda', '0.17-1', ext_options), - ('codetools', '0.2-11', ext_options), - ('foreach', '1.4.2', ext_options), - ('doMC', '1.3.3', ext_options), - ('DBI', '0.3.1', ext_options), - ('foreign', '0.8-63', ext_options), - ('survival', '2.38-1', ext_options), - ('gam', '1.09.1', ext_options), - ('gamlss.data', '4.2-7', ext_options), - ('gamlss.dist', '4.3-4', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-14', ext_options), - ('zoo', '1.7-12', ext_options), - ('xts', '0.9-7', ext_options), - ('TTR', '0.22-0', ext_options), - ('quantmod', '0.4-4', ext_options), - ('lmtest', '0.9-33', ext_options), - ('mnormt', '1.5-1', ext_options), - ('mvtnorm', '1.0-2', ext_options), - ('pcaPP', '1.9-60', ext_options), - ('numDeriv', '2012.9-1', ext_options), - ('lava', '1.4.0', ext_options), - ('prodlim', '1.5.1', ext_options), - ('pscl', '1.4.8', ext_options), - ('RSQLite', '1.0.0', ext_options), - ('BatchJobs', '1.6', ext_options), - ('sandwich', '2.3-2', ext_options), - ('sfsmisc', '1.0-27', ext_options), - ('spatial', '7.3-9', ext_options), - ('VGAM', '0.9-7', ext_options), - ('waveslim', '1.7.5', ext_options), - ('xtable', '1.7-4', ext_options), - ('profileModel', '0.5-9', ext_options), - ('brglm', '0.5-9', ext_options), - ('deSolve', '1.11', ext_options), - ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-34', ext_options), - ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.7.0', ext_options), - ('R.oo', '1.19.0', ext_options), - ('cgdsr', '1.1.33', ext_options), - ('R.utils', '2.0.0', ext_options), - ('R.matlab', '3.2.0', ext_options), + ('Rmpi', '0.6-5', { + 'patches': ['Rmpi-0.6-5_impi5.patch'], + }), + ('abind', '1.4-3'), + ('magic', '1.5-6'), + ('geometry', '0.3-5', { + 'patches': ['geometry-0.3-4-icc.patch'], + }), + ('bit', '1.1-12'), + ('filehash', '2.2-2'), + ('ff', '2.2-13'), + ('bnlearn', '3.7.1'), + ('bootstrap', '2015.2'), + ('combinat', '0.0-8'), + ('deal', '1.2-37'), + ('fdrtool', '1.2.14'), + ('formatR', '1.0'), + ('gtools', '3.4.1'), + ('gdata', '2.13.3'), + ('GSA', '1.03'), + ('highr', '0.4'), + ('infotheo', '1.2.0'), + ('lars', '1.2'), + ('lazy', '1.2-15'), + ('kernlab', '0.9-20'), + ('mime', '0.2'), + ('markdown', '0.7.4'), + ('mlbench', '2.1-1'), + ('NLP', '0.1-6'), + ('mclust', '4.4'), + ('RANN', '2.4.1'), + ('rmeta', '2.16'), + ('segmented', '0.5-1.1'), + ('som', '0.3-5'), + ('SuppDists', '1.1-9.1'), + ('stabledist', '0.6-6'), + ('survivalROC', '1.0.3'), + ('pspline', '1.0-16'), + ('timeDate', '3012.100'), + ('longmemo', '1.0-0'), + ('ADGofTest', '0.3'), + ('ade4', '1.6-2'), + ('AlgDesign', '1.1-7.3'), + ('base64enc', '0.1-2'), + ('BH', '1.55.0-3'), + ('brew', '1.0-6'), + ('Brobdingnag', '1.2-4'), + ('corpcor', '1.6.7'), + ('longitudinal', '1.1.11'), + ('checkmate', '1.5.2'), + ('cubature', '1.1-2'), + ('DEoptimR', '1.0-2'), + ('digest', '0.6.8'), + ('fastmatch', '1.0-4'), + ('ffbase', '0.11.3'), + ('iterators', '1.0.7'), + ('maps', '2.3-9'), + ('nnls', '1.4'), + ('sendmailR', '1.2-1'), + ('spam', '1.0-1'), + ('subplex', '1.1-4'), + ('stringr', '0.6.2'), + ('evaluate', '0.5.5'), + ('logspline', '2.1.5'), + ('ncbit', '2013.03.29'), + ('permute', '0.8-3'), + ('plotrix', '3.5-11'), + ('randomForest', '4.6-10'), + ('scatterplot3d', '0.3-35'), + ('SparseM', '1.6'), + ('tripack', '1.3-6'), + ('irace', '1.06'), + ('rJava', '0.9-6'), + ('lattice', '0.20-30'), + ('RColorBrewer', '1.1-2'), + ('latticeExtra', '0.6-26'), + ('Matrix', '1.1-5'), + ('png', '0.1-7'), + ('Rcpp', '0.11.5'), + ('RcppArmadillo', '0.4.650.1.1'), + ('plyr', '1.8.1'), + ('pROC', '1.7.3'), + ('quadprog', '1.5-5'), + ('BB', '2014.10-1'), + ('BBmisc', '1.9'), + ('fail', '1.2'), + ('rlecuyer', '0.3-3'), + ('snow', '0.3-13'), + ('MASS', '7.3-40'), + ('tree', '1.0-35'), + ('pls', '2.4-3'), + ('class', '7.3-12'), + ('e1071', '1.6-4'), + ('nnet', '7.3-9'), + ('nlme', '3.1-120'), + ('mgcv', '1.8-5'), + ('minqa', '1.2.4'), + ('nloptr', '1.0.4'), + ('RcppEigen', '0.3.2.4.0'), + ('lme4', '1.1-7'), + ('pbkrtest', '0.4-2'), + ('quantreg', '5.11'), + ('car', '2.0-25'), + ('colorspace', '1.2-6'), + ('robustbase', '0.92-3'), + ('sp', '1.0-17'), + ('vcd', '1.3-2'), + ('snowfall', '1.84-6'), + ('rpart', '4.1-9'), + ('mice', '2.22'), + ('urca', '1.2-8'), + ('fracdiff', '1.4-2'), + ('logistf', '1.21'), + ('akima', '0.5-11'), + ('bitops', '1.0-6'), + ('boot', '1.3-15'), + ('mixtools', '1.0.2'), + ('cluster', '2.0.1'), + ('gclus', '1.3.1'), + ('coda', '0.17-1'), + ('codetools', '0.2-11'), + ('foreach', '1.4.2'), + ('doMC', '1.3.3'), + ('DBI', '0.3.1'), + ('foreign', '0.8-63'), + ('survival', '2.38-1'), + ('gam', '1.09.1'), + ('gamlss.data', '4.2-7'), + ('gamlss.dist', '4.3-4'), + ('hwriter', '1.3.2'), + ('KernSmooth', '2.23-14'), + ('zoo', '1.7-12'), + ('xts', '0.9-7'), + ('TTR', '0.22-0'), + ('quantmod', '0.4-4'), + ('lmtest', '0.9-33'), + ('mnormt', '1.5-1'), + ('mvtnorm', '1.0-2'), + ('pcaPP', '1.9-60'), + ('numDeriv', '2012.9-1'), + ('lava', '1.4.0'), + ('prodlim', '1.5.1'), + ('pscl', '1.4.8'), + ('RSQLite', '1.0.0'), + ('BatchJobs', '1.6'), + ('sandwich', '2.3-2'), + ('sfsmisc', '1.0-27'), + ('spatial', '7.3-9'), + ('VGAM', '0.9-7'), + ('waveslim', '1.7.5'), + ('xtable', '1.7-4'), + ('profileModel', '0.5-9'), + ('brglm', '0.5-9'), + ('deSolve', '1.11'), + ('tseriesChaos', '0.1-13'), + ('tseries', '0.10-34'), + ('fastICA', '1.2-0'), + ('R.methodsS3', '1.7.0'), + ('R.oo', '1.19.0'), + ('cgdsr', '1.1.33'), + ('R.utils', '2.0.0'), + ('R.matlab', '3.2.0'), ('BiocGenerics', '0.12.1', bioconductor_options), ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), @@ -239,83 +243,83 @@ exts_list = [ ('GenomicAlignments', '1.2.2', bioconductor_options), ('ShortRead', '1.24.0', bioconductor_options), ('graph', '1.44.1', bioconductor_options), - ('gbm', '2.1.1', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.2-0', ext_options), - ('acepack', '1.3-3.3', ext_options), - ('gtable', '0.1.2', ext_options), - ('reshape2', '1.4.1', ext_options), - ('proto', '0.3-10', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), - ('scales', '0.2.4', ext_options), - ('ggplot2', '1.0.1', ext_options), - ('Hmisc', '3.15-0', ext_options), - ('fastcluster', '1.1.16', ext_options), - ('chron', '2.3-45', ext_options), - ('data.table', '1.9.4', ext_options), - ('igraph', '0.7.1', ext_options), - ('GeneNet', '1.2.12', ext_options), - ('ape', '3.2', ext_options), - ('htmltools', '0.2.6', ext_options), - ('RJSONIO', '1.3-0', ext_options), - ('caTools', '1.17.1', ext_options), - ('gplots', '2.16.0', ext_options), - ('ROCR', '1.0-5', ext_options), - ('httpuv', '1.3.2', ext_options), - ('R6', '2.0.1', ext_options), - ('shiny', '0.11.1', ext_options), - ('adegenet', '1.4-2', ext_options), - ('phylobase', '0.6.8', ext_options), - ('adephylo', '1.1-6', ext_options), - ('animation', '2.3', ext_options), - ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.4.6', ext_options), - ('calibrate', '1.7.2', ext_options), - ('clusterGeneration', '1.3.4', ext_options), - ('raster', '2.3-33', ext_options), - ('dismo', '1.0-12', ext_options), - ('expm', '0.99-1.1', ext_options), - ('extrafontdb', '1.0', ext_options), - ('Rttf2pt1', '1.3.3', ext_options), - ('extrafont', '0.17', ext_options), - ('fields', '8.2-1', ext_options), - ('shapefiles', '0.7', ext_options), - ('fossil', '0.3.7', ext_options), - ('geiger', '2.0.3', ext_options), - ('glmnet', '1.9-8', ext_options), - ('labdsv', '1.6-1', ext_options), - ('MatrixModels', '0.4-0', ext_options), - ('stabs', '0.5-1', ext_options), - ('mboost', '2.4-2', ext_options), - ('msm', '1.5', ext_options), - ('nor1mix', '1.2-0', ext_options), - ('np', '0.60-2', ext_options), - ('polynom', '1.3-8', ext_options), - ('polspline', '1.1.9', ext_options), - ('TH.data', '1.0-6', ext_options), - ('multcomp', '1.4-0', ext_options), - ('gridExtra', '0.9.1', ext_options), - ('rms', '4.3-0', ext_options), - ('RWekajars', '3.7.12-1', ext_options), - ('RWeka', '0.4-24', ext_options), - ('slam', '0.1-32', ext_options), - ('tm', '0.6', ext_options), - ('TraMineR', '1.8-9', ext_options), - ('chemometrics', '1.3.9', ext_options), - ('FNN', '1.1', ext_options), - ('ipred', '0.9-4', ext_options), - ('knitr', '1.9', ext_options), - ('statmod', '1.4.20', ext_options), - ('miscTools', '0.6-16', ext_options), - ('maxLik', '1.2-4', ext_options), - ('mlogit', '0.2-4', ext_options), - ('getopt', '1.20.0', ext_options), - ('gsalib', '2.1', ext_options), - ('reshape', '0.8.5', ext_options), - ('optparse', '1.3.0', ext_options), - ('klaR', '0.6-12', ext_options), - ('neuRosim', '0.2-12', ext_options), + ('gbm', '2.1.1'), + ('dichromat', '2.0-0'), + ('Formula', '1.2-0'), + ('acepack', '1.3-3.3'), + ('gtable', '0.1.2'), + ('reshape2', '1.4.1'), + ('proto', '0.3-10'), + ('munsell', '0.4.2'), + ('labeling', '0.3'), + ('scales', '0.2.4'), + ('ggplot2', '1.0.1'), + ('Hmisc', '3.15-0'), + ('fastcluster', '1.1.16'), + ('chron', '2.3-45'), + ('data.table', '1.9.4'), + ('igraph', '0.7.1'), + ('GeneNet', '1.2.12'), + ('ape', '3.2'), + ('htmltools', '0.2.6'), + ('RJSONIO', '1.3-0'), + ('caTools', '1.17.1'), + ('gplots', '2.16.0'), + ('ROCR', '1.0-5'), + ('httpuv', '1.3.2'), + ('R6', '2.0.1'), + ('shiny', '0.11.1'), + ('adegenet', '1.4-2'), + ('phylobase', '0.6.8'), + ('adephylo', '1.1-6'), + ('animation', '2.3'), + ('bigmemory.sri', '0.1.3'), + ('bigmemory', '4.4.6'), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.4'), + ('raster', '2.3-33'), + ('dismo', '1.0-12'), + ('expm', '0.99-1.1'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3.3'), + ('extrafont', '0.17'), + ('fields', '8.2-1'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.3'), + ('glmnet', '1.9-8'), + ('labdsv', '1.6-1'), + ('MatrixModels', '0.4-0'), + ('stabs', '0.5-1'), + ('mboost', '2.4-2'), + ('msm', '1.5'), + ('nor1mix', '1.2-0'), + ('np', '0.60-2'), + ('polynom', '1.3-8'), + ('polspline', '1.1.9'), + ('TH.data', '1.0-6'), + ('multcomp', '1.4-0'), + ('gridExtra', '0.9.1'), + ('rms', '4.3-0'), + ('RWekajars', '3.7.12-1'), + ('RWeka', '0.4-24'), + ('slam', '0.1-32'), + ('tm', '0.6'), + ('TraMineR', '1.8-9'), + ('chemometrics', '1.3.9'), + ('FNN', '1.1'), + ('ipred', '0.9-4'), + ('knitr', '1.9'), + ('statmod', '1.4.20'), + ('miscTools', '0.6-16'), + ('maxLik', '1.2-4'), + ('mlogit', '0.2-4'), + ('getopt', '1.20.0'), + ('gsalib', '2.1'), + ('reshape', '0.8.5'), + ('optparse', '1.3.0'), + ('klaR', '0.6-12'), + ('neuRosim', '0.2-12'), ('affyio', '1.34.0', bioconductor_options), ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), @@ -331,65 +335,67 @@ exts_list = [ ('oligoClasses', '1.28.0', bioconductor_options), ('edgeR', '3.8.6', bioconductor_options), ('PFAM.db', '3.0.0', bioconductor_options), - ('locfit', '1.5-9.1', ext_options), - ('GGally', '0.5.0', ext_options), + ('locfit', '1.5-9.1'), + ('GGally', '0.5.0'), ('baySeq', '2.0.50', bioconductor_options), - ('beanplot', '1.2', ext_options), - ('clValid', '0.6-6', ext_options), + ('beanplot', '1.2'), + ('clValid', '0.6-6'), ('qvalue', '1.43.0', bioconductor_options), ('impute', '1.40.0', bioconductor_options), - ('matrixStats', '0.14.0', ext_options), - ('samr', '2.0', ext_options), + ('matrixStats', '0.14.0'), + ('samr', '2.0'), ('DEGseq', '1.20.0', bioconductor_options), - ('DiscriMiner', '0.1-29', ext_options), - ('ellipse', '0.3-8', ext_options), - ('leaps', '2.9', ext_options), - ('flashClust', '1.01-2', ext_options), - ('FactoMineR', '1.29', ext_options), - ('modeltools', '0.2-21', ext_options), - ('flexclust', '1.3-4', ext_options), - ('flexmix', '2.3-13', ext_options), - ('prabclus', '2.2-6', ext_options), - ('diptest', '0.75-6', ext_options), - ('trimcluster', '0.1-2', ext_options), - ('fpc', '2.1-9', ext_options), - ('BiasedUrn', '1.06.1', ext_options), + ('DiscriMiner', '0.1-29'), + ('ellipse', '0.3-8'), + ('leaps', '2.9'), + ('flashClust', '1.01-2'), + ('FactoMineR', '1.29'), + ('modeltools', '0.2-21'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-13'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-6'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-9'), + ('BiasedUrn', '1.06.1'), ('hgu133plus2.db', '3.0.0', bioconductor_options), - ('TeachingDemos', '2.9', ext_options), - ('jsonlite', '0.9.14', ext_options), - ('kohonen', '2.0.15', ext_options), - ('base64', '1.1', ext_options), + ('TeachingDemos', '2.9'), + ('jsonlite', '0.9.14'), + ('kohonen', '2.0.15'), + ('base64', '1.1'), ('illuminaio', '0.8.0', bioconductor_options), - ('registry', '0.2', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), - ('doRNG', '1.6', ext_options), + ('registry', '0.2'), + ('pkgmaker', '0.22'), + ('rngtools', '1.2.4'), + ('doRNG', '1.6'), ('bumphunter', '1.6.0', bioconductor_options), ('multtest', '2.22.0', bioconductor_options), ('siggenes', '1.40.0', bioconductor_options), - ('nleqslv', '2.6', ext_options), + ('nleqslv', '2.6'), ('DynDoc', '1.44.0', bioconductor_options), ('genoset', '1.20.0', bioconductor_options), - ('RGCCA', '2.0', ext_options), - ('pheatmap', '1.0.2', ext_options), + ('RGCCA', '2.0'), + ('pheatmap', '1.0.2'), ('multtest', '2.22.0', bioconductor_options), ('NOISeq', '2.8.0', bioconductor_options), - ('openxlsx', '2.4.0', ext_options), + ('openxlsx', '2.4.0'), ('Rgraphviz', '2.10.0', bioconductor_options), - ('pvclust', '1.3-2', ext_options), - ('RCircos', '1.1.2', ext_options), - ('reshape', '0.8.5', ext_options), + ('pvclust', '1.3-2'), + ('RCircos', '1.1.2'), + ('reshape', '0.8.5'), ('RNASeqPower', '1.6.0', bioconductor_options), - ('VennDiagram', '1.6.9', ext_options), - ('xlsxjars', '0.6.1', ext_options), - ('xlsx', '0.5.7', ext_options), + ('VennDiagram', '1.6.9'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), ('Rsubread', '1.16.1', bioconductor_options), - ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('vegan', '2.2-1'), # requires Tcl/Tk ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk - ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), - ('fma', '2.01', ext_options), - ('expsmooth', '2.3', ext_options), - ('fpp', '0.5', ext_options), + ('forecast', '6.1', { + 'patches': ['forecast-6.1_icpc-wd308.patch'], + }), + ('fma', '2.01'), + ('expsmooth', '2.3'), + ('fpp', '0.5'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb index b5c6d77c853..fc8747efae8 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -31,7 +31,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -58,305 +58,307 @@ exts_list = [ 'utils', # non-standard libraries, should be specified with fixed versions! # Rmpi segfaults (on some systems) when built with goolf/1.7.20? - # ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-3', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-5', ext_options), - ('bit', '1.1-12', ext_options), - ('filehash', '2.2-2', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '3.7.1', ext_options), - ('bootstrap', '2015.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.14', ext_options), - ('formatR', '1.2', ext_options), - ('gtools', '3.4.2', ext_options), - ('gdata', '2.13.3', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.5', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-20', ext_options), - ('mime', '0.3', ext_options), - ('markdown', '0.7.7', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-6', ext_options), - ('mclust', '5.0.1', ext_options), - ('RANN', '2.5', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.1', ext_options), - ('som', '0.3-5', ext_options), - ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.6-6', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-16', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.7-2', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-2', ext_options), - ('BH', '1.55.0-3', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.7', ext_options), - ('longitudinal', '1.1.11', ext_options), - ('checkmate', '1.5.2', ext_options), - ('cubature', '1.1-2', ext_options), - ('DEoptimR', '1.0-2', ext_options), - ('digest', '0.6.8', ext_options), - ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.11.3', ext_options), - ('iterators', '1.0.7', ext_options), - ('maps', '2.3-9', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.0-1', ext_options), - ('subplex', '1.1-4', ext_options), - ('stringr', '0.6.2', ext_options), - ('evaluate', '0.7', ext_options), - ('logspline', '2.1.5', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.8-3', ext_options), - ('plotrix', '3.5-11', ext_options), - ('randomForest', '4.6-10', ext_options), - ('scatterplot3d', '0.3-35', ext_options), - ('SparseM', '1.6', ext_options), - ('tripack', '1.3-6', ext_options), - ('irace', '1.06', ext_options), - ('rJava', '0.9-6', ext_options), - ('lattice', '0.20-31', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.2-0', ext_options), - ('png', '0.1-7', ext_options), - ('Rcpp', '0.11.5', ext_options), - ('RcppArmadillo', '0.5.000.0', ext_options), - ('plyr', '1.8.2', ext_options), - ('pROC', '1.7.3', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.9', ext_options), - ('fail', '1.2', ext_options), - ('rlecuyer', '0.3-3', ext_options), - ('snow', '0.3-13', ext_options), - ('MASS', '7.3-40', ext_options), - ('tree', '1.0-35', ext_options), - ('pls', '2.4-3', ext_options), - ('class', '7.3-12', ext_options), - ('e1071', '1.6-4', ext_options), - ('nnet', '7.3-9', ext_options), - ('nlme', '3.1-120', ext_options), - ('minqa', '1.2.4', ext_options), - ('RcppEigen', '0.3.2.4.0', ext_options), - ('quantreg', '5.11', ext_options), - ('mgcv', '1.8-6', ext_options), - ('colorspace', '1.2-6', ext_options), - ('robustbase', '0.92-3', ext_options), - ('sp', '1.1-0', ext_options), - ('vcd', '1.3-2', ext_options), - ('snowfall', '1.84-6', ext_options), - ('rpart', '4.1-9', ext_options), - ('mice', '2.22', ext_options), - ('urca', '1.2-8', ext_options), - ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), - ('akima', '0.5-11', ext_options), - ('bitops', '1.0-6', ext_options), - ('boot', '1.3-15', ext_options), - ('mixtools', '1.0.3', ext_options), - ('cluster', '2.0.1', ext_options), - ('gclus', '1.3.1', ext_options), - ('coda', '0.17-1', ext_options), - ('codetools', '0.2-11', ext_options), - ('foreach', '1.4.2', ext_options), - ('doMC', '1.3.3', ext_options), - ('DBI', '0.3.1', ext_options), - ('foreign', '0.8-63', ext_options), - ('survival', '2.38-1', ext_options), - ('gam', '1.09.1', ext_options), - ('gamlss.data', '4.2-7', ext_options), - ('gamlss.dist', '4.3-4', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-14', ext_options), - ('zoo', '1.7-12', ext_options), - ('xts', '0.9-7', ext_options), - ('TTR', '0.22-0', ext_options), - ('quantmod', '0.4-4', ext_options), - ('lmtest', '0.9-33', ext_options), - ('mnormt', '1.5-2', ext_options), - ('mvtnorm', '1.0-2', ext_options), - ('pcaPP', '1.9-60', ext_options), - ('numDeriv', '2012.9-1', ext_options), - ('lava', '1.4.0', ext_options), - ('prodlim', '1.5.1', ext_options), - ('pscl', '1.4.9', ext_options), - ('RSQLite', '1.0.0', ext_options), - ('BatchJobs', '1.6', ext_options), - ('sandwich', '2.3-3', ext_options), - ('sfsmisc', '1.0-27', ext_options), - ('spatial', '7.3-9', ext_options), - ('VGAM', '0.9-7', ext_options), - ('waveslim', '1.7.5', ext_options), - ('xtable', '1.7-4', ext_options), - ('profileModel', '0.5-9', ext_options), - ('brglm', '0.5-9', ext_options), - ('deSolve', '1.11', ext_options), - ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-34', ext_options), - ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.7.0', ext_options), - ('R.oo', '1.19.0', ext_options), - ('cgdsr', '1.1.33', ext_options), - ('R.utils', '2.0.1', ext_options), - ('R.matlab', '3.2.0', ext_options), - ('gbm', '2.1.1', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.2-1', ext_options), - ('acepack', '1.3-3.3', ext_options), - ('reshape2', '1.4.1', ext_options), - ('gtable', '0.1.2', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), - ('scales', '0.2.4', ext_options), - ('proto', '0.3-10', ext_options), - ('ggplot2', '1.0.1', ext_options), - ('Hmisc', '3.15-0', ext_options), - ('fastcluster', '1.1.16', ext_options), - ('chron', '2.3-45', ext_options), - ('data.table', '1.9.4', ext_options), - ('igraph', '0.7.1', ext_options), - ('GeneNet', '1.2.12', ext_options), - ('ape', '3.2', ext_options), - ('htmltools', '0.2.6', ext_options), - ('RJSONIO', '1.3-0', ext_options), - ('caTools', '1.17.1', ext_options), - ('gplots', '2.16.0', ext_options), - ('ROCR', '1.0-7', ext_options), - ('httpuv', '1.3.2', ext_options), - ('R6', '2.0.1', ext_options), - ('shiny', '0.11.1', ext_options), - ('adegenet', '1.4-2', ext_options), - ('phylobase', '0.6.8', ext_options), - ('adephylo', '1.1-6', ext_options), - ('animation', '2.3', ext_options), - ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.4.6', ext_options), - ('calibrate', '1.7.2', ext_options), - ('clusterGeneration', '1.3.4', ext_options), - ('raster', '2.3-40', ext_options), - ('dismo', '1.0-12', ext_options), - ('expm', '0.99-1.1', ext_options), - ('extrafontdb', '1.0', ext_options), - ('Rttf2pt1', '1.3.3', ext_options), - ('extrafont', '0.17', ext_options), - ('fields', '8.2-1', ext_options), - ('shapefiles', '0.7', ext_options), - ('fossil', '0.3.7', ext_options), - ('geiger', '2.0.3', ext_options), - ('glmnet', '2.0-2', ext_options), - ('labdsv', '1.6-1', ext_options), - ('MatrixModels', '0.4-0', ext_options), - ('stabs', '0.5-1', ext_options), - ('mboost', '2.4-2', ext_options), - ('msm', '1.5', ext_options), - ('nor1mix', '1.2-0', ext_options), - ('np', '0.60-2', ext_options), - ('polynom', '1.3-8', ext_options), - ('quantreg', '5.11', ext_options), - ('polspline', '1.1.9', ext_options), - ('TH.data', '1.0-6', ext_options), - ('multcomp', '1.4-0', ext_options), - ('gridExtra', '0.9.1', ext_options), - ('rms', '4.3-0', ext_options), - ('RWekajars', '3.7.12-1', ext_options), - ('RWeka', '0.4-24', ext_options), - ('slam', '0.1-32', ext_options), - ('tm', '0.6', ext_options), - ('TraMineR', '1.8-9', ext_options), - ('chemometrics', '1.3.9', ext_options), - ('FNN', '1.1', ext_options), - ('ipred', '0.9-4', ext_options), - ('yaml', '2.1.13', ext_options), - ('knitr', '1.10', ext_options), - ('statmod', '1.4.21', ext_options), - ('miscTools', '0.6-16', ext_options), - ('maxLik', '1.2-4', ext_options), - ('mlogit', '0.2-4', ext_options), - ('getopt', '1.20.0', ext_options), - ('gsalib', '2.1', ext_options), - ('reshape', '0.8.5', ext_options), - ('optparse', '1.3.0', ext_options), - ('klaR', '0.6-12', ext_options), - ('neuRosim', '0.2-12', ext_options), - ('locfit', '1.5-9.1', ext_options), - ('GGally', '0.5.0', ext_options), - ('beanplot', '1.2', ext_options), - ('clValid', '0.6-6', ext_options), - ('matrixStats', '0.14.0', ext_options), - ('DiscriMiner', '0.1-29', ext_options), - ('ellipse', '0.3-8', ext_options), - ('leaps', '2.9', ext_options), - ('nloptr', '1.0.4', ext_options), - ('lme4', '1.1-8', ext_options), - ('pbkrtest', '0.4-2', ext_options), - ('car', '2.0-25', ext_options), - ('flashClust', '1.01-2', ext_options), - ('FactoMineR', '1.29', ext_options), - ('modeltools', '0.2-21', ext_options), - ('flexclust', '1.3-4', ext_options), - ('flexmix', '2.3-13', ext_options), - ('prabclus', '2.2-6', ext_options), - ('diptest', '0.75-6', ext_options), - ('trimcluster', '0.1-2', ext_options), - ('fpc', '2.1-9', ext_options), - ('BiasedUrn', '1.06.1', ext_options), - ('TeachingDemos', '2.9', ext_options), - ('jsonlite', '0.9.16', ext_options), - ('kohonen', '2.0.18', ext_options), - ('base64', '1.1', ext_options), - ('registry', '0.2', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), - ('doRNG', '1.6', ext_options), - ('nleqslv', '2.7', ext_options), - ('RGCCA', '2.0', ext_options), - ('pheatmap', '1.0.2', ext_options), - ('openxlsx', '2.4.0', ext_options), - ('pvclust', '1.3-2', ext_options), - ('RCircos', '1.1.2', ext_options), - ('VennDiagram', '1.6.9', ext_options), - ('xlsxjars', '0.6.1', ext_options), - ('xlsx', '0.5.7', ext_options), - ('vegan', '2.3-0', ext_options), - ('forecast', '6.1', ext_options), - ('fma', '2.01', ext_options), - ('expsmooth', '2.3', ext_options), - ('fpp', '0.5', ext_options), - ('XML', '3.98-1.1', ext_options), - ('memoise', '0.2.1', ext_options), - ('crayon', '1.3.1', ext_options), - ('testthat', '0.10.0', ext_options), - ('rmarkdown', '0.7', ext_options), - ('curl', '0.9.1', ext_options), - ('RCurl', '1.95-4.7', ext_options), - ('httr', '0.6.1', ext_options), - ('maptools', '0.8-36', ext_options), - ('deldir', '0.1-9', ext_options), - ('tensor', '1.5', ext_options), - ('polyclip', '1.3-0', ext_options), - ('goftest', '1.0-2', ext_options), - ('spatstat', '1.41-1', ext_options), - ('gdalUtils', '0.3.1', ext_options), - ('pracma', '1.8.3', ext_options), - ('bio3d', '2.2-2', ext_options), - ('penalized', '0.9-45', ext_options), - ('coin', '1.0-24', ext_options), - ('clusterRepro', '0.5-1.1', ext_options), - ('randomForestSRC', '2.0.7', ext_options), - ('sm', '2.2-5.4', ext_options), + # ('Rmpi', '0.6-5', { + # 'patches': ['Rmpi-0.6-5_impi5.patch'], + # }), + ('abind', '1.4-3'), + ('magic', '1.5-6'), + ('geometry', '0.3-5'), + ('bit', '1.1-12'), + ('filehash', '2.2-2'), + ('ff', '2.2-13'), + ('bnlearn', '3.7.1'), + ('bootstrap', '2015.2'), + ('combinat', '0.0-8'), + ('deal', '1.2-37'), + ('fdrtool', '1.2.14'), + ('formatR', '1.2'), + ('gtools', '3.4.2'), + ('gdata', '2.13.3'), + ('GSA', '1.03'), + ('highr', '0.5'), + ('infotheo', '1.2.0'), + ('lars', '1.2'), + ('lazy', '1.2-15'), + ('kernlab', '0.9-20'), + ('mime', '0.3'), + ('markdown', '0.7.7'), + ('mlbench', '2.1-1'), + ('NLP', '0.1-6'), + ('mclust', '5.0.1'), + ('RANN', '2.5'), + ('rmeta', '2.16'), + ('segmented', '0.5-1.1'), + ('som', '0.3-5'), + ('SuppDists', '1.1-9.1'), + ('stabledist', '0.6-6'), + ('survivalROC', '1.0.3'), + ('pspline', '1.0-16'), + ('timeDate', '3012.100'), + ('longmemo', '1.0-0'), + ('ADGofTest', '0.3'), + ('ade4', '1.7-2'), + ('AlgDesign', '1.1-7.3'), + ('base64enc', '0.1-2'), + ('BH', '1.55.0-3'), + ('brew', '1.0-6'), + ('Brobdingnag', '1.2-4'), + ('corpcor', '1.6.7'), + ('longitudinal', '1.1.11'), + ('checkmate', '1.5.2'), + ('cubature', '1.1-2'), + ('DEoptimR', '1.0-2'), + ('digest', '0.6.8'), + ('fastmatch', '1.0-4'), + ('ffbase', '0.11.3'), + ('iterators', '1.0.7'), + ('maps', '2.3-9'), + ('nnls', '1.4'), + ('sendmailR', '1.2-1'), + ('spam', '1.0-1'), + ('subplex', '1.1-4'), + ('stringr', '0.6.2'), + ('evaluate', '0.7'), + ('logspline', '2.1.5'), + ('ncbit', '2013.03.29'), + ('permute', '0.8-3'), + ('plotrix', '3.5-11'), + ('randomForest', '4.6-10'), + ('scatterplot3d', '0.3-35'), + ('SparseM', '1.6'), + ('tripack', '1.3-6'), + ('irace', '1.06'), + ('rJava', '0.9-6'), + ('lattice', '0.20-31'), + ('RColorBrewer', '1.1-2'), + ('latticeExtra', '0.6-26'), + ('Matrix', '1.2-0'), + ('png', '0.1-7'), + ('Rcpp', '0.11.5'), + ('RcppArmadillo', '0.5.000.0'), + ('plyr', '1.8.2'), + ('pROC', '1.7.3'), + ('quadprog', '1.5-5'), + ('BB', '2014.10-1'), + ('BBmisc', '1.9'), + ('fail', '1.2'), + ('rlecuyer', '0.3-3'), + ('snow', '0.3-13'), + ('MASS', '7.3-40'), + ('tree', '1.0-35'), + ('pls', '2.4-3'), + ('class', '7.3-12'), + ('e1071', '1.6-4'), + ('nnet', '7.3-9'), + ('nlme', '3.1-120'), + ('minqa', '1.2.4'), + ('RcppEigen', '0.3.2.4.0'), + ('quantreg', '5.11'), + ('mgcv', '1.8-6'), + ('colorspace', '1.2-6'), + ('robustbase', '0.92-3'), + ('sp', '1.1-0'), + ('vcd', '1.3-2'), + ('snowfall', '1.84-6'), + ('rpart', '4.1-9'), + ('mice', '2.22'), + ('urca', '1.2-8'), + ('fracdiff', '1.4-2'), + ('logistf', '1.21'), + ('akima', '0.5-11'), + ('bitops', '1.0-6'), + ('boot', '1.3-15'), + ('mixtools', '1.0.3'), + ('cluster', '2.0.1'), + ('gclus', '1.3.1'), + ('coda', '0.17-1'), + ('codetools', '0.2-11'), + ('foreach', '1.4.2'), + ('doMC', '1.3.3'), + ('DBI', '0.3.1'), + ('foreign', '0.8-63'), + ('survival', '2.38-1'), + ('gam', '1.09.1'), + ('gamlss.data', '4.2-7'), + ('gamlss.dist', '4.3-4'), + ('hwriter', '1.3.2'), + ('KernSmooth', '2.23-14'), + ('zoo', '1.7-12'), + ('xts', '0.9-7'), + ('TTR', '0.22-0'), + ('quantmod', '0.4-4'), + ('lmtest', '0.9-33'), + ('mnormt', '1.5-2'), + ('mvtnorm', '1.0-2'), + ('pcaPP', '1.9-60'), + ('numDeriv', '2012.9-1'), + ('lava', '1.4.0'), + ('prodlim', '1.5.1'), + ('pscl', '1.4.9'), + ('RSQLite', '1.0.0'), + ('BatchJobs', '1.6'), + ('sandwich', '2.3-3'), + ('sfsmisc', '1.0-27'), + ('spatial', '7.3-9'), + ('VGAM', '0.9-7'), + ('waveslim', '1.7.5'), + ('xtable', '1.7-4'), + ('profileModel', '0.5-9'), + ('brglm', '0.5-9'), + ('deSolve', '1.11'), + ('tseriesChaos', '0.1-13'), + ('tseries', '0.10-34'), + ('fastICA', '1.2-0'), + ('R.methodsS3', '1.7.0'), + ('R.oo', '1.19.0'), + ('cgdsr', '1.1.33'), + ('R.utils', '2.0.1'), + ('R.matlab', '3.2.0'), + ('gbm', '2.1.1'), + ('dichromat', '2.0-0'), + ('Formula', '1.2-1'), + ('acepack', '1.3-3.3'), + ('reshape2', '1.4.1'), + ('gtable', '0.1.2'), + ('munsell', '0.4.2'), + ('labeling', '0.3'), + ('scales', '0.2.4'), + ('proto', '0.3-10'), + ('ggplot2', '1.0.1'), + ('Hmisc', '3.15-0'), + ('fastcluster', '1.1.16'), + ('chron', '2.3-45'), + ('data.table', '1.9.4'), + ('igraph', '0.7.1'), + ('GeneNet', '1.2.12'), + ('ape', '3.2'), + ('htmltools', '0.2.6'), + ('RJSONIO', '1.3-0'), + ('caTools', '1.17.1'), + ('gplots', '2.16.0'), + ('ROCR', '1.0-7'), + ('httpuv', '1.3.2'), + ('R6', '2.0.1'), + ('shiny', '0.11.1'), + ('adegenet', '1.4-2'), + ('phylobase', '0.6.8'), + ('adephylo', '1.1-6'), + ('animation', '2.3'), + ('bigmemory.sri', '0.1.3'), + ('bigmemory', '4.4.6'), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.4'), + ('raster', '2.3-40'), + ('dismo', '1.0-12'), + ('expm', '0.99-1.1'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3.3'), + ('extrafont', '0.17'), + ('fields', '8.2-1'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.3'), + ('glmnet', '2.0-2'), + ('labdsv', '1.6-1'), + ('MatrixModels', '0.4-0'), + ('stabs', '0.5-1'), + ('mboost', '2.4-2'), + ('msm', '1.5'), + ('nor1mix', '1.2-0'), + ('np', '0.60-2'), + ('polynom', '1.3-8'), + ('quantreg', '5.11'), + ('polspline', '1.1.9'), + ('TH.data', '1.0-6'), + ('multcomp', '1.4-0'), + ('gridExtra', '0.9.1'), + ('rms', '4.3-0'), + ('RWekajars', '3.7.12-1'), + ('RWeka', '0.4-24'), + ('slam', '0.1-32'), + ('tm', '0.6'), + ('TraMineR', '1.8-9'), + ('chemometrics', '1.3.9'), + ('FNN', '1.1'), + ('ipred', '0.9-4'), + ('yaml', '2.1.13'), + ('knitr', '1.10'), + ('statmod', '1.4.21'), + ('miscTools', '0.6-16'), + ('maxLik', '1.2-4'), + ('mlogit', '0.2-4'), + ('getopt', '1.20.0'), + ('gsalib', '2.1'), + ('reshape', '0.8.5'), + ('optparse', '1.3.0'), + ('klaR', '0.6-12'), + ('neuRosim', '0.2-12'), + ('locfit', '1.5-9.1'), + ('GGally', '0.5.0'), + ('beanplot', '1.2'), + ('clValid', '0.6-6'), + ('matrixStats', '0.14.0'), + ('DiscriMiner', '0.1-29'), + ('ellipse', '0.3-8'), + ('leaps', '2.9'), + ('nloptr', '1.0.4'), + ('lme4', '1.1-8'), + ('pbkrtest', '0.4-2'), + ('car', '2.0-25'), + ('flashClust', '1.01-2'), + ('FactoMineR', '1.29'), + ('modeltools', '0.2-21'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-13'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-6'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-9'), + ('BiasedUrn', '1.06.1'), + ('TeachingDemos', '2.9'), + ('jsonlite', '0.9.16'), + ('kohonen', '2.0.18'), + ('base64', '1.1'), + ('registry', '0.2'), + ('pkgmaker', '0.22'), + ('rngtools', '1.2.4'), + ('doRNG', '1.6'), + ('nleqslv', '2.7'), + ('RGCCA', '2.0'), + ('pheatmap', '1.0.2'), + ('openxlsx', '2.4.0'), + ('pvclust', '1.3-2'), + ('RCircos', '1.1.2'), + ('VennDiagram', '1.6.9'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), + ('vegan', '2.3-0'), + ('forecast', '6.1'), + ('fma', '2.01'), + ('expsmooth', '2.3'), + ('fpp', '0.5'), + ('XML', '3.98-1.1'), + ('memoise', '0.2.1'), + ('crayon', '1.3.1'), + ('testthat', '0.10.0'), + ('rmarkdown', '0.7'), + ('curl', '0.9.1'), + ('RCurl', '1.95-4.7'), + ('httr', '0.6.1'), + ('maptools', '0.8-36'), + ('deldir', '0.1-9'), + ('tensor', '1.5'), + ('polyclip', '1.3-0'), + ('goftest', '1.0-2'), + ('spatstat', '1.41-1'), + ('gdalUtils', '0.3.1'), + ('pracma', '1.8.3'), + ('bio3d', '2.2-2'), + ('penalized', '0.9-45'), + ('coin', '1.0-24'), + ('clusterRepro', '0.5-1.1'), + ('randomForestSRC', '2.0.7'), + ('sm', '2.2-5.4'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb index 685023f39b4..bf999bcdca7 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -31,7 +31,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -57,360 +57,368 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-3', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.2-2', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '3.8.1', ext_options), - ('bootstrap', '2015.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.15', ext_options), - ('formatR', '1.2', ext_options), - ('gtools', '3.5.0', ext_options), - ('gdata', '2.17.0', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.5', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-20', ext_options), - ('mime', '0.3', ext_options), - ('markdown', '0.7.7', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-8', ext_options), - ('mclust', '5.0.2', ext_options), - ('RANN', '2.5', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.1', ext_options), - ('som', '0.3-5', ext_options), - ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.7-0', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-17', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.7-2', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-2', ext_options), - ('BH', '1.58.0-1', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.8', ext_options), - ('longitudinal', '1.1.12', ext_options), - ('checkmate', '1.6.0', ext_options), - ('cubature', '1.1-2', ext_options), - ('DEoptimR', '1.0-2', ext_options), - ('digest', '0.6.8', ext_options), - ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.12.1', ext_options), - ('iterators', '1.0.7', ext_options), - ('maps', '2.3-10', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.0-1', ext_options), - ('subplex', '1.1-6', ext_options), - ('stringi', '0.5-5', ext_options), - ('magrittr', '1.5', ext_options), - ('stringr', '1.0.0', ext_options), - ('evaluate', '0.7', ext_options), - ('logspline', '2.1.8', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.8-4', ext_options), - ('plotrix', '3.5-12', ext_options), - ('randomForest', '4.6-10', ext_options), - ('scatterplot3d', '0.3-35', ext_options), - ('SparseM', '1.6', ext_options), - ('tripack', '1.3-6', ext_options), - ('irace', '1.06', ext_options), - ('rJava', '0.9-6', ext_options), - ('lattice', '0.20-31', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.2-2', ext_options), - ('png', '0.1-7', ext_options), - ('Rcpp', '0.11.6', ext_options), - ('RcppArmadillo', '0.5.200.1.0', ext_options), - ('plyr', '1.8.3', ext_options), - ('pROC', '1.8', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.9', ext_options), - ('fail', '1.2', ext_options), - ('rlecuyer', '0.3-3', ext_options), - ('snow', '0.3-13', ext_options), - ('MASS', '7.3-42', ext_options), - ('tree', '1.0-36', ext_options), - ('pls', '2.4-3', ext_options), - ('class', '7.3-13', ext_options), - ('e1071', '1.6-4', ext_options), - ('nnet', '7.3-10', ext_options), - ('nlme', '3.1-121', ext_options), - ('minqa', '1.2.4', ext_options), - ('RcppEigen', '0.3.2.4.0', ext_options), - ('quantreg', '5.11', ext_options), - ('mgcv', '1.8-6', ext_options), - ('colorspace', '1.2-6', ext_options), - ('robustbase', '0.92-4', ext_options), - ('sp', '1.1-1', ext_options), - ('zoo', '1.7-12', ext_options), - ('lmtest', '0.9-34', ext_options), - ('vcd', '1.4-1', ext_options), - ('snowfall', '1.84-6', ext_options), - ('rpart', '4.1-10', ext_options), - ('mice', '2.22', ext_options), - ('urca', '1.2-8', ext_options), - ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), - ('akima', '0.5-11', ext_options), - ('bitops', '1.0-6', ext_options), - ('boot', '1.3-17', ext_options), - ('mixtools', '1.0.3', ext_options), - ('cluster', '2.0.2', ext_options), - ('gclus', '1.3.1', ext_options), - ('coda', '0.17-1', ext_options), - ('codetools', '0.2-11', ext_options), - ('foreach', '1.4.2', ext_options), - ('doMC', '1.3.3', ext_options), - ('DBI', '0.3.1', ext_options), - ('foreign', '0.8-65', ext_options), - ('survival', '2.38-3', ext_options), - ('gam', '1.12', ext_options), - ('gamlss.data', '4.2-7', ext_options), - ('gamlss.dist', '4.3-4', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-15', ext_options), - ('xts', '0.9-7', ext_options), - ('TTR', '0.23-0', ext_options), - ('quantmod', '0.4-4', ext_options), - ('mnormt', '1.5-3', ext_options), - ('mvtnorm', '1.0-2', ext_options), - ('pcaPP', '1.9-60', ext_options), - ('numDeriv', '2014.2-1', ext_options), - ('lava', '1.4.1', ext_options), - ('prodlim', '1.5.1', ext_options), - ('pscl', '1.4.9', ext_options), - ('RSQLite', '1.0.0', ext_options), - ('BatchJobs', '1.6', ext_options), - ('sandwich', '2.3-3', ext_options), - ('sfsmisc', '1.0-27', ext_options), - ('spatial', '7.3-10', ext_options), - ('VGAM', '0.9-8', ext_options), - ('waveslim', '1.7.5', ext_options), - ('xtable', '1.7-4', ext_options), - ('profileModel', '0.5-9', ext_options), - ('brglm', '0.5-9', ext_options), - ('deSolve', '1.12', ext_options), - ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-34', ext_options), - ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.7.0', ext_options), - ('R.oo', '1.19.0', ext_options), - ('cgdsr', '1.1.33', ext_options), - ('R.utils', '2.1.0', ext_options), - ('R.matlab', '3.2.0', ext_options), - ('gbm', '2.1.1', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.2-1', ext_options), - ('acepack', '1.3-3.3', ext_options), - ('reshape2', '1.4.1', ext_options), - ('gtable', '0.1.2', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), - ('scales', '0.2.5', ext_options), - ('proto', '0.3-10', ext_options), - ('ggplot2', '1.0.1', ext_options), - ('gridExtra', '0.9.1', ext_options), - ('Hmisc', '3.16-0', ext_options), - ('fastcluster', '1.1.16', ext_options), - ('chron', '2.3-47', ext_options), - ('data.table', '1.9.4', ext_options), - ('registry', '0.3', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), - ('doParallel', '1.0.8', ext_options), - ('gridBase', '0.4-7', ext_options), - ('NMF', '0.20.6', ext_options), - ('irlba', '1.0.3', ext_options), - ('igraph', '1.0.1', ext_options), - ('GeneNet', '1.2.12', ext_options), - ('ape', '3.3', ext_options), - ('htmltools', '0.2.6', ext_options), - ('RJSONIO', '1.3-0', ext_options), - ('caTools', '1.17.1', ext_options), - ('gplots', '2.17.0', ext_options), - ('ROCR', '1.0-7', ext_options), - ('httpuv', '1.3.2', ext_options), - ('R6', '2.1.0', ext_options), - ('jsonlite', '0.9.16', ext_options), - ('shiny', '0.12.1', ext_options), - ('seqinr', '3.1-3', ext_options), - ('LearnBayes', '2.15', ext_options), - ('deldir', '0.1-9', ext_options), - ('spdep', '0.5-88', ext_options), - ('assertthat', '0.1', ext_options), - ('lazyeval', '0.1.10', ext_options), - ('dplyr', '0.4.2', ext_options), - ('adegenet', '2.0.0', ext_options), - ('phylobase', '0.6.8', ext_options), - ('adephylo', '1.1-6', ext_options), - ('animation', '2.3', ext_options), - ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.4.6', ext_options), - ('calibrate', '1.7.2', ext_options), - ('clusterGeneration', '1.3.4', ext_options), - ('raster', '2.4-15', ext_options), - ('dismo', '1.0-12', ext_options), - ('expm', '0.99-1.1', ext_options), - ('extrafontdb', '1.0', ext_options), - ('Rttf2pt1', '1.3.3', ext_options), - ('extrafont', '0.17', ext_options), - ('fields', '8.2-1', ext_options), - ('shapefiles', '0.7', ext_options), - ('fossil', '0.3.7', ext_options), - ('geiger', '2.0.3', ext_options), - ('glmnet', '2.0-2', ext_options), - ('rgl', '0.95.1247', ext_options), - ('labdsv', '1.7-0', ext_options), - ('MatrixModels', '0.4-0', ext_options), - ('stabs', '0.5-1', ext_options), - ('mboost', '2.4-2', ext_options), - ('msm', '1.5', ext_options), - ('nor1mix', '1.2-0', ext_options), - ('np', '0.60-2', ext_options), - ('polynom', '1.3-8', ext_options), - ('polspline', '1.1.11', ext_options), - ('TH.data', '1.0-6', ext_options), - ('multcomp', '1.4-0', ext_options), - ('rms', '4.3-1', ext_options), - ('RWekajars', '3.7.12-1', ext_options), - ('RWeka', '0.4-24', ext_options), - ('slam', '0.1-32', ext_options), - ('tm', '0.6-2', ext_options), - ('TraMineR', '1.8-9', ext_options), - ('chemometrics', '1.3.9', ext_options), - ('FNN', '1.1', ext_options), - ('ipred', '0.9-4', ext_options), - ('yaml', '2.1.13', ext_options), - ('knitr', '1.10.5', ext_options), - ('statmod', '1.4.21', ext_options), - ('miscTools', '0.6-16', ext_options), - ('maxLik', '1.2-4', ext_options), - ('mlogit', '0.2-4', ext_options), - ('getopt', '1.20.0', ext_options), - ('gsalib', '2.1', ext_options), - ('reshape', '0.8.5', ext_options), - ('optparse', '1.3.0', ext_options), - ('klaR', '0.6-12', ext_options), - ('neuRosim', '0.2-12', ext_options), - ('locfit', '1.5-9.1', ext_options), - ('GGally', '0.5.0', ext_options), - ('beanplot', '1.2', ext_options), - ('clValid', '0.6-6', ext_options), - ('matrixStats', '0.14.2', ext_options), - ('DiscriMiner', '0.1-29', ext_options), - ('ellipse', '0.3-8', ext_options), - ('leaps', '2.9', ext_options), - ('nloptr', '1.0.4', ext_options), - ('lme4', '1.1-8', ext_options), - ('pbkrtest', '0.4-2', ext_options), - ('car', '2.0-25', ext_options), - ('flashClust', '1.01-2', ext_options), - ('FactoMineR', '1.31.3', ext_options), - ('modeltools', '0.2-21', ext_options), - ('flexclust', '1.3-4', ext_options), - ('flexmix', '2.3-13', ext_options), - ('prabclus', '2.2-6', ext_options), - ('diptest', '0.75-7', ext_options), - ('trimcluster', '0.1-2', ext_options), - ('fpc', '2.1-9', ext_options), - ('BiasedUrn', '1.06.1', ext_options), - ('TeachingDemos', '2.9', ext_options), - ('jsonlite', '0.9.16', ext_options), - ('kohonen', '2.0.18', ext_options), - ('base64', '1.1', ext_options), - ('doRNG', '1.6', ext_options), - ('nleqslv', '2.8', ext_options), - ('RGCCA', '2.0', ext_options), - ('pheatmap', '1.0.7', ext_options), - ('openxlsx', '3.0.0', ext_options), - ('pvclust', '1.3-2', ext_options), - ('RCircos', '1.1.2', ext_options), - ('VennDiagram', '1.6.9', ext_options), - ('xlsxjars', '0.6.1', ext_options), - ('xlsx', '0.5.7', ext_options), - ('vegan', '2.3-0', ext_options), - ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), - ('fma', '2.01', ext_options), - ('expsmooth', '2.3', ext_options), - ('fpp', '0.5', ext_options), - ('XML', '3.98-1.3', ext_options), - ('memoise', '0.2.1', ext_options), - ('crayon', '1.3.1', ext_options), - ('testthat', '0.10.0', ext_options), - ('rmarkdown', '0.7', ext_options), - ('curl', '0.9.1', ext_options), - ('httr', '1.0.0', ext_options), - ('maptools', '0.8-36', ext_options), - ('deldir', '0.1-9', ext_options), - ('tensor', '1.5', ext_options), - ('polyclip', '1.3-2', ext_options), - ('goftest', '1.0-3', ext_options), - ('spatstat', '1.42-2', ext_options), - ('gdalUtils', '0.3.1', ext_options), - ('pracma', '1.8.3', ext_options), - ('RCurl', '1.95-4.7', ext_options), - ('bio3d', '2.2-2', ext_options), - ('AUC', '0.3.0', ext_options), - ('interpretR', '0.2.3', ext_options), - ('SuperLearner', '2.0-15', ext_options), - ('lpSolve', '5.6.13', ext_options), - ('mediation', '4.4.5', ext_options), - ('caret', '6.0-57', ext_options), - ('adabag', '4.1', ext_options), - ('parallelMap', '1.3', ext_options), - ('ParamHelpers', '1.5', ext_options), - ('ggvis', '0.4.2', ext_options), - ('mlr', '2.4', ext_options), - ('unbalanced', '2.0', ext_options), - ('RSNNS', '0.4-7', ext_options), - ('abc.data', '1.0', ext_options), - ('abc', '2.1', ext_options), - ('lhs', '0.10', ext_options), - ('tensorA', '0.36', ext_options), - ('EasyABC', '1.5', ext_options), - ('shape', '1.4.2', ext_options), - ('tidyr', '0.3.1', ext_options), - ('whisker', '0.3-2', ext_options), - ('rstudioapi', '0.4.0', ext_options), - ('roxygen2', '5.0.1', ext_options), - ('git2r', '0.13.1', ext_options), - ('xml2', '0.1.2', ext_options), - ('rversions', '1.0.2', ext_options), - ('devtools', '1.9.1', ext_options), - ('Rook', '1.1-1', ext_options), - ('rjson', '0.2.15', ext_options), - ('Cairo', '1.5-9', ext_options), - ('RMTstat', '0.3', ext_options), - ('Lmoments', '1.1-6', ext_options), - ('distillery', '1.0-2', ext_options), - ('extRemes', '2.0-7', ext_options), - ('pixmap', '0.4-11', ext_options), - ('tkrplot', '0.0-23', ext_options), - ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-9', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), - ('ks', '1.10.1', ext_options), - ('logcondens', '2.1.4', ext_options), - ('Iso', '0.0-17', ext_options), - ('penalized', '0.9-45', ext_options), - ('coin', '1.0-24', ext_options), - ('clusterRepro', '0.5-1.1', ext_options), - ('randomForestSRC', '2.0.7', ext_options), - ('sm', '2.2-5.4', ext_options), + ('Rmpi', '0.6-5', { + 'patches': ['Rmpi-0.6-5_impi5.patch'], + }), + ('abind', '1.4-3'), + ('magic', '1.5-6'), + ('geometry', '0.3-5', { + 'patches': ['geometry-0.3-4-icc.patch'], + }), + ('bit', '1.1-12'), + ('filehash', '2.2-2'), + ('ff', '2.2-13'), + ('bnlearn', '3.8.1'), + ('bootstrap', '2015.2'), + ('combinat', '0.0-8'), + ('deal', '1.2-37'), + ('fdrtool', '1.2.15'), + ('formatR', '1.2'), + ('gtools', '3.5.0'), + ('gdata', '2.17.0'), + ('GSA', '1.03'), + ('highr', '0.5'), + ('infotheo', '1.2.0'), + ('lars', '1.2'), + ('lazy', '1.2-15'), + ('kernlab', '0.9-20'), + ('mime', '0.3'), + ('markdown', '0.7.7'), + ('mlbench', '2.1-1'), + ('NLP', '0.1-8'), + ('mclust', '5.0.2'), + ('RANN', '2.5'), + ('rmeta', '2.16'), + ('segmented', '0.5-1.1'), + ('som', '0.3-5'), + ('SuppDists', '1.1-9.1'), + ('stabledist', '0.7-0'), + ('survivalROC', '1.0.3'), + ('pspline', '1.0-17'), + ('timeDate', '3012.100'), + ('longmemo', '1.0-0'), + ('ADGofTest', '0.3'), + ('ade4', '1.7-2'), + ('AlgDesign', '1.1-7.3'), + ('base64enc', '0.1-2'), + ('BH', '1.58.0-1'), + ('brew', '1.0-6'), + ('Brobdingnag', '1.2-4'), + ('corpcor', '1.6.8'), + ('longitudinal', '1.1.12'), + ('checkmate', '1.6.0'), + ('cubature', '1.1-2'), + ('DEoptimR', '1.0-2'), + ('digest', '0.6.8'), + ('fastmatch', '1.0-4'), + ('ffbase', '0.12.1'), + ('iterators', '1.0.7'), + ('maps', '2.3-10'), + ('nnls', '1.4'), + ('sendmailR', '1.2-1'), + ('spam', '1.0-1'), + ('subplex', '1.1-6'), + ('stringi', '0.5-5'), + ('magrittr', '1.5'), + ('stringr', '1.0.0'), + ('evaluate', '0.7'), + ('logspline', '2.1.8'), + ('ncbit', '2013.03.29'), + ('permute', '0.8-4'), + ('plotrix', '3.5-12'), + ('randomForest', '4.6-10'), + ('scatterplot3d', '0.3-35'), + ('SparseM', '1.6'), + ('tripack', '1.3-6'), + ('irace', '1.06'), + ('rJava', '0.9-6'), + ('lattice', '0.20-31'), + ('RColorBrewer', '1.1-2'), + ('latticeExtra', '0.6-26'), + ('Matrix', '1.2-2'), + ('png', '0.1-7'), + ('Rcpp', '0.11.6'), + ('RcppArmadillo', '0.5.200.1.0'), + ('plyr', '1.8.3'), + ('pROC', '1.8'), + ('quadprog', '1.5-5'), + ('BB', '2014.10-1'), + ('BBmisc', '1.9'), + ('fail', '1.2'), + ('rlecuyer', '0.3-3'), + ('snow', '0.3-13'), + ('MASS', '7.3-42'), + ('tree', '1.0-36'), + ('pls', '2.4-3'), + ('class', '7.3-13'), + ('e1071', '1.6-4'), + ('nnet', '7.3-10'), + ('nlme', '3.1-121'), + ('minqa', '1.2.4'), + ('RcppEigen', '0.3.2.4.0'), + ('quantreg', '5.11'), + ('mgcv', '1.8-6'), + ('colorspace', '1.2-6'), + ('robustbase', '0.92-4'), + ('sp', '1.1-1'), + ('zoo', '1.7-12'), + ('lmtest', '0.9-34'), + ('vcd', '1.4-1'), + ('snowfall', '1.84-6'), + ('rpart', '4.1-10'), + ('mice', '2.22'), + ('urca', '1.2-8'), + ('fracdiff', '1.4-2'), + ('logistf', '1.21'), + ('akima', '0.5-11'), + ('bitops', '1.0-6'), + ('boot', '1.3-17'), + ('mixtools', '1.0.3'), + ('cluster', '2.0.2'), + ('gclus', '1.3.1'), + ('coda', '0.17-1'), + ('codetools', '0.2-11'), + ('foreach', '1.4.2'), + ('doMC', '1.3.3'), + ('DBI', '0.3.1'), + ('foreign', '0.8-65'), + ('survival', '2.38-3'), + ('gam', '1.12'), + ('gamlss.data', '4.2-7'), + ('gamlss.dist', '4.3-4'), + ('hwriter', '1.3.2'), + ('KernSmooth', '2.23-15'), + ('xts', '0.9-7'), + ('TTR', '0.23-0'), + ('quantmod', '0.4-4'), + ('mnormt', '1.5-3'), + ('mvtnorm', '1.0-2'), + ('pcaPP', '1.9-60'), + ('numDeriv', '2014.2-1'), + ('lava', '1.4.1'), + ('prodlim', '1.5.1'), + ('pscl', '1.4.9'), + ('RSQLite', '1.0.0'), + ('BatchJobs', '1.6'), + ('sandwich', '2.3-3'), + ('sfsmisc', '1.0-27'), + ('spatial', '7.3-10'), + ('VGAM', '0.9-8'), + ('waveslim', '1.7.5'), + ('xtable', '1.7-4'), + ('profileModel', '0.5-9'), + ('brglm', '0.5-9'), + ('deSolve', '1.12'), + ('tseriesChaos', '0.1-13'), + ('tseries', '0.10-34'), + ('fastICA', '1.2-0'), + ('R.methodsS3', '1.7.0'), + ('R.oo', '1.19.0'), + ('cgdsr', '1.1.33'), + ('R.utils', '2.1.0'), + ('R.matlab', '3.2.0'), + ('gbm', '2.1.1'), + ('dichromat', '2.0-0'), + ('Formula', '1.2-1'), + ('acepack', '1.3-3.3'), + ('reshape2', '1.4.1'), + ('gtable', '0.1.2'), + ('munsell', '0.4.2'), + ('labeling', '0.3'), + ('scales', '0.2.5'), + ('proto', '0.3-10'), + ('ggplot2', '1.0.1'), + ('gridExtra', '0.9.1'), + ('Hmisc', '3.16-0'), + ('fastcluster', '1.1.16'), + ('chron', '2.3-47'), + ('data.table', '1.9.4'), + ('registry', '0.3'), + ('pkgmaker', '0.22'), + ('rngtools', '1.2.4'), + ('doParallel', '1.0.8'), + ('gridBase', '0.4-7'), + ('NMF', '0.20.6'), + ('irlba', '1.0.3'), + ('igraph', '1.0.1'), + ('GeneNet', '1.2.12'), + ('ape', '3.3'), + ('htmltools', '0.2.6'), + ('RJSONIO', '1.3-0'), + ('caTools', '1.17.1'), + ('gplots', '2.17.0'), + ('ROCR', '1.0-7'), + ('httpuv', '1.3.2'), + ('R6', '2.1.0'), + ('jsonlite', '0.9.16'), + ('shiny', '0.12.1'), + ('seqinr', '3.1-3'), + ('LearnBayes', '2.15'), + ('deldir', '0.1-9'), + ('spdep', '0.5-88'), + ('assertthat', '0.1'), + ('lazyeval', '0.1.10'), + ('dplyr', '0.4.2'), + ('adegenet', '2.0.0'), + ('phylobase', '0.6.8'), + ('adephylo', '1.1-6'), + ('animation', '2.3'), + ('bigmemory.sri', '0.1.3'), + ('bigmemory', '4.4.6'), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.4'), + ('raster', '2.4-15'), + ('dismo', '1.0-12'), + ('expm', '0.99-1.1'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3.3'), + ('extrafont', '0.17'), + ('fields', '8.2-1'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.3'), + ('glmnet', '2.0-2'), + ('rgl', '0.95.1247'), + ('labdsv', '1.7-0'), + ('MatrixModels', '0.4-0'), + ('stabs', '0.5-1'), + ('mboost', '2.4-2'), + ('msm', '1.5'), + ('nor1mix', '1.2-0'), + ('np', '0.60-2'), + ('polynom', '1.3-8'), + ('polspline', '1.1.11'), + ('TH.data', '1.0-6'), + ('multcomp', '1.4-0'), + ('rms', '4.3-1'), + ('RWekajars', '3.7.12-1'), + ('RWeka', '0.4-24'), + ('slam', '0.1-32'), + ('tm', '0.6-2'), + ('TraMineR', '1.8-9'), + ('chemometrics', '1.3.9'), + ('FNN', '1.1'), + ('ipred', '0.9-4'), + ('yaml', '2.1.13'), + ('knitr', '1.10.5'), + ('statmod', '1.4.21'), + ('miscTools', '0.6-16'), + ('maxLik', '1.2-4'), + ('mlogit', '0.2-4'), + ('getopt', '1.20.0'), + ('gsalib', '2.1'), + ('reshape', '0.8.5'), + ('optparse', '1.3.0'), + ('klaR', '0.6-12'), + ('neuRosim', '0.2-12'), + ('locfit', '1.5-9.1'), + ('GGally', '0.5.0'), + ('beanplot', '1.2'), + ('clValid', '0.6-6'), + ('matrixStats', '0.14.2'), + ('DiscriMiner', '0.1-29'), + ('ellipse', '0.3-8'), + ('leaps', '2.9'), + ('nloptr', '1.0.4'), + ('lme4', '1.1-8'), + ('pbkrtest', '0.4-2'), + ('car', '2.0-25'), + ('flashClust', '1.01-2'), + ('FactoMineR', '1.31.3'), + ('modeltools', '0.2-21'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-13'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-7'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-9'), + ('BiasedUrn', '1.06.1'), + ('TeachingDemos', '2.9'), + ('jsonlite', '0.9.16'), + ('kohonen', '2.0.18'), + ('base64', '1.1'), + ('doRNG', '1.6'), + ('nleqslv', '2.8'), + ('RGCCA', '2.0'), + ('pheatmap', '1.0.7'), + ('openxlsx', '3.0.0'), + ('pvclust', '1.3-2'), + ('RCircos', '1.1.2'), + ('VennDiagram', '1.6.9'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), + ('vegan', '2.3-0'), + ('forecast', '6.1', { + 'patches': ['forecast-6.1_icpc-wd308.patch'], + }), + ('fma', '2.01'), + ('expsmooth', '2.3'), + ('fpp', '0.5'), + ('XML', '3.98-1.3'), + ('memoise', '0.2.1'), + ('crayon', '1.3.1'), + ('testthat', '0.10.0'), + ('rmarkdown', '0.7'), + ('curl', '0.9.1'), + ('httr', '1.0.0'), + ('maptools', '0.8-36'), + ('deldir', '0.1-9'), + ('tensor', '1.5'), + ('polyclip', '1.3-2'), + ('goftest', '1.0-3'), + ('spatstat', '1.42-2'), + ('gdalUtils', '0.3.1'), + ('pracma', '1.8.3'), + ('RCurl', '1.95-4.7'), + ('bio3d', '2.2-2'), + ('AUC', '0.3.0'), + ('interpretR', '0.2.3'), + ('SuperLearner', '2.0-15'), + ('lpSolve', '5.6.13'), + ('mediation', '4.4.5'), + ('caret', '6.0-57'), + ('adabag', '4.1'), + ('parallelMap', '1.3'), + ('ParamHelpers', '1.5'), + ('ggvis', '0.4.2'), + ('mlr', '2.4'), + ('unbalanced', '2.0'), + ('RSNNS', '0.4-7'), + ('abc.data', '1.0'), + ('abc', '2.1'), + ('lhs', '0.10'), + ('tensorA', '0.36'), + ('EasyABC', '1.5'), + ('shape', '1.4.2'), + ('tidyr', '0.3.1'), + ('whisker', '0.3-2'), + ('rstudioapi', '0.4.0'), + ('roxygen2', '5.0.1'), + ('git2r', '0.13.1'), + ('xml2', '0.1.2'), + ('rversions', '1.0.2'), + ('devtools', '1.9.1'), + ('Rook', '1.1-1'), + ('rjson', '0.2.15'), + ('Cairo', '1.5-9'), + ('RMTstat', '0.3'), + ('Lmoments', '1.1-6'), + ('distillery', '1.0-2'), + ('extRemes', '2.0-7'), + ('pixmap', '0.4-11'), + ('tkrplot', '0.0-23'), + ('misc3d', '0.8-4'), + ('multicool', '0.1-9', { + 'patches': [('multicool-0.1-9_icpc-wd308.patch', 1)], + }), + ('ks', '1.10.1'), + ('logcondens', '2.1.4'), + ('Iso', '0.0-17'), + ('penalized', '0.9-45'), + ('coin', '1.0-24'), + ('clusterRepro', '0.5-1.1'), + ('randomForestSRC', '2.0.7'), + ('sm', '2.2-5.4'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb index b972f1163cf..28a924627e0 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb @@ -31,7 +31,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -57,360 +57,368 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-3', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.2-2', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '3.8.1', ext_options), - ('bootstrap', '2015.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.15', ext_options), - ('formatR', '1.2', ext_options), - ('gtools', '3.5.0', ext_options), - ('gdata', '2.17.0', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.5', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-20', ext_options), - ('mime', '0.3', ext_options), - ('markdown', '0.7.7', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-8', ext_options), - ('mclust', '5.0.2', ext_options), - ('RANN', '2.5', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.1', ext_options), - ('som', '0.3-5', ext_options), - ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.7-0', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-17', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.7-2', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-2', ext_options), - ('BH', '1.58.0-1', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.8', ext_options), - ('longitudinal', '1.1.12', ext_options), - ('checkmate', '1.6.0', ext_options), - ('cubature', '1.1-2', ext_options), - ('DEoptimR', '1.0-2', ext_options), - ('digest', '0.6.8', ext_options), - ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.12.1', ext_options), - ('iterators', '1.0.7', ext_options), - ('maps', '2.3-10', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.0-1', ext_options), - ('subplex', '1.1-6', ext_options), - ('stringi', '0.5-5', ext_options), - ('magrittr', '1.5', ext_options), - ('stringr', '1.0.0', ext_options), - ('evaluate', '0.7', ext_options), - ('logspline', '2.1.8', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.8-4', ext_options), - ('plotrix', '3.5-12', ext_options), - ('randomForest', '4.6-10', ext_options), - ('scatterplot3d', '0.3-35', ext_options), - ('SparseM', '1.6', ext_options), - ('tripack', '1.3-6', ext_options), - ('irace', '1.06', ext_options), - ('rJava', '0.9-6', ext_options), - ('lattice', '0.20-31', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.2-2', ext_options), - ('png', '0.1-7', ext_options), - ('Rcpp', '0.11.6', ext_options), - ('RcppArmadillo', '0.5.200.1.0', ext_options), - ('plyr', '1.8.3', ext_options), - ('pROC', '1.8', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.9', ext_options), - ('fail', '1.2', ext_options), - ('rlecuyer', '0.3-3', ext_options), - ('snow', '0.3-13', ext_options), - ('MASS', '7.3-42', ext_options), - ('tree', '1.0-36', ext_options), - ('pls', '2.4-3', ext_options), - ('class', '7.3-13', ext_options), - ('e1071', '1.6-4', ext_options), - ('nnet', '7.3-10', ext_options), - ('nlme', '3.1-121', ext_options), - ('minqa', '1.2.4', ext_options), - ('RcppEigen', '0.3.2.4.0', ext_options), - ('quantreg', '5.11', ext_options), - ('mgcv', '1.8-6', ext_options), - ('colorspace', '1.2-6', ext_options), - ('robustbase', '0.92-4', ext_options), - ('sp', '1.1-1', ext_options), - ('zoo', '1.7-12', ext_options), - ('lmtest', '0.9-34', ext_options), - ('vcd', '1.4-1', ext_options), - ('snowfall', '1.84-6', ext_options), - ('rpart', '4.1-10', ext_options), - ('mice', '2.22', ext_options), - ('urca', '1.2-8', ext_options), - ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), - ('akima', '0.5-11', ext_options), - ('bitops', '1.0-6', ext_options), - ('boot', '1.3-17', ext_options), - ('mixtools', '1.0.3', ext_options), - ('cluster', '2.0.2', ext_options), - ('gclus', '1.3.1', ext_options), - ('coda', '0.17-1', ext_options), - ('codetools', '0.2-11', ext_options), - ('foreach', '1.4.2', ext_options), - ('doMC', '1.3.3', ext_options), - ('DBI', '0.3.1', ext_options), - ('foreign', '0.8-65', ext_options), - ('survival', '2.38-3', ext_options), - ('gam', '1.12', ext_options), - ('gamlss.data', '4.2-7', ext_options), - ('gamlss.dist', '4.3-4', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-15', ext_options), - ('xts', '0.9-7', ext_options), - ('TTR', '0.23-0', ext_options), - ('quantmod', '0.4-4', ext_options), - ('mnormt', '1.5-3', ext_options), - 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('Iso', '0.0-17'), + ('penalized', '0.9-45'), + ('coin', '1.0-24'), + ('clusterRepro', '0.5-1.1'), + ('randomForestSRC', '2.0.7'), + ('sm', '2.2-5.4'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index bd244047ad8..c2396a2d58d 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -43,7 +43,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -68,394 +68,406 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-3', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.3', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '3.9', ext_options), - ('bootstrap', '2015.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.15', ext_options), - ('formatR', '1.2.1', ext_options), - ('gtools', '3.5.0', ext_options), - ('gdata', '2.17.0', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.5.1', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-22', ext_options), - ('mime', '0.4', ext_options), - ('markdown', '0.7.7', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-8', ext_options), - ('mclust', '5.1', ext_options), - ('RANN', '2.5', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.4', ext_options), - ('som', '0.3-5', ext_options), - ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.7-0', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-17', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.7-3', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-3', ext_options), - ('BH', '1.60.0-1', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.8', ext_options), - ('longitudinal', '1.1.12', ext_options), - ('checkmate', '1.6.3', ext_options), - ('cubature', '1.1-2', ext_options), - ('DEoptimR', '1.0-4', ext_options), - ('digest', '0.6.8', ext_options), - ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.12.1', ext_options), - ('iterators', '1.0.8', ext_options), - ('maps', '3.0.2', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.3-0', ext_options), - ('subplex', '1.1-6', ext_options), - ('stringi', '1.0-1', ext_options), - ('magrittr', '1.5', ext_options), - ('stringr', '1.0.0', ext_options), - ('evaluate', '0.8', ext_options), - ('logspline', '2.1.8', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.8-4', ext_options), - ('plotrix', '3.6-1', ext_options), - ('randomForest', '4.6-12', ext_options), - ('scatterplot3d', '0.3-36', ext_options), - ('SparseM', '1.7', ext_options), - ('tripack', '1.3-7', ext_options), - ('irace', '1.07', ext_options), - ('rJava', '0.9-7', ext_options), - ('lattice', '0.20-33', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.2-3', ext_options), - ('png', '0.1-7', ext_options), - ('Rcpp', '0.12.2', ext_options), - ('RcppArmadillo', '0.6.400.2.2', ext_options), - ('plyr', '1.8.3', ext_options), - ('pROC', '1.8', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.9', ext_options), - ('fail', '1.3', ext_options), - ('rlecuyer', '0.3-4', ext_options), - ('snow', '0.4-1', ext_options), - ('MASS', '7.3-45', ext_options), - ('tree', '1.0-36', ext_options), - ('pls', '2.5-0', ext_options), - ('class', '7.3-14', ext_options), - ('e1071', '1.6-7', ext_options), - ('nnet', '7.3-11', ext_options), - ('nlme', '3.1-122', ext_options), - ('minqa', '1.2.4', ext_options), - ('RcppEigen', '0.3.2.5.1', ext_options), - ('MatrixModels', '0.4-1', ext_options), - ('quantreg', '5.19', ext_options), - ('mgcv', '1.8-10', ext_options), - ('colorspace', '1.2-6', ext_options), - ('robustbase', '0.92-5', ext_options), - ('sp', '1.2-1', ext_options), - ('zoo', '1.7-12', ext_options), - ('lmtest', '0.9-34', ext_options), - ('vcd', '1.4-1', ext_options), - ('snowfall', '1.84-6.1', ext_options), - ('rpart', '4.1-10', ext_options), - ('survival', '2.38-3', ext_options), - ('mice', '2.25', ext_options), - ('urca', '1.2-8', ext_options), - ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), - ('akima', '0.5-12', ext_options), - ('bitops', '1.0-6', ext_options), - ('boot', '1.3-17', ext_options), - ('mixtools', '1.0.3', ext_options), - ('cluster', '2.0.3', ext_options), - ('gclus', '1.3.1', ext_options), - ('coda', '0.18-1', ext_options), - ('codetools', '0.2-14', ext_options), - ('foreach', '1.4.3', ext_options), - ('doMC', '1.3.4', ext_options), - ('DBI', '0.3.1', ext_options), - ('foreign', '0.8-66', ext_options), - ('gam', '1.12', ext_options), - ('gamlss.data', '4.3-2', ext_options), - ('gamlss.dist', '4.3-5', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-15', ext_options), - ('xts', '0.9-7', ext_options), - ('TTR', '0.23-0', ext_options), - ('quantmod', '0.4-5', ext_options), - ('mnormt', '1.5-3', ext_options), - ('mvtnorm', '1.0-3', ext_options), - ('pcaPP', '1.9-60', ext_options), - ('numDeriv', '2014.2-1', ext_options), - ('lava', '1.4.1', ext_options), - ('prodlim', '1.5.7', ext_options), - ('pscl', '1.4.9', ext_options), - ('RSQLite', '1.0.0', ext_options), - ('BatchJobs', '1.6', ext_options), - ('sandwich', '2.3-4', ext_options), - ('sfsmisc', '1.0-28', ext_options), - ('spatial', '7.3-11', ext_options), - ('VGAM', '1.0-0', ext_options), - ('waveslim', '1.7.5', ext_options), - ('xtable', '1.8-0', ext_options), - ('profileModel', '0.5-9', ext_options), - ('brglm', '0.5-9', ext_options), - ('deSolve', '1.12', ext_options), - ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-34', ext_options), - ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.7.0', ext_options), - ('R.oo', '1.19.0', ext_options), - ('cgdsr', '1.2.5', ext_options), - ('R.utils', '2.2.0', ext_options), - ('R.matlab', '3.3.0', ext_options), - ('gbm', '2.1.1', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.2-1', ext_options), - ('acepack', '1.3-3.3', ext_options), - ('reshape2', '1.4.1', ext_options), - ('gtable', '0.1.2', ext_options), - ('munsell', '0.4.2', ext_options), - ('labeling', '0.3', ext_options), - ('scales', '0.3.0', ext_options), - ('proto', '0.3-10', ext_options), - ('ggplot2', '2.0.0', ext_options), - ('gridExtra', '2.0.0', ext_options), - ('Hmisc', '3.17-1', ext_options), - ('fastcluster', '1.1.16', ext_options), - ('chron', '2.3-47', ext_options), - ('data.table', '1.9.6', ext_options), - ('registry', '0.3', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), - ('doParallel', '1.0.10', ext_options), - ('gridBase', '0.4-7', ext_options), - ('NMF', '0.20.6', ext_options), - ('irlba', '2.0.0', ext_options), - ('igraph', '1.0.1', ext_options), - ('GeneNet', '1.2.13', ext_options), - ('ape', '3.4', ext_options), - ('htmltools', '0.3', ext_options), - ('RJSONIO', '1.3-0', ext_options), - ('caTools', '1.17.1', ext_options), - ('gplots', '2.17.0', ext_options), - ('ROCR', '1.0-7', ext_options), - ('httpuv', '1.3.3', ext_options), - ('R6', '2.1.1', ext_options), - ('jsonlite', '0.9.19', ext_options), - ('rjson', '0.2.15', ext_options), - ('shiny', '0.12.2', ext_options), - ('seqinr', '3.1-3', ext_options), - ('LearnBayes', '2.15', ext_options), - ('deldir', '0.1-9', ext_options), - ('spdep', '0.5-92', ext_options), - ('assertthat', '0.1', ext_options), - ('lazyeval', '0.1.10', ext_options), - ('dplyr', '0.4.3', ext_options), - ('adegenet', '2.0.0', ext_options), - ('rncl', '0.6.0', ext_options), - ('XML', '3.98-1.3', ext_options), - ('memoise', '0.2.1', ext_options), - ('crayon', '1.3.1', ext_options), - ('praise', '1.0.0', ext_options), - ('testthat', '0.11.0', ext_options), - ('yaml', '2.1.13', ext_options), - ('knitr', '1.11', ext_options), - ('rmarkdown', '0.9.2', ext_options), - ('curl', '0.9.4', ext_options), - ('httr', '1.0.0', ext_options), - ('reshape', '0.8.5', ext_options), - ('bold', '0.3.0', ext_options), - ('taxize', '0.7.0', ext_options), - ('tidyr', '0.3.1', ext_options), - ('uuid', '0.1-2', ext_options), - ('RNeXML', '2.0.5', ext_options), - ('phylobase', '0.8.0', ext_options), - ('adephylo', '1.1-6', ext_options), - ('animation', '2.4', ext_options), - ('bigmemory.sri', '0.1.3', ext_options), - ('bigmemory', '4.5.8', dict(ext_options.items() + [('patches', ['bigmemory-4.5.8_icpc-wd308.patch'])])), - ('calibrate', '1.7.2', ext_options), - ('clusterGeneration', '1.3.4', ext_options), - ('raster', '2.5-2', ext_options), - ('dismo', '1.0-12', ext_options), - ('expm', '0.999-0', ext_options), - ('extrafontdb', '1.0', ext_options), - ('Rttf2pt1', '1.3.3', ext_options), - ('extrafont', '0.17', ext_options), - ('fields', '8.3-6', ext_options), - ('shapefiles', '0.7', ext_options), - ('fossil', '0.3.7', ext_options), - ('geiger', '2.0.6', ext_options), - ('glmnet', '2.0-2', ext_options), - ('rgl', '0.95.1441', ext_options), - ('labdsv', '1.7-0', ext_options), - ('stabs', '0.5-1', ext_options), - ('mboost', '2.5-0', ext_options), - ('msm', '1.6', ext_options), - ('nor1mix', '1.2-1', ext_options), - ('np', '0.60-2', ext_options), - ('polynom', '1.3-8', ext_options), - ('polspline', '1.1.12', ext_options), - ('TH.data', '1.0-6', ext_options), - ('multcomp', '1.4-1', ext_options), - ('rms', '4.4-1', ext_options), - ('RWekajars', '3.7.12-1', ext_options), - ('RWeka', '0.4-24', ext_options), - ('slam', '0.1-32', ext_options), - ('tm', '0.6-2', ext_options), - ('TraMineR', '1.8-11', ext_options), - ('chemometrics', '1.3.9', ext_options), - ('FNN', '1.1', ext_options), - ('ipred', '0.9-5', ext_options), - ('statmod', '1.4.23', ext_options), - ('miscTools', '0.6-16', ext_options), - ('maxLik', '1.3-4', ext_options), - ('mlogit', '0.2-4', ext_options), - ('getopt', '1.20.0', ext_options), - ('gsalib', '2.1', ext_options), - ('optparse', '1.3.2', ext_options), - ('klaR', '0.6-12', ext_options), - ('neuRosim', '0.2-12', ext_options), - ('locfit', '1.5-9.1', ext_options), - ('GGally', '1.0.0', ext_options), - ('beanplot', '1.2', ext_options), - ('clValid', '0.6-6', ext_options), - ('matrixStats', '0.50.1', ext_options), - ('DiscriMiner', '0.1-29', ext_options), - ('ellipse', '0.3-8', ext_options), - ('leaps', '2.9', ext_options), - ('nloptr', '1.0.4', ext_options), - ('lme4', '1.1-10', ext_options), - ('pbkrtest', '0.4-4', ext_options), - ('car', '2.1-1', ext_options), - ('flashClust', '1.01-2', ext_options), - ('FactoMineR', '1.31.4', ext_options), - ('modeltools', '0.2-21', ext_options), - ('flexclust', '1.3-4', ext_options), - ('flexmix', '2.3-13', ext_options), - ('prabclus', '2.2-6', ext_options), - ('diptest', '0.75-7', ext_options), - ('trimcluster', '0.1-2', ext_options), - ('fpc', '2.1-10', ext_options), - ('BiasedUrn', '1.07', ext_options), - ('TeachingDemos', '2.9', ext_options), - ('kohonen', '2.0.19', ext_options), - ('base64', '1.1', ext_options), - ('doRNG', '1.6', ext_options), - ('nleqslv', '2.9.1', ext_options), - ('RGCCA', '2.0', ext_options), - ('pheatmap', '1.0.8', ext_options), - ('openxlsx', '3.0.0', ext_options), - ('pvclust', '2.0-0', ext_options), - ('RCircos', '1.1.3', ext_options), - ('lambda.r', '1.1.7', ext_options), - ('futile.options', '1.0.0', ext_options), - ('futile.logger', '1.4.1', ext_options), - ('VennDiagram', '1.6.16', ext_options), - ('xlsxjars', '0.6.1', ext_options), - ('xlsx', '0.5.7', ext_options), - ('vegan', '2.3-2', ext_options), - ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), - ('fma', '2.01', ext_options), - ('expsmooth', '2.3', ext_options), - ('fpp', '0.5', ext_options), - ('maptools', '0.8-37', ext_options), - ('deldir', '0.1-9', ext_options), - ('tensor', '1.5', ext_options), - ('polyclip', '1.3-2', ext_options), - ('goftest', '1.0-3', ext_options), - ('spatstat', '1.44-1', ext_options), - ('rgdal', '1.1-3', ext_options), - ('gdalUtils', '2.0.1.7', ext_options), - ('pracma', '1.8.8', ext_options), - ('RCurl', '1.95-4.7', ext_options), - ('bio3d', '2.2-4', ext_options), - ('AUC', '0.3.0', ext_options), - ('interpretR', '0.2.3', ext_options), - ('SuperLearner', '2.0-15', ext_options), - ('lpSolve', '5.6.13', ext_options), - ('mediation', '4.4.5', ext_options), - ('caret', '6.0-64', ext_options), - ('adabag', '4.1', ext_options), - ('parallelMap', '1.3', ext_options), - ('ParamHelpers', '1.6', ext_options), - ('ggvis', '0.4.2', ext_options), - ('mlr', '2.7', ext_options), - ('unbalanced', '2.0', ext_options), - ('RSNNS', '0.4-7', ext_options), - ('abc.data', '1.0', ext_options), - ('abc', '2.1', ext_options), - ('lhs', '0.10', ext_options), - ('tensorA', '0.36', ext_options), - ('EasyABC', '1.5', ext_options), - ('shape', '1.4.2', ext_options), - ('whisker', '0.3-2', ext_options), - ('rstudioapi', '0.4.0', ext_options), - ('roxygen2', '5.0.1', ext_options), - ('git2r', '0.13.1', ext_options), - ('xml2', '0.1.2', ext_options), - ('rversions', '1.0.2', ext_options), - ('devtools', '1.9.1', ext_options), - ('Rook', '1.1-1', ext_options), - ('rjson', '0.2.15', ext_options), - ('Cairo', '1.5-9', ext_options), - ('RMTstat', '0.3', ext_options), - ('Lmoments', '1.1-6', ext_options), - ('distillery', '1.0-2', ext_options), - ('extRemes', '2.0-7', ext_options), - ('pixmap', '0.4-11', ext_options), - ('tkrplot', '0.0-23', ext_options), - ('misc3d', '0.8-4', ext_options), - ('multicool', '0.1-9', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), - ('ks', '1.10.1', ext_options), - ('logcondens', '2.1.4', ext_options), - ('Iso', '0.0-17', ext_options), - ('penalized', '0.9-45', ext_options), - ('coin', '1.1-2', ext_options), - ('clusterRepro', '0.5-1.1', ext_options), - ('randomForestSRC', '2.0.7', ext_options), - ('sm', '2.2-5.4', ext_options), - ('psych', '1.5.8', ext_options), - ('pbivnorm', '0.6.0', ext_options), - ('lavaan', '0.5-20', ext_options), - ('matrixcalc', '1.0-3', ext_options), - ('arm', '1.8-6', ext_options), - ('mi', '1.0', ext_options), - ('htmlwidgets', '0.6', ext_options), - ('visNetwork', '0.2.1', ext_options), - ('DiagrammeR', '0.8.2', ext_options), - ('sem', '3.1-6', ext_options), - ('jpeg', '0.1-8', ext_options), - ('sna', '2.3-2', ext_options), - ('glasso', '1.8', dict(ext_options.items() + [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])), - ('huge', '1.2.7', ext_options), - ('d3Network', '0.5.2.1', ext_options), - ('ggm', '2.3', ext_options), - ('qgraph', '1.3.2', ext_options), - ('diveRsity', '1.9.89', ext_options), - ('doSNOW', '1.0.14', ext_options), - ('phangorn', '2.0.2', ext_options), - ('geepack', '1.2-0.1', ext_options), - ('lubridate', '1.5.6', ext_options), - ('biom', '0.3.12', ext_options), - ('pim', '2.0.0.2', ext_options), + ('Rmpi', '0.6-5', { + 'patches': ['Rmpi-0.6-5_impi5.patch'], + }), + ('abind', '1.4-3'), + ('magic', '1.5-6'), + ('geometry', '0.3-6', { + 'patches': ['geometry-0.3-4-icc.patch'], + }), + ('bit', '1.1-12'), + ('filehash', '2.3'), + ('ff', '2.2-13'), + ('bnlearn', '3.9'), + ('bootstrap', '2015.2'), + ('combinat', '0.0-8'), + ('deal', '1.2-37'), + ('fdrtool', '1.2.15'), + ('formatR', '1.2.1'), + ('gtools', '3.5.0'), + ('gdata', '2.17.0'), + ('GSA', '1.03'), + ('highr', '0.5.1'), + ('infotheo', '1.2.0'), + ('lars', '1.2'), + ('lazy', '1.2-15'), + ('kernlab', '0.9-22'), + ('mime', '0.4'), + ('markdown', '0.7.7'), + ('mlbench', '2.1-1'), + ('NLP', '0.1-8'), + ('mclust', '5.1'), + ('RANN', '2.5'), + ('rmeta', '2.16'), + ('segmented', '0.5-1.4'), + ('som', '0.3-5'), + ('SuppDists', '1.1-9.1'), + ('stabledist', '0.7-0'), + ('survivalROC', '1.0.3'), + ('pspline', '1.0-17'), + ('timeDate', '3012.100'), + ('longmemo', '1.0-0'), + ('ADGofTest', '0.3'), + ('ade4', '1.7-3'), + ('AlgDesign', '1.1-7.3'), + ('base64enc', '0.1-3'), + ('BH', '1.60.0-1'), + ('brew', '1.0-6'), + ('Brobdingnag', '1.2-4'), + ('corpcor', '1.6.8'), + ('longitudinal', '1.1.12'), + ('checkmate', '1.6.3'), + ('cubature', '1.1-2'), + ('DEoptimR', '1.0-4'), + ('digest', '0.6.8'), + ('fastmatch', '1.0-4'), + ('ffbase', '0.12.1'), + ('iterators', '1.0.8'), + ('maps', '3.0.2'), + ('nnls', '1.4'), + ('sendmailR', '1.2-1'), + ('spam', '1.3-0'), + ('subplex', '1.1-6'), + ('stringi', '1.0-1'), + ('magrittr', '1.5'), + ('stringr', '1.0.0'), + ('evaluate', '0.8'), + ('logspline', '2.1.8'), + ('ncbit', '2013.03.29'), + ('permute', '0.8-4'), + ('plotrix', '3.6-1'), + ('randomForest', '4.6-12'), + ('scatterplot3d', '0.3-36'), + ('SparseM', '1.7'), + ('tripack', '1.3-7'), + ('irace', '1.07'), + ('rJava', '0.9-7'), + ('lattice', '0.20-33'), + ('RColorBrewer', '1.1-2'), + ('latticeExtra', '0.6-26'), + ('Matrix', '1.2-3'), + ('png', '0.1-7'), + ('Rcpp', '0.12.2'), + ('RcppArmadillo', '0.6.400.2.2'), + ('plyr', '1.8.3'), + ('pROC', '1.8'), + ('quadprog', '1.5-5'), + ('BB', '2014.10-1'), + ('BBmisc', '1.9'), + ('fail', '1.3'), + ('rlecuyer', '0.3-4'), + ('snow', '0.4-1'), + ('MASS', '7.3-45'), + ('tree', '1.0-36'), + ('pls', '2.5-0'), + ('class', '7.3-14'), + ('e1071', '1.6-7'), + ('nnet', '7.3-11'), + ('nlme', '3.1-122'), + ('minqa', '1.2.4'), + ('RcppEigen', '0.3.2.5.1'), + ('MatrixModels', '0.4-1'), + ('quantreg', '5.19'), + ('mgcv', '1.8-10'), + ('colorspace', '1.2-6'), + ('robustbase', '0.92-5'), + ('sp', '1.2-1'), + ('zoo', '1.7-12'), + ('lmtest', '0.9-34'), + ('vcd', '1.4-1'), + ('snowfall', '1.84-6.1'), + ('rpart', '4.1-10'), + ('survival', '2.38-3'), + ('mice', '2.25'), + ('urca', '1.2-8'), + ('fracdiff', '1.4-2'), + ('logistf', '1.21'), + ('akima', '0.5-12'), + ('bitops', '1.0-6'), + ('boot', '1.3-17'), + ('mixtools', '1.0.3'), + ('cluster', '2.0.3'), + ('gclus', '1.3.1'), + ('coda', '0.18-1'), + ('codetools', '0.2-14'), + ('foreach', '1.4.3'), + ('doMC', '1.3.4'), + ('DBI', '0.3.1'), + ('foreign', '0.8-66'), + ('gam', '1.12'), + ('gamlss.data', '4.3-2'), + ('gamlss.dist', '4.3-5'), + ('hwriter', '1.3.2'), + ('KernSmooth', '2.23-15'), + ('xts', '0.9-7'), + ('TTR', '0.23-0'), + ('quantmod', '0.4-5'), + ('mnormt', '1.5-3'), + ('mvtnorm', '1.0-3'), + ('pcaPP', '1.9-60'), + ('numDeriv', '2014.2-1'), + ('lava', '1.4.1'), + ('prodlim', '1.5.7'), + ('pscl', '1.4.9'), + ('RSQLite', '1.0.0'), + ('BatchJobs', '1.6'), + ('sandwich', '2.3-4'), + ('sfsmisc', '1.0-28'), + ('spatial', '7.3-11'), + ('VGAM', '1.0-0'), + ('waveslim', '1.7.5'), + ('xtable', '1.8-0'), + ('profileModel', '0.5-9'), + ('brglm', '0.5-9'), + ('deSolve', '1.12'), + ('tseriesChaos', '0.1-13'), + ('tseries', '0.10-34'), + ('fastICA', '1.2-0'), + ('R.methodsS3', '1.7.0'), + ('R.oo', '1.19.0'), + ('cgdsr', '1.2.5'), + ('R.utils', '2.2.0'), + ('R.matlab', '3.3.0'), + ('gbm', '2.1.1'), + ('dichromat', '2.0-0'), + ('Formula', '1.2-1'), + ('acepack', '1.3-3.3'), + ('reshape2', '1.4.1'), + ('gtable', '0.1.2'), + ('munsell', '0.4.2'), + ('labeling', '0.3'), + ('scales', '0.3.0'), + ('proto', '0.3-10'), + ('ggplot2', '2.0.0'), + ('gridExtra', '2.0.0'), + ('Hmisc', '3.17-1'), + ('fastcluster', '1.1.16'), + ('chron', '2.3-47'), + ('data.table', '1.9.6'), + ('registry', '0.3'), + ('pkgmaker', '0.22'), + ('rngtools', '1.2.4'), + ('doParallel', '1.0.10'), + ('gridBase', '0.4-7'), + ('NMF', '0.20.6'), + ('irlba', '2.0.0'), + ('igraph', '1.0.1'), + ('GeneNet', '1.2.13'), + ('ape', '3.4'), + ('htmltools', '0.3'), + ('RJSONIO', '1.3-0'), + ('caTools', '1.17.1'), + ('gplots', '2.17.0'), + ('ROCR', '1.0-7'), + ('httpuv', '1.3.3'), + ('R6', '2.1.1'), + ('jsonlite', '0.9.19'), + ('rjson', '0.2.15'), + ('shiny', '0.12.2'), + ('seqinr', '3.1-3'), + ('LearnBayes', '2.15'), + ('deldir', '0.1-9'), + ('spdep', '0.5-92'), + ('assertthat', '0.1'), + ('lazyeval', '0.1.10'), + ('dplyr', '0.4.3'), + ('adegenet', '2.0.0'), + ('rncl', '0.6.0'), + ('XML', '3.98-1.3'), + ('memoise', '0.2.1'), + ('crayon', '1.3.1'), + ('praise', '1.0.0'), + ('testthat', '0.11.0'), + ('yaml', '2.1.13'), + ('knitr', '1.11'), + ('rmarkdown', '0.9.2'), + ('curl', '0.9.4'), + ('httr', '1.0.0'), + ('reshape', '0.8.5'), + ('bold', '0.3.0'), + ('taxize', '0.7.0'), + ('tidyr', '0.3.1'), + ('uuid', '0.1-2'), + ('RNeXML', '2.0.5'), + ('phylobase', '0.8.0'), + ('adephylo', '1.1-6'), + ('animation', '2.4'), + ('bigmemory.sri', '0.1.3'), + ('bigmemory', '4.5.8', { + 'patches': ['bigmemory-4.5.8_icpc-wd308.patch'], + }), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.4'), + ('raster', '2.5-2'), + ('dismo', '1.0-12'), + ('expm', '0.999-0'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3.3'), + ('extrafont', '0.17'), + ('fields', '8.3-6'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.6'), + ('glmnet', '2.0-2'), + ('rgl', '0.95.1441'), + ('labdsv', '1.7-0'), + ('stabs', '0.5-1'), + ('mboost', '2.5-0'), + ('msm', '1.6'), + ('nor1mix', '1.2-1'), + ('np', '0.60-2'), + ('polynom', '1.3-8'), + ('polspline', '1.1.12'), + ('TH.data', '1.0-6'), + ('multcomp', '1.4-1'), + ('rms', '4.4-1'), + ('RWekajars', '3.7.12-1'), + ('RWeka', '0.4-24'), + ('slam', '0.1-32'), + ('tm', '0.6-2'), + ('TraMineR', '1.8-11'), + ('chemometrics', '1.3.9'), + ('FNN', '1.1'), + ('ipred', '0.9-5'), + ('statmod', '1.4.23'), + ('miscTools', '0.6-16'), + ('maxLik', '1.3-4'), + ('mlogit', '0.2-4'), + ('getopt', '1.20.0'), + ('gsalib', '2.1'), + ('optparse', '1.3.2'), + ('klaR', '0.6-12'), + ('neuRosim', '0.2-12'), + ('locfit', '1.5-9.1'), + ('GGally', '1.0.0'), + ('beanplot', '1.2'), + ('clValid', '0.6-6'), + ('matrixStats', '0.50.1'), + ('DiscriMiner', '0.1-29'), + ('ellipse', '0.3-8'), + ('leaps', '2.9'), + ('nloptr', '1.0.4'), + ('lme4', '1.1-10'), + ('pbkrtest', '0.4-4'), + ('car', '2.1-1'), + ('flashClust', '1.01-2'), + ('FactoMineR', '1.31.4'), + ('modeltools', '0.2-21'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-13'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-7'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-10'), + ('BiasedUrn', '1.07'), + ('TeachingDemos', '2.9'), + ('kohonen', '2.0.19'), + ('base64', '1.1'), + ('doRNG', '1.6'), + ('nleqslv', '2.9.1'), + ('RGCCA', '2.0'), + ('pheatmap', '1.0.8'), + ('openxlsx', '3.0.0'), + ('pvclust', '2.0-0'), + ('RCircos', '1.1.3'), + ('lambda.r', '1.1.7'), + ('futile.options', '1.0.0'), + ('futile.logger', '1.4.1'), + ('VennDiagram', '1.6.16'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), + ('vegan', '2.3-2'), + ('forecast', '6.1', { + 'patches': ['forecast-6.1_icpc-wd308.patch'], + }), + ('fma', '2.01'), + ('expsmooth', '2.3'), + ('fpp', '0.5'), + ('maptools', '0.8-37'), + ('deldir', '0.1-9'), + ('tensor', '1.5'), + ('polyclip', '1.3-2'), + ('goftest', '1.0-3'), + ('spatstat', '1.44-1'), + ('rgdal', '1.1-3'), + ('gdalUtils', '2.0.1.7'), + ('pracma', '1.8.8'), + ('RCurl', '1.95-4.7'), + ('bio3d', '2.2-4'), + ('AUC', '0.3.0'), + ('interpretR', '0.2.3'), + ('SuperLearner', '2.0-15'), + ('lpSolve', '5.6.13'), + ('mediation', '4.4.5'), + ('caret', '6.0-64'), + ('adabag', '4.1'), + ('parallelMap', '1.3'), + ('ParamHelpers', '1.6'), + ('ggvis', '0.4.2'), + ('mlr', '2.7'), + ('unbalanced', '2.0'), + ('RSNNS', '0.4-7'), + ('abc.data', '1.0'), + ('abc', '2.1'), + ('lhs', '0.10'), + ('tensorA', '0.36'), + ('EasyABC', '1.5'), + ('shape', '1.4.2'), + ('whisker', '0.3-2'), + ('rstudioapi', '0.4.0'), + ('roxygen2', '5.0.1'), + ('git2r', '0.13.1'), + ('xml2', '0.1.2'), + ('rversions', '1.0.2'), + ('devtools', '1.9.1'), + ('Rook', '1.1-1'), + ('rjson', '0.2.15'), + ('Cairo', '1.5-9'), + ('RMTstat', '0.3'), + ('Lmoments', '1.1-6'), + ('distillery', '1.0-2'), + ('extRemes', '2.0-7'), + ('pixmap', '0.4-11'), + ('tkrplot', '0.0-23'), + ('misc3d', '0.8-4'), + ('multicool', '0.1-9', { + 'patches': [('multicool-0.1-9_icpc-wd308.patch', 1)], + }), + ('ks', '1.10.1'), + ('logcondens', '2.1.4'), + ('Iso', '0.0-17'), + ('penalized', '0.9-45'), + ('coin', '1.1-2'), + ('clusterRepro', '0.5-1.1'), + ('randomForestSRC', '2.0.7'), + ('sm', '2.2-5.4'), + ('psych', '1.5.8'), + ('pbivnorm', '0.6.0'), + ('lavaan', '0.5-20'), + ('matrixcalc', '1.0-3'), + ('arm', '1.8-6'), + ('mi', '1.0'), + ('htmlwidgets', '0.6'), + ('visNetwork', '0.2.1'), + ('DiagrammeR', '0.8.2'), + ('sem', '3.1-6'), + ('jpeg', '0.1-8'), + ('sna', '2.3-2'), + ('glasso', '1.8', { + 'patches': [('glasso-1.8-ifort-no-fixed.patch', 1)], + }), + ('huge', '1.2.7'), + ('d3Network', '0.5.2.1'), + ('ggm', '2.3'), + ('qgraph', '1.3.2'), + ('diveRsity', '1.9.89'), + ('doSNOW', '1.0.14'), + ('phangorn', '2.0.2'), + ('geepack', '1.2-0.1'), + ('lubridate', '1.5.6'), + ('biom', '0.3.12'), + ('pim', '2.0.0.2'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 6dbcaf2eb2b..219fdd363f6 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -34,7 +34,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -60,394 +60,406 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-3', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.3', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '3.9', ext_options), - ('bootstrap', '2015.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.15', ext_options), - ('formatR', '1.2.1', ext_options), - ('gtools', '3.5.0', ext_options), - ('gdata', '2.17.0', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.5.1', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-22', ext_options), - ('mime', '0.4', ext_options), - ('markdown', '0.7.7', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-8', ext_options), - ('mclust', '5.1', ext_options), - ('RANN', '2.5', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.4', ext_options), - ('som', '0.3-5', ext_options), - ('SuppDists', '1.1-9.1', ext_options), - ('stabledist', '0.7-0', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-17', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.7-3', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-3', ext_options), - ('BH', '1.60.0-1', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.8', ext_options), - ('longitudinal', '1.1.12', ext_options), - ('checkmate', '1.6.3', ext_options), - ('cubature', '1.1-2', ext_options), - ('DEoptimR', '1.0-4', ext_options), - ('digest', '0.6.8', ext_options), - ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.12.1', ext_options), - ('iterators', '1.0.8', ext_options), - ('maps', '3.0.2', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.3-0', ext_options), - ('subplex', '1.1-6', ext_options), - ('stringi', '1.0-1', ext_options), - ('magrittr', '1.5', ext_options), - ('stringr', '1.0.0', ext_options), - ('evaluate', '0.8', ext_options), - ('logspline', '2.1.8', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.8-4', ext_options), - ('plotrix', '3.6-1', ext_options), - ('randomForest', '4.6-12', ext_options), - ('scatterplot3d', '0.3-36', ext_options), - ('SparseM', '1.7', ext_options), - ('tripack', '1.3-7', ext_options), - ('irace', '1.07', ext_options), - ('rJava', '0.9-7', ext_options), - ('lattice', '0.20-33', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-26', ext_options), - ('Matrix', '1.2-3', ext_options), - ('png', '0.1-7', 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'0.3.0'), + ('taxize', '0.7.0'), + ('tidyr', '0.3.1'), + ('uuid', '0.1-2'), + ('RNeXML', '2.0.5'), + ('phylobase', '0.8.0'), + ('adephylo', '1.1-6'), + ('animation', '2.4'), + ('bigmemory.sri', '0.1.3'), + ('bigmemory', '4.5.8', { + 'patches': ['bigmemory-4.5.8_icpc-wd308.patch'], + }), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.4'), + ('raster', '2.5-2'), + ('dismo', '1.0-12'), + ('expm', '0.999-0'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3.3'), + ('extrafont', '0.17'), + ('fields', '8.3-6'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.6'), + ('glmnet', '2.0-2'), + ('rgl', '0.95.1441'), + ('labdsv', '1.7-0'), + ('stabs', '0.5-1'), + ('mboost', '2.5-0'), + ('msm', '1.6'), + ('nor1mix', '1.2-1'), + ('np', '0.60-2'), + ('polynom', '1.3-8'), + ('polspline', '1.1.12'), + ('TH.data', '1.0-6'), + ('multcomp', '1.4-1'), + ('rms', '4.4-1'), + ('RWekajars', '3.7.12-1'), + ('RWeka', '0.4-24'), + ('slam', '0.1-32'), + ('tm', '0.6-2'), + ('TraMineR', '1.8-11'), + ('chemometrics', '1.3.9'), + ('FNN', '1.1'), + ('ipred', '0.9-5'), + ('statmod', '1.4.23'), + ('miscTools', '0.6-16'), + ('maxLik', '1.3-4'), + ('mlogit', '0.2-4'), + ('getopt', '1.20.0'), + ('gsalib', '2.1'), + ('optparse', '1.3.2'), + ('klaR', '0.6-12'), + ('neuRosim', '0.2-12'), + ('locfit', '1.5-9.1'), + ('GGally', '1.0.0'), + ('beanplot', '1.2'), + ('clValid', '0.6-6'), + ('matrixStats', '0.50.1'), + ('DiscriMiner', '0.1-29'), + ('ellipse', '0.3-8'), + ('leaps', '2.9'), + ('nloptr', '1.0.4'), + ('lme4', '1.1-10'), + ('pbkrtest', '0.4-4'), + ('car', '2.1-1'), + ('flashClust', '1.01-2'), + ('FactoMineR', '1.31.4'), + ('modeltools', '0.2-21'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-13'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-7'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-10'), + ('BiasedUrn', '1.07'), + ('TeachingDemos', '2.9'), + ('kohonen', '2.0.19'), + ('base64', '1.1'), + ('doRNG', '1.6'), + ('nleqslv', '2.9.1'), + ('RGCCA', '2.0'), + ('pheatmap', '1.0.8'), + ('openxlsx', '3.0.0'), + ('pvclust', '2.0-0'), + ('RCircos', '1.1.3'), + ('lambda.r', '1.1.7'), + ('futile.options', '1.0.0'), + ('futile.logger', '1.4.1'), + ('VennDiagram', '1.6.16'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), + ('vegan', '2.3-2'), + ('forecast', '6.1', { + 'patches': ['forecast-6.1_icpc-wd308.patch'], + }), + ('fma', '2.01'), + ('expsmooth', '2.3'), + ('fpp', '0.5'), + ('maptools', '0.8-37'), + ('deldir', '0.1-9'), + ('tensor', '1.5'), + ('polyclip', '1.3-2'), + ('goftest', '1.0-3'), + ('spatstat', '1.44-1'), + ('rgdal', '1.1-3'), + ('gdalUtils', '2.0.1.7'), + ('pracma', '1.8.8'), + ('RCurl', '1.95-4.7'), + ('bio3d', '2.2-4'), + ('AUC', '0.3.0'), + ('interpretR', '0.2.3'), + ('SuperLearner', '2.0-15'), + ('lpSolve', '5.6.13'), + ('mediation', '4.4.5'), + ('caret', '6.0-64'), + ('adabag', '4.1'), + ('parallelMap', '1.3'), + ('ParamHelpers', '1.6'), + ('ggvis', '0.4.2'), + ('mlr', '2.7'), + ('unbalanced', '2.0'), + ('RSNNS', '0.4-7'), + ('abc.data', '1.0'), + ('abc', '2.1'), + ('lhs', '0.10'), + ('tensorA', '0.36'), + ('EasyABC', '1.5'), + ('shape', '1.4.2'), + ('whisker', '0.3-2'), + ('rstudioapi', '0.4.0'), + ('roxygen2', '5.0.1'), + ('git2r', '0.13.1'), + ('xml2', '0.1.2'), + ('rversions', '1.0.2'), + ('devtools', '1.9.1'), + ('Rook', '1.1-1'), + ('rjson', '0.2.15'), + ('Cairo', '1.5-9'), + ('RMTstat', '0.3'), + ('Lmoments', '1.1-6'), + ('distillery', '1.0-2'), + ('extRemes', '2.0-7'), + ('pixmap', '0.4-11'), + ('tkrplot', '0.0-23'), + ('misc3d', '0.8-4'), + ('multicool', '0.1-9', { + 'patches': [('multicool-0.1-9_icpc-wd308.patch', 1)], + }), + ('ks', '1.10.1'), + ('logcondens', '2.1.4'), + ('Iso', '0.0-17'), + ('penalized', '0.9-45'), + ('coin', '1.1-2'), + ('clusterRepro', '0.5-1.1'), + ('randomForestSRC', '2.0.7'), + ('sm', '2.2-5.4'), + ('psych', '1.5.8'), + ('pbivnorm', '0.6.0'), + ('lavaan', '0.5-20'), + ('matrixcalc', '1.0-3'), + ('arm', '1.8-6'), + ('mi', '1.0'), + ('htmlwidgets', '0.6'), + ('visNetwork', '0.2.1'), + ('DiagrammeR', '0.8.2'), + ('sem', '3.1-6'), + ('jpeg', '0.1-8'), + ('sna', '2.3-2'), + ('glasso', '1.8', { + 'patches': [('glasso-1.8-ifort-no-fixed.patch', 1)], + }), + ('huge', '1.2.7'), + ('d3Network', '0.5.2.1'), + ('ggm', '2.3'), + ('qgraph', '1.3.2'), + ('diveRsity', '1.9.89'), + ('doSNOW', '1.0.14'), + ('phangorn', '2.0.2'), + ('geepack', '1.2-0.1'), + ('lubridate', '1.5.6'), + ('biom', '0.3.12'), + ('pim', '2.0.0.2'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb index 6dbfc8db3d8..ebe33155b56 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb @@ -44,14 +44,13 @@ configopts += " --with-recommended-packages=no" # since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK easybuild_version = '3.5.0' -name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ], - 'source_tmpl': name_tmpl, + 'source_tmpl': '%(name)s_%(version)s.tar.gz', } @@ -71,409 +70,421 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-6', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-3', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.3', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '4.0', ext_options), - ('bootstrap', '2015.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.15', ext_options), - ('formatR', '1.4', ext_options), - ('gtools', '3.5.0', ext_options), - ('gdata', '2.17.0', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.6', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-24', ext_options), - ('mime', '0.5', ext_options), - ('markdown', '0.7.7', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-9', ext_options), - ('mclust', '5.2', ext_options), - ('RANN', '2.5', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.4', ext_options), - ('som', '0.3-5.1', ext_options), - ('SuppDists', '1.1-9.2', ext_options), - ('stabledist', '0.7-0', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-17', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.7-4', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-3', ext_options), - ('BH', '1.60.0-2', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.8', ext_options), - ('longitudinal', '1.1.12', ext_options), - ('backports', '1.0.3', ext_options), - ('checkmate', '1.8.1', ext_options), - ('cubature', '1.1-2', ext_options), - ('DEoptimR', '1.0-6', ext_options), - ('digest', '0.6.9', ext_options), - ('fastmatch', '1.0-4', ext_options), - ('ffbase', '0.12.3', ext_options), - ('iterators', '1.0.8', ext_options), - ('maps', '3.1.0', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.3-0', ext_options), - ('subplex', '1.1-6', ext_options), - ('stringi', '1.1.1', ext_options), - ('magrittr', '1.5', ext_options), - ('stringr', '1.0.0', ext_options), - ('evaluate', '0.9', ext_options), - ('logspline', '2.1.9', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.9-0', ext_options), - ('plotrix', '3.6-2', ext_options), - ('randomForest', '4.6-12', ext_options), - ('scatterplot3d', '0.3-37', ext_options), - ('SparseM', '1.7', ext_options), - ('tripack', '1.3-7', ext_options), - ('irace', '1.07', ext_options), - ('rJava', '0.9-8', ext_options), - ('lattice', '0.20-33', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-28', ext_options), - ('Matrix', '1.2-6', ext_options), - ('png', '0.1-7', ext_options), - ('Rcpp', '0.12.5', ext_options), - ('RcppArmadillo', '0.7.100.3.1', ext_options), - ('plyr', '1.8.4', ext_options), - ('pROC', '1.8', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.9', ext_options), - ('fail', '1.3', ext_options), - ('rlecuyer', '0.3-4', ext_options), - ('snow', '0.4-1', ext_options), - ('MASS', '7.3-45', ext_options), - ('tree', '1.0-37', ext_options), - ('pls', '2.5-0', ext_options), - ('class', '7.3-14', ext_options), - ('e1071', '1.6-7', ext_options), - ('nnet', '7.3-12', ext_options), - ('nlme', '3.1-128', ext_options), - ('minqa', '1.2.4', ext_options), - ('RcppEigen', '0.3.2.8.1', ext_options), - ('MatrixModels', '0.4-1', ext_options), - ('quantreg', '5.26', ext_options), - ('mgcv', '1.8-12', ext_options), - ('colorspace', '1.2-6', ext_options), - ('robustbase', '0.92-6', ext_options), - ('sp', '1.2-3', ext_options), - ('zoo', '1.7-13', ext_options), - ('lmtest', '0.9-34', ext_options), - ('vcd', '1.4-1', ext_options), - ('snowfall', '1.84-6.1', ext_options), - ('rpart', '4.1-10', ext_options), - ('survival', '2.39-5', ext_options), - ('mice', '2.25', ext_options), - ('urca', '1.2-9', ext_options), - ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.21', ext_options), - ('akima', '0.5-12', ext_options), - ('bitops', '1.0-6', ext_options), - ('boot', '1.3-18', ext_options), - ('mixtools', '1.0.4', ext_options), - ('cluster', '2.0.4', ext_options), - ('gclus', '1.3.1', ext_options), - ('coda', '0.18-1', ext_options), - ('codetools', '0.2-14', ext_options), - ('foreach', '1.4.3', ext_options), - ('doMC', '1.3.4', ext_options), - ('DBI', '0.4-1', ext_options), - ('foreign', '0.8-66', ext_options), - ('gam', '1.12', ext_options), - ('gamlss.data', '4.3-4', ext_options), - ('gamlss.dist', '4.3-6', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-15', ext_options), - ('xts', '0.9-7', ext_options), - ('TTR', '0.23-1', ext_options), - ('quantmod', '0.4-5', ext_options), - ('mnormt', '1.5-4', ext_options), - ('mvtnorm', '1.0-5', ext_options), - ('pcaPP', '1.9-60', ext_options), - ('numDeriv', '2014.2-1', ext_options), - ('lava', '1.4.3', ext_options), - ('prodlim', '1.5.7', ext_options), - ('pscl', '1.4.9', ext_options), - ('RSQLite', '1.0.0', ext_options), - ('BatchJobs', '1.6', ext_options), - ('sandwich', '2.3-4', ext_options), - ('sfsmisc', '1.1-0', ext_options), - ('spatial', '7.3-11', ext_options), - ('VGAM', '1.0-2', ext_options), - ('waveslim', '1.7.5', ext_options), - ('xtable', '1.8-2', ext_options), - ('profileModel', '0.5-9', ext_options), - ('brglm', '0.5-9', ext_options), - ('deSolve', '1.13', ext_options), - ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-35', ext_options), - ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.7.1', ext_options), - ('R.oo', '1.20.0', ext_options), - ('cgdsr', '1.2.5', ext_options), - ('R.utils', '2.3.0', ext_options), - ('R.matlab', '3.6.0', ext_options), - ('gbm', '2.1.1', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.2-1', ext_options), - ('acepack', '1.3-3.3', ext_options), - ('reshape2', '1.4.1', ext_options), - ('gtable', '0.2.0', ext_options), - ('munsell', '0.4.3', ext_options), - ('labeling', '0.3', ext_options), - ('scales', '0.4.0', ext_options), - ('proto', '0.3-10', ext_options), - ('ggplot2', '2.1.0', ext_options), - ('gridExtra', '2.2.1', ext_options), - ('chron', 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('logcondens', '2.1.4'), + ('Iso', '0.0-17'), + ('penalized', '0.9-47'), + ('clusterRepro', '0.5-1.1'), + ('randomForestSRC', '2.2.0'), + ('sm', '2.2-5.4'), + ('psych', '1.6.6'), + ('pbivnorm', '0.6.0'), + ('lavaan', '0.5-20'), + ('matrixcalc', '1.0-3'), + ('arm', '1.8-6'), + ('mi', '1.0'), + ('htmlwidgets', '0.6'), + ('visNetwork', '1.0.1'), + ('DiagrammeR', '0.8.2'), + ('sem', '3.1-7'), + ('jpeg', '0.1-8'), + ('sna', '2.3-2'), + ('glasso', '1.8', { + 'patches': [('glasso-1.8-ifort-no-fixed.patch', 1)], + }), + ('huge', '1.2.7'), + ('d3Network', '0.5.2.1'), + ('ggm', '2.3'), + ('qgraph', '1.3.4'), + ('diveRsity', '1.9.89'), + ('doSNOW', '1.0.14'), + ('phangorn', '2.0.4'), + ('geepack', '1.2-0.2'), + ('lubridate', '1.5.6'), + ('biom', '0.3.12'), + ('pim', '2.0.0.2'), + ('minpack.lm', '1.2-1'), + ('rootSolve', '1.7'), + ('diagram', '1.6.3'), + ('FME', '1.3.5'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb index ad737a3871c..99ecdc6fbb3 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -51,7 +51,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -76,434 +76,436 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-6', ext_options), - ('abind', '1.4-5', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-6', ext_options), - ('bit', '1.1-12', ext_options), - ('filehash', '2.3', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '4.1', ext_options), - ('bootstrap', '2017.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.15', ext_options), - ('formatR', '1.4', ext_options), - ('gtools', '3.5.0', ext_options), - ('gdata', '2.17.0', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.6', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-25', ext_options), - ('mime', '0.5', ext_options), - ('markdown', '0.7.7', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-10', ext_options), - ('mclust', '5.2.2', ext_options), - ('RANN', '2.5', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.4', ext_options), - ('som', '0.3-5.1', ext_options), - ('SuppDists', '1.1-9.4', ext_options), - ('stabledist', '0.7-1', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-17', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.7-5', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-3', ext_options), - ('BH', '1.62.0-1', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.8', ext_options), - ('longitudinal', '1.1.12', ext_options), - ('backports', '1.0.5', ext_options), - ('checkmate', '1.8.2', ext_options), - ('Rcpp', '0.12.9', ext_options), - ('cubature', '1.3-6', ext_options), - ('DEoptimR', '1.0-8', ext_options), - ('digest', '0.6.12', ext_options), - ('fastmatch', '1.1-0', ext_options), - ('ffbase', '0.12.3', ext_options), - ('iterators', '1.0.8', ext_options), - ('maps', '3.1.1', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.4-0', ext_options), - ('subplex', '1.2-2', ext_options), - ('stringi', '1.1.2', ext_options), - ('magrittr', '1.5', ext_options), - ('stringr', '1.2.0', ext_options), - ('evaluate', '0.10', ext_options), - ('logspline', '2.1.9', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.9-4', ext_options), - ('plotrix', '3.6-4', ext_options), - ('randomForest', '4.6-12', ext_options), - ('scatterplot3d', '0.3-38', ext_options), - ('SparseM', '1.76', ext_options), - ('tripack', '1.3-8', ext_options), - ('irace', '2.1', ext_options), - ('rJava', '0.9-8', ext_options), - ('lattice', '0.20-34', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-28', ext_options), - ('Matrix', '1.2-8', ext_options), - ('png', '0.1-7', ext_options), - ('RcppArmadillo', '0.7.700.0.0', ext_options), - ('plyr', '1.8.4', ext_options), - ('pROC', '1.9.1', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.11', ext_options), - ('fail', '1.3', ext_options), - ('rlecuyer', '0.3-4', ext_options), - ('snow', '0.4-2', ext_options), - ('MASS', '7.3-45', ext_options), - ('tree', '1.0-37', ext_options), - ('pls', '2.6-0', ext_options), - ('class', '7.3-14', ext_options), - ('e1071', '1.6-8', ext_options), - ('nnet', '7.3-12', ext_options), - ('nlme', '3.1-131', ext_options), - ('minqa', '1.2.4', ext_options), - ('RcppEigen', '0.3.2.9.0', ext_options), - ('MatrixModels', '0.4-1', ext_options), - ('quantreg', '5.29', ext_options), - ('mgcv', '1.8-17', ext_options), - ('colorspace', '1.3-2', ext_options), - ('robustbase', '0.92-7', ext_options), - ('sp', '1.2-4', ext_options), - ('zoo', '1.7-14', ext_options), - ('lmtest', '0.9-35', ext_options), - ('vcd', '1.4-3', ext_options), - ('snowfall', '1.84-6.1', ext_options), - ('rpart', '4.1-10', ext_options), - ('survival', '2.40-1', ext_options), - ('mice', '2.30', ext_options), - ('urca', '1.3-0', ext_options), - ('fracdiff', '1.4-2', ext_options), - ('logistf', '1.22', ext_options), - ('akima', '0.6-2', ext_options), - ('bitops', '1.0-6', ext_options), - ('boot', '1.3-18', ext_options), - ('mixtools', '1.1.0', ext_options), - ('cluster', '2.0.5', ext_options), - ('gclus', '1.3.1', ext_options), - ('coda', '0.19-1', ext_options), - ('codetools', '0.2-15', ext_options), - ('foreach', '1.4.3', ext_options), - ('doMC', '1.3.4', ext_options), - ('DBI', '0.6', ext_options), - ('foreign', '0.8-67', ext_options), - ('gam', '1.14', ext_options), - ('gamlss.data', '5.0-0', ext_options), - ('gamlss.dist', '5.0-0', ext_options), - ('hwriter', '1.3.2', ext_options), - ('KernSmooth', '2.23-15', ext_options), - ('xts', '0.9-7', ext_options), - ('TTR', '0.23-1', ext_options), - ('quantmod', '0.4-7', ext_options), - ('mnormt', '1.5-5', ext_options), - ('mvtnorm', '1.0-6', ext_options), - ('pcaPP', '1.9-61', ext_options), - ('numDeriv', '2016.8-1', ext_options), - ('lava', '1.4.7', ext_options), - ('prodlim', '1.6.1', ext_options), - ('pscl', '1.4.9', ext_options), - ('memoise', '1.0.0', ext_options), - ('plogr', '0.1-1', ext_options), - ('RSQLite', '1.1-2', ext_options), - ('BatchJobs', '1.6', ext_options), - ('sandwich', '2.3-4', ext_options), - ('sfsmisc', '1.1-0', ext_options), - ('spatial', '7.3-11', ext_options), - ('VGAM', '1.0-3', ext_options), - ('waveslim', '1.7.5', ext_options), - ('xtable', '1.8-2', ext_options), - ('profileModel', '0.5-9', ext_options), - ('brglm', '0.5-9', ext_options), - ('deSolve', '1.14', ext_options), - ('tseriesChaos', '0.1-13', ext_options), - ('tseries', '0.10-38', ext_options), - ('fastICA', '1.2-0', ext_options), - ('R.methodsS3', '1.7.1', ext_options), - ('R.oo', '1.21.0', ext_options), - ('cgdsr', '1.2.5', ext_options), - ('R.utils', '2.5.0', ext_options), - ('R.matlab', '3.6.1', ext_options), - ('gbm', '2.1.1', ext_options), - ('dichromat', '2.0-0', ext_options), - ('Formula', '1.2-1', ext_options), - ('acepack', '1.4.1', ext_options), - ('reshape2', '1.4.2', ext_options), - ('gtable', '0.2.0', ext_options), - ('munsell', '0.4.3', ext_options), - ('labeling', '0.3', ext_options), - ('scales', '0.4.1', ext_options), - ('proto', '1.0.0', ext_options), - ('lazyeval', '0.2.0', ext_options), - ('assertthat', '0.1', ext_options), - ('tibble', '1.2', ext_options), - ('ggplot2', '2.2.1', ext_options), - ('gridExtra', '2.2.1', ext_options), - ('chron', '2.3-50', ext_options), - ('data.table', '1.10.4', ext_options), - ('viridis', '0.3.4', ext_options), - ('yaml', '2.1.14', ext_options), - ('jsonlite', '1.3', ext_options), - ('htmltools', '0.3.5', ext_options), - ('htmlwidgets', '0.8', ext_options), - ('knitr', '1.15.1', ext_options), - ('htmlTable', '1.9', ext_options), - ('Hmisc', '4.0-2', ext_options), - ('fastcluster', '1.1.22', ext_options), - ('registry', '0.3', ext_options), - ('pkgmaker', '0.22', ext_options), - ('rngtools', '1.2.4', ext_options), - ('doParallel', '1.0.10', ext_options), - ('gridBase', '0.4-7', ext_options), - ('NMF', '0.20.6', ext_options), - ('irlba', '2.1.2', ext_options), - ('igraph', '1.0.1', ext_options), - ('GeneNet', '1.2.13', ext_options), - ('ape', '4.1', ext_options), - ('RJSONIO', '1.3-0', ext_options), - ('caTools', 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('ks', '1.10.5', ext_options), - ('logcondens', '2.1.5', ext_options), - ('Iso', '0.0-17', ext_options), - ('penalized', '0.9-50', ext_options), - ('clusterRepro', '0.5-1.1', ext_options), - ('randomForestSRC', '2.4.2', ext_options), - ('sm', '2.2-5.4', ext_options), - ('psych', '1.6.12', ext_options), - ('pbivnorm', '0.6.0', ext_options), - ('lavaan', '0.5-23.1097', ext_options), - ('matrixcalc', '1.0-3', ext_options), - ('arm', '1.9-3', ext_options), - ('mi', '1.0', ext_options), - ('visNetwork', '1.0.3', ext_options), - ('rgexf', '0.15.3', ext_options), - ('influenceR', '0.1.0', ext_options), - ('DiagrammeR', '0.9.0', ext_options), - ('sem', '3.1-8', ext_options), - ('jpeg', '0.1-8', ext_options), - ('network', '1.13.0', ext_options), - ('statnet.common', '3.3.0', ext_options), - ('sna', '2.4', ext_options), - ('glasso', '1.8', ext_options), - ('huge', '1.2.7', ext_options), - ('d3Network', '0.5.2.1', ext_options), - ('ggm', '2.3', ext_options), - ('qgraph', '1.4.2', ext_options), - ('diveRsity', '1.9.89', ext_options), - ('doSNOW', '1.0.14', ext_options), - ('phangorn', '2.1.1', ext_options), - ('geepack', '1.2-1', ext_options), - ('lubridate', '1.6.0', ext_options), - ('biom', '0.3.12', ext_options), - ('pim', '2.0.0.2', ext_options), - ('minpack.lm', '1.2-1', ext_options), - ('rootSolve', '1.7', ext_options), - ('diagram', '1.6.3', ext_options), - ('FME', '1.3.5', ext_options), - ('bmp', '0.2', ext_options), - ('readbitmap', '0.1-4', ext_options), - ('purrr', '0.2.2', ext_options), - ('downloader', '0.4', ext_options), - ('imager', '0.40.1', ext_options), + ('Rmpi', '0.6-6'), + ('abind', '1.4-5'), + ('magic', '1.5-6'), + ('geometry', '0.3-6'), + ('bit', '1.1-12'), + ('filehash', '2.3'), + ('ff', '2.2-13'), + ('bnlearn', '4.1'), + ('bootstrap', '2017.2'), + ('combinat', '0.0-8'), + ('deal', '1.2-37'), + ('fdrtool', '1.2.15'), + ('formatR', '1.4'), + ('gtools', '3.5.0'), + ('gdata', '2.17.0'), + ('GSA', '1.03'), + ('highr', '0.6'), + ('infotheo', '1.2.0'), + ('lars', '1.2'), + ('lazy', '1.2-15'), + ('kernlab', '0.9-25'), + ('mime', '0.5'), + ('markdown', '0.7.7'), + ('mlbench', '2.1-1'), + ('NLP', '0.1-10'), + ('mclust', '5.2.2'), + ('RANN', '2.5'), + ('rmeta', '2.16'), + ('segmented', '0.5-1.4'), + ('som', '0.3-5.1'), + ('SuppDists', '1.1-9.4'), + ('stabledist', '0.7-1'), + ('survivalROC', '1.0.3'), + ('pspline', '1.0-17'), + ('timeDate', '3012.100'), + ('longmemo', '1.0-0'), + ('ADGofTest', '0.3'), + ('ade4', '1.7-5'), + ('AlgDesign', '1.1-7.3'), + ('base64enc', '0.1-3'), + ('BH', '1.62.0-1'), + ('brew', '1.0-6'), + ('Brobdingnag', '1.2-4'), + ('corpcor', '1.6.8'), + ('longitudinal', '1.1.12'), + ('backports', '1.0.5'), + ('checkmate', '1.8.2'), + ('Rcpp', '0.12.9'), + ('cubature', '1.3-6'), + ('DEoptimR', '1.0-8'), + ('digest', '0.6.12'), + ('fastmatch', '1.1-0'), + ('ffbase', '0.12.3'), + ('iterators', '1.0.8'), + ('maps', '3.1.1'), + ('nnls', '1.4'), + ('sendmailR', '1.2-1'), + ('spam', '1.4-0'), + ('subplex', '1.2-2'), + ('stringi', '1.1.2'), + ('magrittr', '1.5'), + ('stringr', '1.2.0'), + ('evaluate', '0.10'), + ('logspline', '2.1.9'), + ('ncbit', '2013.03.29'), + ('permute', '0.9-4'), + ('plotrix', '3.6-4'), + ('randomForest', '4.6-12'), + ('scatterplot3d', '0.3-38'), + ('SparseM', '1.76'), + ('tripack', '1.3-8'), + ('irace', '2.1'), + ('rJava', '0.9-8'), + ('lattice', '0.20-34'), + ('RColorBrewer', '1.1-2'), + ('latticeExtra', '0.6-28'), + ('Matrix', '1.2-8'), + ('png', '0.1-7'), + ('RcppArmadillo', '0.7.700.0.0'), + ('plyr', '1.8.4'), + ('pROC', '1.9.1'), + ('quadprog', '1.5-5'), + ('BB', '2014.10-1'), + ('BBmisc', '1.11'), + ('fail', '1.3'), + ('rlecuyer', '0.3-4'), + ('snow', '0.4-2'), + ('MASS', '7.3-45'), + ('tree', '1.0-37'), + ('pls', '2.6-0'), + ('class', '7.3-14'), + ('e1071', '1.6-8'), + ('nnet', '7.3-12'), + ('nlme', '3.1-131'), + ('minqa', '1.2.4'), + ('RcppEigen', '0.3.2.9.0'), + ('MatrixModels', '0.4-1'), + ('quantreg', '5.29'), + ('mgcv', '1.8-17'), + ('colorspace', '1.3-2'), + ('robustbase', '0.92-7'), + ('sp', '1.2-4'), + ('zoo', '1.7-14'), + ('lmtest', '0.9-35'), + ('vcd', '1.4-3'), + ('snowfall', '1.84-6.1'), + ('rpart', '4.1-10'), + ('survival', '2.40-1'), + ('mice', '2.30'), + ('urca', '1.3-0'), + ('fracdiff', '1.4-2'), + ('logistf', '1.22'), + ('akima', '0.6-2'), + ('bitops', '1.0-6'), + ('boot', '1.3-18'), + ('mixtools', '1.1.0'), + ('cluster', '2.0.5'), + ('gclus', '1.3.1'), + ('coda', '0.19-1'), + ('codetools', '0.2-15'), + ('foreach', '1.4.3'), + ('doMC', '1.3.4'), + ('DBI', '0.6'), + ('foreign', '0.8-67'), + ('gam', '1.14'), + ('gamlss.data', '5.0-0'), + ('gamlss.dist', '5.0-0'), + ('hwriter', '1.3.2'), + ('KernSmooth', '2.23-15'), + ('xts', '0.9-7'), + ('TTR', '0.23-1'), + ('quantmod', '0.4-7'), + ('mnormt', '1.5-5'), + ('mvtnorm', '1.0-6'), + ('pcaPP', '1.9-61'), + ('numDeriv', '2016.8-1'), + ('lava', '1.4.7'), + ('prodlim', '1.6.1'), + ('pscl', '1.4.9'), + ('memoise', '1.0.0'), + ('plogr', '0.1-1'), + ('RSQLite', '1.1-2'), + ('BatchJobs', '1.6'), + ('sandwich', '2.3-4'), + ('sfsmisc', '1.1-0'), + ('spatial', '7.3-11'), + ('VGAM', '1.0-3'), + ('waveslim', '1.7.5'), + ('xtable', '1.8-2'), + ('profileModel', '0.5-9'), + ('brglm', '0.5-9'), + ('deSolve', '1.14'), + ('tseriesChaos', '0.1-13'), + ('tseries', '0.10-38'), + ('fastICA', '1.2-0'), + ('R.methodsS3', '1.7.1'), + ('R.oo', '1.21.0'), + ('cgdsr', '1.2.5'), + ('R.utils', '2.5.0'), + ('R.matlab', '3.6.1'), + ('gbm', '2.1.1'), + ('dichromat', '2.0-0'), + ('Formula', '1.2-1'), + ('acepack', '1.4.1'), + ('reshape2', '1.4.2'), + ('gtable', '0.2.0'), + ('munsell', '0.4.3'), + ('labeling', '0.3'), + ('scales', '0.4.1'), + ('proto', '1.0.0'), + ('lazyeval', '0.2.0'), + ('assertthat', '0.1'), + ('tibble', '1.2'), + ('ggplot2', '2.2.1'), + ('gridExtra', '2.2.1'), + ('chron', '2.3-50'), + ('data.table', '1.10.4'), + ('viridis', '0.3.4'), + ('yaml', '2.1.14'), + ('jsonlite', '1.3'), + ('htmltools', '0.3.5'), + ('htmlwidgets', '0.8'), + ('knitr', '1.15.1'), + ('htmlTable', '1.9'), + ('Hmisc', '4.0-2'), + ('fastcluster', '1.1.22'), + ('registry', '0.3'), + ('pkgmaker', '0.22'), + ('rngtools', '1.2.4'), + ('doParallel', '1.0.10'), + ('gridBase', '0.4-7'), + ('NMF', '0.20.6'), + ('irlba', '2.1.2'), + ('igraph', '1.0.1'), + ('GeneNet', '1.2.13'), + ('ape', '4.1'), + ('RJSONIO', '1.3-0'), + ('caTools', '1.17.1'), + ('gplots', '3.0.1'), + ('ROCR', '1.0-7'), + ('httpuv', '1.3.3'), + ('R6', '2.2.0'), + ('rjson', '0.2.15'), + ('sourcetools', '0.1.5'), + ('shiny', '1.0.0'), + ('seqinr', '3.3-3'), + ('LearnBayes', '2.15'), + ('deldir', '0.1-12'), + ('gmodels', '2.16.2'), + ('expm', '0.999-1'), + ('spdep', '0.6-11'), + ('dplyr', '0.5.0'), + ('vegan', '2.4-2'), + ('adegenet', '2.0.1'), + ('prettyunits', '1.0.2'), + ('progress', '1.1.2'), + ('rncl', '0.8.2'), + ('XML', '3.98-1.5'), + ('crayon', '1.3.2'), + ('praise', '1.0.0'), + ('testthat', '1.0.2'), + ('rprojroot', '1.2'), + ('rmarkdown', '1.3'), + ('curl', '2.3'), + ('openssl', '0.9.6'), + ('httr', '1.2.1'), + ('reshape', '0.8.6'), + ('xml2', '1.1.1'), + ('bold', '0.4.0'), + ('triebeard', '0.3.0'), + ('urltools', '1.6.0'), + ('httpcode', '0.2.0'), + ('crul', '0.3.0'), + ('rredlist', '0.3.0'), + ('rentrez', '1.0.4'), + ('rotl', '3.0.3'), + ('solrium', '0.4.0'), + ('ritis', '0.5.4'), + ('worrms', '0.1.0'), + ('natserv', '0.1.4'), + ('taxize', '0.8.4'), + ('tidyr', '0.6.1'), + ('uuid', '0.1-2'), + ('RNeXML', '2.0.7'), + ('phylobase', '0.8.2'), + ('adephylo', '1.1-10'), + ('animation', '2.4'), + ('bigmemory.sri', '0.1.3'), + ('bigmemory', '4.5.19'), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.4'), + ('raster', '2.5-8'), + ('dismo', '1.1-4'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3.4'), + ('extrafont', '0.17'), + ('fields', '8.10'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.6'), + ('glmnet', '2.0-5'), + ('rgl', '0.98.1'), + ('labdsv', '1.8-0'), + ('stabs', '0.6-2'), + ('modeltools', '0.2-21'), + ('strucchange', '1.5-1'), + ('TH.data', '1.0-8'), + ('multcomp', '1.4-6'), + ('coin', '1.1-3'), + ('party', '1.2-2'), + ('mboost', '2.7-0'), + ('msm', '1.6.4'), + ('nor1mix', '1.2-2'), + ('np', '0.60-2'), + ('polynom', '1.3-9'), + ('polspline', '1.1.12'), + ('rms', '5.1-0'), + ('RWekajars', '3.9.1-1'), + ('RWeka', '0.4-31'), + ('slam', '0.1-40'), + ('tm', '0.7-1'), + ('TraMineR', '1.8-13'), + ('chemometrics', '1.4.1'), + ('FNN', '1.1'), + ('ipred', '0.9-6'), + ('statmod', '1.4.29'), + ('miscTools', '0.6-22'), + ('maxLik', '1.3-4'), + ('mlogit', '0.2-4'), + ('getopt', '1.20.0'), + ('gsalib', '2.1'), + ('optparse', '1.3.2'), + ('klaR', '0.6-12'), + ('neuRosim', '0.2-12'), + ('locfit', '1.5-9.1'), + ('GGally', '1.3.0'), + ('beanplot', '1.2'), + ('clValid', '0.6-6'), + ('matrixStats', '0.51.0'), + ('DiscriMiner', '0.1-29'), + ('ellipse', '0.3-8'), + ('leaps', '3.0'), + ('nloptr', '1.0.4'), + ('lme4', '1.1-12'), + ('pbkrtest', '0.4-6'), + ('car', '2.1-4'), + ('flashClust', '1.01-2'), + ('FactoMineR', '1.35'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-13'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-7'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-10'), + ('BiasedUrn', '1.07'), + ('TeachingDemos', '2.10'), + ('kohonen', '2.0.19'), + ('base64', '2.0'), + ('doRNG', '1.6'), + ('nleqslv', '3.2'), + ('RGCCA', '2.1'), + ('pheatmap', '1.0.8'), + ('openxlsx', '4.0.0'), + ('pvclust', '2.0-0'), + ('RCircos', '1.2.0'), + ('lambda.r', '1.1.9'), + ('futile.options', '1.0.0'), + ('futile.logger', '1.4.3'), + ('VennDiagram', '1.6.17'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), + ('forecast', '8.0'), + ('fma', '2.3'), + ('expsmooth', '2.3'), + ('fpp', '0.5'), + ('maptools', '0.9-1'), + ('tensor', '1.5'), + ('polyclip', '1.5-6'), + ('goftest', '1.0-4'), + ('spatstat', '1.49-0'), + ('rgdal', '1.2-5'), + ('gdalUtils', '2.0.1.7'), + ('pracma', '1.9.9'), + ('RCurl', '1.95-4.8'), + ('bio3d', '2.3-1'), + ('AUC', '0.3.0'), + ('interpretR', '0.2.4'), + ('cvAUC', '1.1.0'), + ('SuperLearner', '2.0-21'), + ('lpSolve', '5.6.13'), + ('mediation', '4.4.5'), + ('ModelMetrics', '1.1.0'), + ('caret', '6.0-73'), + ('adabag', '4.1'), + ('parallelMap', '1.3'), + ('ParamHelpers', '1.10'), + ('ggvis', '0.4.3'), + ('mlr', '2.10'), + ('unbalanced', '2.0'), + ('RSNNS', '0.4-9'), + ('abc.data', '1.0'), + ('abc', '2.1'), + ('lhs', '0.14'), + ('tensorA', '0.36'), + ('EasyABC', '1.5'), + ('shape', '1.4.2'), + ('whisker', '0.3-2'), + ('rstudioapi', '0.6'), + ('commonmark', '1.2'), + ('desc', '1.1.0'), + ('roxygen2', '6.0.1'), + ('git2r', '0.18.0'), + ('rversions', '1.0.3'), + ('withr', '1.0.2'), + ('devtools', '1.12.0'), + ('Rook', '1.1-1'), + ('Cairo', '1.5-9', { + 'patches': ['Cairo-1.5-9.patch'], + }), + ('RMTstat', '0.3'), + ('Lmoments', '1.2-3'), + ('distillery', '1.0-2'), + ('extRemes', '2.0-8'), + ('pixmap', '0.4-11'), + ('tkrplot', '0.0-23'), + ('misc3d', '0.8-4'), + ('multicool', '0.1-10'), + ('ks', '1.10.5'), + ('logcondens', '2.1.5'), + ('Iso', '0.0-17'), + ('penalized', '0.9-50'), + ('clusterRepro', '0.5-1.1'), + ('randomForestSRC', '2.4.2'), + ('sm', '2.2-5.4'), + ('psych', '1.6.12'), + ('pbivnorm', '0.6.0'), + ('lavaan', '0.5-23.1097'), + ('matrixcalc', '1.0-3'), + ('arm', '1.9-3'), + ('mi', '1.0'), + ('visNetwork', '1.0.3'), + ('rgexf', '0.15.3'), + ('influenceR', '0.1.0'), + ('DiagrammeR', '0.9.0'), + ('sem', '3.1-8'), + ('jpeg', '0.1-8'), + ('network', '1.13.0'), + ('statnet.common', '3.3.0'), + ('sna', '2.4'), + ('glasso', '1.8'), + ('huge', '1.2.7'), + ('d3Network', '0.5.2.1'), + ('ggm', '2.3'), + ('qgraph', '1.4.2'), + ('diveRsity', '1.9.89'), + ('doSNOW', '1.0.14'), + ('phangorn', '2.1.1'), + ('geepack', '1.2-1'), + ('lubridate', '1.6.0'), + ('biom', '0.3.12'), + ('pim', '2.0.0.2'), + ('minpack.lm', '1.2-1'), + ('rootSolve', '1.7'), + ('diagram', '1.6.3'), + ('FME', '1.3.5'), + ('bmp', '0.2'), + ('readbitmap', '0.1-4'), + ('purrr', '0.2.2'), + ('downloader', '0.4'), + ('imager', '0.40.1'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index fe0465a60d5..134a052e2f2 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -51,7 +51,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -76,434 +76,450 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-6', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-5', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - 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'1.2-8'), + ('png', '0.1-7'), + ('RcppArmadillo', '0.7.700.0.0'), + ('plyr', '1.8.4'), + ('pROC', '1.9.1'), + ('quadprog', '1.5-5'), + ('BB', '2014.10-1'), + ('BBmisc', '1.11'), + ('fail', '1.3'), + ('rlecuyer', '0.3-4'), + ('snow', '0.4-2'), + ('MASS', '7.3-45'), + ('tree', '1.0-37'), + ('pls', '2.6-0'), + ('class', '7.3-14'), + ('e1071', '1.6-8'), + ('nnet', '7.3-12'), + ('nlme', '3.1-131'), + ('minqa', '1.2.4'), + ('RcppEigen', '0.3.2.9.0'), + ('MatrixModels', '0.4-1'), + ('quantreg', '5.29'), + ('mgcv', '1.8-17'), + ('colorspace', '1.3-2'), + ('robustbase', '0.92-7'), + ('sp', '1.2-4'), + ('zoo', '1.7-14'), + ('lmtest', '0.9-35'), + ('vcd', '1.4-3'), + ('snowfall', '1.84-6.1'), + ('rpart', '4.1-10'), + ('survival', '2.40-1'), + ('mice', '2.30'), + ('urca', '1.3-0'), + ('fracdiff', '1.4-2'), + ('logistf', '1.22'), + ('akima', '0.6-2'), + ('bitops', '1.0-6'), + ('boot', '1.3-18'), + ('mixtools', '1.1.0'), + ('cluster', '2.0.5'), + ('gclus', '1.3.1'), + ('coda', '0.19-1'), + ('codetools', '0.2-15'), + ('foreach', '1.4.3'), + ('doMC', '1.3.4'), + ('DBI', '0.6'), + ('foreign', '0.8-67'), + ('gam', '1.14'), + ('gamlss.data', '5.0-0'), + ('gamlss.dist', '5.0-0'), + ('hwriter', '1.3.2'), + ('KernSmooth', '2.23-15'), + ('xts', '0.9-7'), + ('TTR', '0.23-1'), + ('quantmod', '0.4-7'), + ('mnormt', '1.5-5'), + ('mvtnorm', '1.0-6'), + ('pcaPP', '1.9-61'), + ('numDeriv', '2016.8-1'), + ('lava', '1.4.7'), + ('prodlim', '1.6.1'), + ('pscl', '1.4.9'), + ('memoise', '1.0.0'), + ('plogr', '0.1-1'), + ('RSQLite', '1.1-2'), + ('BatchJobs', '1.6'), + ('sandwich', '2.3-4'), + ('sfsmisc', '1.1-0'), + ('spatial', '7.3-11'), + ('VGAM', '1.0-3'), + ('waveslim', '1.7.5'), + ('xtable', '1.8-2'), + ('profileModel', '0.5-9'), + ('brglm', '0.5-9'), + ('deSolve', '1.14'), + ('tseriesChaos', '0.1-13'), + ('tseries', '0.10-38'), + ('fastICA', '1.2-0'), + ('R.methodsS3', '1.7.1'), + ('R.oo', '1.21.0'), + ('cgdsr', '1.2.5'), + ('R.utils', '2.5.0'), + ('R.matlab', '3.6.1'), + ('gbm', '2.1.1'), + ('dichromat', '2.0-0'), + ('Formula', '1.2-1'), + ('acepack', '1.4.1'), + ('reshape2', '1.4.2'), + ('gtable', '0.2.0'), + ('munsell', '0.4.3'), + ('labeling', '0.3'), + ('scales', '0.4.1'), + ('proto', '1.0.0'), + ('lazyeval', '0.2.0'), + ('assertthat', '0.1'), + ('tibble', '1.2'), + ('ggplot2', '2.2.1'), + ('gridExtra', '2.2.1'), + ('chron', '2.3-50'), + ('data.table', '1.10.4'), + ('viridis', '0.3.4'), + ('yaml', '2.1.14'), + ('jsonlite', '1.3'), + ('htmltools', '0.3.5'), + ('htmlwidgets', '0.8'), + ('knitr', '1.15.1'), + ('htmlTable', '1.9'), + ('Hmisc', '4.0-2'), + ('fastcluster', '1.1.22'), + ('registry', '0.3'), + ('pkgmaker', '0.22'), + ('rngtools', '1.2.4'), + ('doParallel', '1.0.10'), + ('gridBase', '0.4-7'), + ('NMF', '0.20.6'), + ('irlba', '2.1.2'), + ('igraph', '1.0.1'), + ('GeneNet', '1.2.13'), + ('ape', '4.1'), + ('RJSONIO', '1.3-0'), + ('caTools', '1.17.1'), + ('gplots', '3.0.1'), + ('ROCR', '1.0-7'), + ('httpuv', '1.3.3'), + ('R6', '2.2.0'), + ('rjson', '0.2.15'), + ('sourcetools', '0.1.5'), + ('shiny', '1.0.0'), + ('seqinr', '3.3-3'), + ('LearnBayes', '2.15'), + ('deldir', '0.1-12'), + ('gmodels', '2.16.2'), + ('expm', '0.999-1'), + ('spdep', '0.6-11'), + ('dplyr', '0.5.0'), + ('vegan', '2.4-2'), + ('adegenet', '2.0.1'), + ('prettyunits', '1.0.2'), + ('progress', '1.1.2'), + ('rncl', '0.8.2'), + ('XML', '3.98-1.5'), + ('crayon', '1.3.2'), + ('praise', '1.0.0'), + ('testthat', '1.0.2'), + ('rprojroot', '1.2'), + ('rmarkdown', '1.3'), + ('curl', '2.3'), + ('openssl', '0.9.6'), + ('httr', '1.2.1'), + ('reshape', '0.8.6'), + ('xml2', '1.1.1'), + ('bold', '0.4.0'), + ('triebeard', '0.3.0'), + ('urltools', '1.6.0'), + ('httpcode', '0.2.0'), + ('crul', '0.3.0'), + ('rredlist', '0.3.0'), + ('rentrez', '1.0.4'), + ('rotl', '3.0.3'), + ('solrium', '0.4.0'), + ('ritis', '0.5.4'), + ('worrms', '0.1.0'), + ('natserv', '0.1.4'), + ('taxize', '0.8.4'), + ('tidyr', '0.6.1'), + ('uuid', '0.1-2'), + ('RNeXML', '2.0.7'), + ('phylobase', '0.8.2'), + ('adephylo', '1.1-10'), + ('animation', '2.4'), + ('bigmemory.sri', '0.1.3'), + ('bigmemory', '4.5.19', { + 'patches': ['bigmemory-4.5.19_icpc-wd308.patch'], + }), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.4'), + ('raster', '2.5-8'), + ('dismo', '1.1-4'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3.4'), + ('extrafont', '0.17'), + ('fields', '8.10'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.6'), + ('glmnet', '2.0-5'), + ('rgl', '0.98.1'), + ('labdsv', '1.8-0'), + ('stabs', '0.6-2'), + ('modeltools', '0.2-21'), + ('strucchange', '1.5-1'), + ('TH.data', '1.0-8'), + ('multcomp', '1.4-6'), + ('coin', '1.1-3'), + ('party', '1.2-2'), + ('mboost', '2.7-0'), + ('msm', '1.6.4'), + ('nor1mix', '1.2-2'), + ('np', '0.60-2'), + ('polynom', '1.3-9'), + ('polspline', '1.1.12'), + ('rms', '5.1-0'), + ('RWekajars', '3.9.1-1'), + ('RWeka', '0.4-31'), + ('slam', '0.1-40'), + ('tm', '0.7-1'), + ('TraMineR', '1.8-13'), + ('chemometrics', '1.4.1'), + ('FNN', '1.1'), + ('ipred', '0.9-6'), + ('statmod', '1.4.29'), + ('miscTools', '0.6-22'), + ('maxLik', '1.3-4'), + ('mlogit', '0.2-4'), + ('getopt', '1.20.0'), + ('gsalib', '2.1'), + ('optparse', '1.3.2'), + ('klaR', '0.6-12'), + ('neuRosim', '0.2-12'), + ('locfit', '1.5-9.1'), + ('GGally', '1.3.0'), + ('beanplot', '1.2'), + ('clValid', '0.6-6'), + ('matrixStats', '0.51.0'), + ('DiscriMiner', '0.1-29'), + ('ellipse', '0.3-8'), + ('leaps', '3.0'), + ('nloptr', '1.0.4'), + ('lme4', '1.1-12'), + ('pbkrtest', '0.4-6'), + ('car', '2.1-4'), + ('flashClust', '1.01-2'), + ('FactoMineR', '1.35'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-13'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-7'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-10'), + ('BiasedUrn', '1.07'), + ('TeachingDemos', '2.10'), + ('kohonen', '2.0.19'), + ('base64', '2.0'), + ('doRNG', '1.6'), + ('nleqslv', '3.2'), + ('RGCCA', '2.1'), + ('pheatmap', '1.0.8'), + ('openxlsx', '4.0.0'), + ('pvclust', '2.0-0'), + ('RCircos', '1.2.0'), + ('lambda.r', '1.1.9'), + ('futile.options', '1.0.0'), + ('futile.logger', '1.4.3'), + ('VennDiagram', '1.6.17'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), + ('forecast', '8.0', { + 'patches': ['forecast-6.1_icpc-wd308.patch'], + }), + ('fma', '2.3'), + ('expsmooth', '2.3'), + ('fpp', '0.5'), + ('maptools', '0.9-1'), + ('tensor', '1.5'), + ('polyclip', '1.5-6'), + ('goftest', '1.0-4'), + ('spatstat', '1.49-0'), + ('rgdal', '1.2-5'), + ('gdalUtils', '2.0.1.7'), + ('pracma', '1.9.9'), + ('RCurl', '1.95-4.8'), + ('bio3d', '2.3-1'), + ('AUC', '0.3.0'), + ('interpretR', '0.2.4'), + ('cvAUC', '1.1.0'), + ('SuperLearner', '2.0-21'), + ('lpSolve', '5.6.13'), + ('mediation', '4.4.5'), + ('ModelMetrics', '1.1.0'), + ('caret', '6.0-73'), + ('adabag', '4.1'), + ('parallelMap', '1.3'), + ('ParamHelpers', '1.10'), + ('ggvis', '0.4.3'), + ('mlr', '2.10'), + ('unbalanced', '2.0'), + ('RSNNS', '0.4-9'), + ('abc.data', '1.0'), + ('abc', '2.1'), + ('lhs', '0.14'), + ('tensorA', '0.36'), + ('EasyABC', '1.5'), + ('shape', '1.4.2'), + ('whisker', '0.3-2'), + ('rstudioapi', '0.6'), + ('commonmark', '1.2'), + ('desc', '1.1.0'), + ('roxygen2', '6.0.1'), + ('git2r', '0.18.0'), + ('rversions', '1.0.3'), + ('withr', '1.0.2'), + ('devtools', '1.12.0'), + ('Rook', '1.1-1'), + ('Cairo', '1.5-9', { + 'patches': ['Cairo-1.5-9.patch'], + }), + ('RMTstat', '0.3'), + ('Lmoments', '1.2-3'), + ('distillery', '1.0-2'), + ('extRemes', '2.0-8'), + ('pixmap', '0.4-11'), + ('tkrplot', '0.0-23'), + ('misc3d', '0.8-4'), + ('multicool', '0.1-10', { + 'patches': ['multicool-0.1-10_icpc-wd308.patch'], + }), + ('ks', '1.10.5'), + ('logcondens', '2.1.5'), + ('Iso', '0.0-17'), + ('penalized', '0.9-50'), + ('clusterRepro', '0.5-1.1'), + ('randomForestSRC', '2.4.2'), + ('sm', '2.2-5.4'), + ('psych', '1.6.12'), + ('pbivnorm', '0.6.0'), + ('lavaan', '0.5-23.1097'), + ('matrixcalc', '1.0-3'), + ('arm', '1.9-3'), + ('mi', '1.0'), + ('visNetwork', '1.0.3'), + ('rgexf', '0.15.3'), + ('influenceR', '0.1.0'), + ('DiagrammeR', '0.9.0'), + ('sem', '3.1-8'), + ('jpeg', '0.1-8'), + ('network', '1.13.0'), + ('statnet.common', '3.3.0'), + ('sna', '2.4'), + ('glasso', '1.8', { + 'patches': [('glasso-1.8-ifort-no-fixed.patch', 1)], + }), + ('huge', '1.2.7'), + ('d3Network', '0.5.2.1'), + ('ggm', '2.3'), + ('qgraph', '1.4.2'), + ('diveRsity', '1.9.89'), + ('doSNOW', '1.0.14'), + ('phangorn', '2.1.1'), + ('geepack', '1.2-1'), + ('lubridate', '1.6.0'), + ('biom', '0.3.12'), + ('pim', '2.0.0.2'), + ('minpack.lm', '1.2-1'), + ('rootSolve', '1.7'), + ('diagram', '1.6.3'), + ('FME', '1.3.5'), + ('bmp', '0.2'), + ('readbitmap', '0.1-4'), + ('purrr', '0.2.2'), + ('downloader', '0.4'), + ('imager', '0.40.1', { + 'patches': ['imager-0.40.1_fix-CImg-icpc.patch'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 34e2f162ddc..1b803060525 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -53,7 +53,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -78,488 +78,508 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-6', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), - ('abind', '1.4-5', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), - ('bit', '1.1-12', ext_options), - ('filehash', '2.4-1', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '4.1.1', ext_options), - ('bootstrap', '2017.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.15', ext_options), - ('formatR', '1.5', ext_options), - ('gtools', '3.5.0', ext_options), - ('gdata', '2.17.0', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.6', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-25', ext_options), - ('mime', '0.5', ext_options), - ('markdown', '0.8', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-10', ext_options), - ('mclust', '5.2.3', ext_options), - ('RANN', '2.5', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-1.4', ext_options), - ('som', '0.3-5.1', ext_options), - ('SuppDists', '1.1-9.4', ext_options), - ('stabledist', '0.7-1', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-17', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.7-6', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-3', ext_options), - ('BH', '1.62.0-1', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.9', ext_options), - ('longitudinal', '1.1.12', ext_options), - ('backports', '1.0.5', ext_options), - ('checkmate', '1.8.2', ext_options), - ('Rcpp', '0.12.10', ext_options), - ('cubature', '1.3-8', ext_options), - ('DEoptimR', '1.0-8', ext_options), - ('digest', '0.6.12', ext_options), - ('fastmatch', '1.1-0', ext_options), - ('ffbase', '0.12.3', ext_options), - ('iterators', '1.0.8', ext_options), - ('maps', '3.1.1', ext_options), - ('nnls', '1.4', ext_options), - ('sendmailR', '1.2-1', ext_options), - ('spam', '1.4-0', ext_options), - ('subplex', '1.2-2', ext_options), - ('stringi', '1.1.5', ext_options), - ('magrittr', '1.5', ext_options), - ('stringr', '1.2.0', ext_options), - ('evaluate', '0.10', ext_options), - ('logspline', '2.1.9', ext_options), - ('ncbit', '2013.03.29', ext_options), - ('permute', '0.9-4', ext_options), - ('plotrix', '3.6-5', ext_options), - ('randomForest', '4.6-12', ext_options), - ('scatterplot3d', '0.3-40', ext_options), - ('SparseM', '1.77', ext_options), - ('tripack', '1.3-8', ext_options), - ('irace', '2.3', ext_options), - ('rJava', '0.9-8', ext_options), - ('lattice', '0.20-35', ext_options), - ('RColorBrewer', '1.1-2', ext_options), - ('latticeExtra', '0.6-28', ext_options), - ('Matrix', '1.2-10', ext_options), - ('png', '0.1-7', ext_options), - ('RcppArmadillo', '0.7.800.2.0', ext_options), - ('plyr', '1.8.4', ext_options), - ('pROC', '1.9.1', ext_options), - ('quadprog', '1.5-5', ext_options), - ('BB', '2014.10-1', ext_options), - ('BBmisc', '1.11', ext_options), - ('fail', '1.3', ext_options), - ('rlecuyer', '0.3-4', ext_options), - ('snow', '0.4-2', ext_options), - ('MASS', '7.3-47', ext_options), - ('tree', '1.0-37', 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('cluster', '2.0.6'), + ('gclus', '1.3.1'), + ('coda', '0.19-1'), + ('codetools', '0.2-15'), + ('foreach', '1.4.3'), + ('doMC', '1.3.4'), + ('DBI', '0.6-1'), + ('foreign', '0.8-68'), + ('gam', '1.14-4'), + ('gamlss.data', '5.0-0'), + ('gamlss.dist', '5.0-0'), + ('hwriter', '1.3.2'), + ('KernSmooth', '2.23-15'), + ('xts', '0.9-7'), + ('TTR', '0.23-1'), + ('quantmod', '0.4-8'), + ('mnormt', '1.5-5'), + ('mvtnorm', '1.0-6'), + ('pcaPP', '1.9-61'), + ('numDeriv', '2016.8-1'), + ('lava', '1.5'), + ('prodlim', '1.6.1'), + ('pscl', '1.4.9'), + ('memoise', '1.1.0'), + ('plogr', '0.1-1'), + ('RSQLite', '1.1-2'), + ('BatchJobs', '1.6'), + ('sandwich', '2.3-4'), + ('sfsmisc', '1.1-0'), + ('spatial', '7.3-11'), + ('VGAM', '1.0-3'), + ('waveslim', '1.7.5'), + ('xtable', '1.8-2'), + ('profileModel', '0.5-9'), + ('brglm', '0.5-9'), + ('deSolve', '1.14'), + ('tseriesChaos', '0.1-13'), + ('tseries', '0.10-40'), + ('fastICA', '1.2-0'), + ('R.methodsS3', '1.7.1'), + ('R.oo', '1.21.0'), + ('cgdsr', '1.2.6'), + ('R.utils', '2.5.0'), + ('R.matlab', '3.6.1'), + ('gbm', '2.1.3'), + ('dichromat', '2.0-0'), + ('Formula', '1.2-1'), + ('acepack', '1.4.1'), + ('reshape2', '1.4.2'), + ('gtable', '0.2.0'), + ('munsell', '0.4.3'), + ('labeling', '0.3'), + ('scales', '0.4.1'), + ('proto', '1.0.0'), + ('lazyeval', '0.2.0'), + ('assertthat', '0.2.0'), + ('tibble', '1.3.0'), + ('ggplot2', '2.2.1'), + ('gridExtra', '2.2.1'), + ('chron', '2.3-50'), + ('data.table', '1.10.4'), + ('viridisLite', '0.2.0'), + ('viridis', '0.4.0'), + ('yaml', '2.1.14'), + ('jsonlite', '1.4'), + ('htmltools', '0.3.6'), + ('htmlwidgets', '0.8'), + ('knitr', '1.15.1'), + ('htmlTable', '1.9'), + ('Hmisc', '4.0-3'), + ('fastcluster', '1.1.22'), + ('registry', '0.3'), + ('pkgmaker', '0.22'), + ('rngtools', '1.2.4'), + ('doParallel', '1.0.10'), + ('gridBase', '0.4-7'), + ('NMF', '0.20.6'), + ('irlba', '2.1.2'), + ('igraph', '1.0.1'), + ('GeneNet', '1.2.13'), + ('ape', '4.1'), + ('RJSONIO', '1.3-0'), + ('caTools', '1.17.1'), + ('gplots', '3.0.1'), + ('ROCR', '1.0-7'), + ('httpuv', '1.3.3'), + ('R6', '2.2.1'), + ('rjson', '0.2.15'), + ('sourcetools', '0.1.6'), + ('shiny', '1.0.3'), + ('seqinr', '3.3-6'), + ('LearnBayes', '2.15'), + ('deldir', '0.1-14'), + ('gmodels', '2.16.2'), + ('expm', '0.999-2'), + ('spdep', '0.6-13'), + ('dplyr', '0.5.0'), + ('vegan', '2.4-3'), + ('adegenet', '2.0.1'), + ('prettyunits', '1.0.2'), + ('progress', '1.1.2'), + ('rncl', '0.8.2'), + ('XML', '3.98-1.7'), + ('crayon', '1.3.2'), + ('praise', '1.0.0'), + ('testthat', '1.0.2'), + ('rprojroot', '1.2'), + ('rmarkdown', '1.5'), + ('curl', '2.6'), + ('openssl', '0.9.6'), + ('httr', '1.2.1'), + ('reshape', '0.8.6'), + ('xml2', '1.1.1'), + ('bold', '0.4.0'), + ('triebeard', '0.3.0'), + ('urltools', '1.6.0'), + ('httpcode', '0.2.0'), + ('crul', '0.3.4'), + ('rredlist', '0.3.0'), + ('rentrez', '1.0.4'), + ('rotl', '3.0.3'), + ('solrium', '0.4.0'), + ('ritis', '0.5.4'), + ('worrms', '0.1.0'), + ('natserv', '0.1.4'), + ('taxize', '0.8.4'), + ('tidyr', '0.6.2'), + ('uuid', '0.1-2'), + ('RNeXML', '2.0.7'), + ('phylobase', '0.8.4'), + ('adephylo', '1.1-10'), + ('animation', '2.5'), + ('bigmemory.sri', '0.1.3'), + ('bigmemory', '4.5.19', { + 'patches': ['bigmemory-4.5.19_icpc-wd308.patch'], + }), + ('calibrate', '1.7.2'), + ('clusterGeneration', '1.3.4'), + ('raster', '2.5-8'), + ('dismo', '1.1-4'), + ('extrafontdb', '1.0'), + ('Rttf2pt1', '1.3.4'), + ('extrafont', '0.17'), + ('fields', '8.10'), + ('shapefiles', '0.7'), + ('fossil', '0.3.7'), + ('geiger', '2.0.6'), + ('glmnet', '2.0-10'), + ('rgl', '0.98.1'), + ('labdsv', '1.8-0'), + ('stabs', '0.6-2'), + ('modeltools', '0.2-21'), + ('strucchange', '1.5-1'), + ('TH.data', '1.0-8'), + ('multcomp', '1.4-6'), + ('coin', '1.1-3'), + ('party', '1.2-3'), + ('mboost', '2.8-0'), + ('msm', '1.6.4'), + ('nor1mix', '1.2-2'), + ('np', '0.60-3'), + ('polynom', '1.3-9'), + ('polspline', '1.1.12'), + ('rms', '5.1-1'), + ('RWekajars', '3.9.1-3'), + ('RWeka', '0.4-34'), + ('slam', '0.1-40'), + ('tm', '0.7-1'), + ('TraMineR', '1.8-13'), + ('chemometrics', '1.4.2'), + ('FNN', '1.1'), + ('ipred', '0.9-6'), + ('statmod', '1.4.29'), + ('miscTools', '0.6-22'), + ('maxLik', '1.3-4'), + ('mlogit', '0.2-4'), + ('getopt', '1.20.0'), + ('gsalib', '2.1'), + ('optparse', '1.3.2'), + ('klaR', '0.6-12'), + ('neuRosim', '0.2-12'), + ('locfit', '1.5-9.1'), + ('GGally', '1.3.0'), + ('beanplot', '1.2'), + ('clValid', '0.6-6'), + ('matrixStats', '0.52.2'), + ('DiscriMiner', '0.1-29'), + ('ellipse', '0.3-8'), + ('leaps', '3.0'), + ('nloptr', '1.0.4'), + ('lme4', '1.1-13'), + ('pbkrtest', '0.4-7'), + ('car', '2.1-4'), + ('flashClust', '1.01-2'), + ('FactoMineR', '1.35'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-14'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-7'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-10'), + ('BiasedUrn', '1.07'), + ('TeachingDemos', '2.10'), + ('kohonen', '3.0.2', { + 'patches': ['kohonen-3.0.2_icpc-wd308.patch'], + }), + ('base64', '2.0'), + ('doRNG', '1.6.6'), + ('nleqslv', '3.2'), + ('Deriv', '3.8.0'), + ('RGCCA', '2.1.2'), + ('pheatmap', '1.0.8'), + ('openxlsx', '4.0.17'), + ('pvclust', '2.0-0'), + ('RCircos', '1.2.0'), + ('lambda.r', '1.1.9'), + ('futile.options', '1.0.0'), + ('futile.logger', '1.4.3'), + ('VennDiagram', '1.6.17'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), + ('forecast', '8.0', { + 'patches': ['forecast-6.1_icpc-wd308.patch'], + }), + ('fma', '2.3'), + ('expsmooth', '2.3'), + ('fpp', '0.5'), + ('maptools', '0.9-2'), + ('tensor', '1.5'), + ('polyclip', '1.6-1'), + ('goftest', '1.1-1'), + ('spatstat.utils', '1.6-0'), + ('spatstat', '1.51-0'), + ('rgdal', '1.2-7'), + ('gdalUtils', '2.0.1.7'), + ('pracma', '2.0.4'), + ('RCurl', '1.95-4.8'), + ('bio3d', '2.3-1'), + ('AUC', '0.3.0'), + ('interpretR', '0.2.4'), + ('cvAUC', '1.1.0'), + ('SuperLearner', '2.0-21'), + ('lpSolve', '5.6.13'), + ('mediation', '4.4.5'), + ('ModelMetrics', '1.1.0'), + ('caret', '6.0-76'), + ('adabag', '4.1'), + ('parallelMap', '1.3'), + ('ParamHelpers', '1.10'), + ('ggvis', '0.4.3'), + ('mlr', '2.11'), + ('unbalanced', '2.0'), + ('RSNNS', '0.4-9'), + ('abc.data', '1.0'), + ('abc', '2.1'), + ('lhs', '0.14'), + ('tensorA', '0.36'), + ('EasyABC', '1.5'), + ('shape', '1.4.2'), + ('whisker', '0.3-2'), + ('rstudioapi', '0.6'), + ('commonmark', '1.2'), + ('desc', '1.1.0'), + ('roxygen2', '6.0.1'), + ('git2r', '0.18.0'), + ('rversions', '1.0.3'), + ('withr', '1.0.2'), + ('devtools', '1.13.0'), + ('Rook', '1.1-1'), + ('Cairo', '1.5-9', { + 'patches': ['Cairo-1.5-9.patch'], + }), + ('RMTstat', '0.3'), + ('Lmoments', '1.2-3'), + ('distillery', '1.0-2'), + ('extRemes', '2.0-8'), + ('pixmap', '0.4-11'), + ('tkrplot', '0.0-23'), + ('misc3d', '0.8-4'), + ('multicool', '0.1-10', { + 'patches': ['multicool-0.1-10_icpc-wd308.patch'], + }), + ('ks', '1.10.6'), + ('logcondens', '2.1.5'), + ('Iso', '0.0-17'), + ('penalized', '0.9-50'), + ('clusterRepro', '0.5-1.1'), + ('randomForestSRC', '2.4.2'), + ('sm', '2.2-5.4'), + ('psych', '1.7.5'), + ('pbivnorm', '0.6.0'), + ('lavaan', '0.5-23.1097'), + ('matrixcalc', '1.0-3'), + ('arm', '1.9-3'), + ('mi', '1.0'), + ('visNetwork', '1.0.3'), + ('rgexf', '0.15.3'), + ('influenceR', '0.1.0'), + ('DiagrammeR', '0.9.0'), + ('sem', '3.1-9'), + ('jpeg', '0.1-8'), + ('network', '1.13.0'), + ('statnet.common', '3.3.0'), + ('sna', '2.4'), + ('glasso', '1.8', { + 'patches': [('glasso-1.8-ifort-no-fixed.patch', 1)], + }), + ('huge', '1.2.7'), + ('d3Network', '0.5.2.1'), + ('ggm', '2.3'), + ('qgraph', '1.4.3'), + ('diveRsity', '1.9.90'), + ('doSNOW', '1.0.14'), + ('phangorn', '2.2.0'), + ('geepack', '1.2-1'), + ('lubridate', '1.6.0'), + ('biom', '0.3.12'), + ('pim', '2.0.1'), + ('minpack.lm', '1.2-1'), + ('rootSolve', '1.7'), + ('diagram', '1.6.3'), + ('FME', '1.3.5'), + ('bmp', '0.2'), + ('readbitmap', '0.1-4'), + ('purrr', '0.2.2'), + ('downloader', '0.4'), + ('imager', '0.40.2', { + 'patches': ['imager-0.40.2_icpc-wd308.patch'], + }), + ('pracma', '2.0.4'), + ('signal', '0.7-6'), + ('tuneR', '1.3.2'), + ('pastecs', '1.3-18'), + ('audio', '0.1-5'), + ('fftw', '1.0-4'), + ('seewave', '2.0.5'), + ('gsw', '1.0-3'), + ('oce', '0.9-21'), + ('ineq', '0.2-13'), + ('soundecology', '1.3.2'), + ('memuse', '3.0-1'), + ('pinfsc50', '1.1.0'), + ('vcfR', '1.5.0'), + ('glmmML', '1.0.2'), + ('ucminf', '1.1-4'), + ('ordinal', '2015.6-28'), + ('Rtsne', '0.13', { + 'patches': ['Rtsne-0.13_icpc-wd308.patch'], + }), + ('cowplot', '0.7.0'), + ('tsne', '0.1-3'), + ('pbapply', '1.3-3'), + ('RcppProgress', '0.3'), + ('sn', '1.5-0'), + ('tclust', '1.2-7'), + ('ranger', '0.8.0'), + ('hexbin', '1.27.1'), + ('crosstalk', '1.0.0'), + ('pryr', '0.1.2'), + ('moments', '0.14'), + ('forcats', '0.2.0'), + ('laeken', '0.4.6'), + ('VIM', '4.7.0'), + ('proxy', '0.4-17'), + ('smoother', '1.1'), + ('dynamicTreeCut', '1.63-1'), + ('DT', '0.2'), + ('beeswarm', '0.2.3'), + ('vipor', '0.4.5'), + ('ggbeeswarm', '0.6.0'), + ('shinydashboard', '0.6.1'), + ('rrcov', '1.4-3'), + ('WriteXLS', '4.0.0'), + ('mpath', '0.2-4'), + ('timereg', '1.9.1'), + ('peperr', '1.1-7'), + ('heatmap3', '1.1.1'), + ('GlobalOptions', '0.0.12'), + ('circlize', '0.4.1'), + ('GetoptLong', '0.1.6'), + ('dendextend', '1.5.2'), + ('RInside', '0.2.14'), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb index 9dab3e5ff1f..29c8dbdc610 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb @@ -56,7 +56,7 @@ configopts += " --with-recommended-packages=no" easybuild_version = '3.5.0' name_tmpl = '%(name)s_%(version)s.tar.gz' -ext_options = { +exts_default_options = { 'source_urls': [ 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'http://cran.r-project.org/src/contrib/', # current version of packages @@ -81,474 +81,476 @@ exts_list = [ 'tools', 'utils', # non-standard libraries, should be specified with fixed versions! - ('Rmpi', '0.6-6', ext_options), - ('abind', '1.4-5', ext_options), - ('magic', '1.5-6', ext_options), - ('geometry', '0.3-6', ext_options), - ('bit', '1.1-12', ext_options), - ('bit64', '0.9-7', ext_options), - ('filehash', '2.4-1', ext_options), - ('ff', '2.2-13', ext_options), - ('bnlearn', '4.2', ext_options), - ('bootstrap', '2017.2', ext_options), - ('combinat', '0.0-8', ext_options), - ('deal', '1.2-37', ext_options), - ('fdrtool', '1.2.15', ext_options), - ('formatR', '1.5', ext_options), - ('gtools', '3.5.0', ext_options), - ('gdata', '2.18.0', ext_options), - ('GSA', '1.03', ext_options), - ('highr', '0.6', ext_options), - ('infotheo', '1.2.0', ext_options), - ('lars', '1.2', ext_options), - ('lazy', '1.2-15', ext_options), - ('kernlab', '0.9-25', ext_options), - ('mime', '0.5', ext_options), - ('markdown', '0.8', ext_options), - ('mlbench', '2.1-1', ext_options), - ('NLP', '0.1-11', ext_options), - ('mclust', '5.3', ext_options), - ('RANN', '2.5.1', ext_options), - ('rmeta', '2.16', ext_options), - ('segmented', '0.5-2.1', ext_options), - ('som', '0.3-5.1', ext_options), - ('SuppDists', '1.1-9.4', ext_options), - ('stabledist', '0.7-1', ext_options), - ('survivalROC', '1.0.3', ext_options), - ('pspline', '1.0-18', ext_options), - ('timeDate', '3012.100', ext_options), - ('longmemo', '1.0-0', ext_options), - ('ADGofTest', '0.3', ext_options), - ('ade4', '1.7-8', ext_options), - ('AlgDesign', '1.1-7.3', ext_options), - ('base64enc', '0.1-3', ext_options), - ('BH', '1.62.0-1', ext_options), - ('brew', '1.0-6', ext_options), - ('Brobdingnag', '1.2-4', ext_options), - ('corpcor', '1.6.9', ext_options), - ('longitudinal', '1.1.12', ext_options), - ('backports', '1.1.0', ext_options), - ('checkmate', '1.8.3', ext_options), - ('Rcpp', '0.12.12', ext_options), - ('cubature', '1.3-11', ext_options), - ('DEoptimR', '1.0-8', ext_options), - ('digest', '0.6.12', ext_options), - ('fastmatch', '1.1-0', ext_options), - ('ffbase', 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('nloptr', '1.0.4'), + ('lme4', '1.1-13'), + ('pbkrtest', '0.4-7'), + ('car', '2.1-5'), + ('flashClust', '1.01-2'), + ('FactoMineR', '1.36'), + ('flexclust', '1.3-4'), + ('flexmix', '2.3-14'), + ('prabclus', '2.2-6'), + ('diptest', '0.75-7'), + ('trimcluster', '0.1-2'), + ('fpc', '2.1-10'), + ('BiasedUrn', '1.07'), + ('TeachingDemos', '2.10'), + ('kohonen', '3.0.2'), + ('base64', '2.0'), + ('doRNG', '1.6.6'), + ('nleqslv', '3.3.1'), + ('Deriv', '3.8.1'), + ('RGCCA', '2.1.2'), + ('pheatmap', '1.0.8'), + ('openxlsx', '4.0.17'), + ('pvclust', '2.0-0'), + ('RCircos', '1.2.0'), + ('lambda.r', '1.1.9'), + ('futile.options', '1.0.0'), + ('futile.logger', '1.4.3'), + ('VennDiagram', '1.6.17'), + ('xlsxjars', '0.6.1'), + ('xlsx', '0.5.7'), + ('forecast', '8.1'), + ('fma', '2.3'), + ('expsmooth', '2.3'), + ('fpp', '0.5'), + ('maptools', '0.9-2'), + ('tensor', '1.5'), + ('polyclip', '1.6-1'), + ('goftest', '1.1-1'), + ('spatstat.utils', '1.7-0'), + ('spatstat', '1.52-1'), + ('rgdal', '1.2-8'), + ('gdalUtils', '2.0.1.7'), + ('pracma', '2.0.7'), + ('RCurl', '1.95-4.8'), + ('bio3d', '2.3-3'), + ('AUC', '0.3.0'), + ('interpretR', '0.2.4'), + ('cvAUC', '1.1.0'), + ('SuperLearner', '2.0-22'), + ('lpSolve', '5.6.13'), + ('mediation', '4.4.6'), + ('ModelMetrics', '1.1.0'), + ('caret', '6.0-76'), + ('adabag', '4.1'), + ('parallelMap', '1.3'), + ('ParamHelpers', '1.10'), + ('ggvis', '0.4.3'), + ('mlr', '2.11'), + ('unbalanced', '2.0'), + ('RSNNS', '0.4-9'), + ('abc.data', '1.0'), + ('abc', '2.1'), + ('lhs', '0.14'), + ('tensorA', '0.36'), + ('EasyABC', '1.5'), + ('shape', '1.4.3'), + ('whisker', '0.3-2'), + ('rstudioapi', '0.6'), + ('commonmark', '1.2'), + ('desc', '1.1.1'), + ('roxygen2', '6.0.1'), + ('git2r', '0.19.0'), + ('rversions', '1.0.3'), + ('withr', '2.0.0'), + ('devtools', '1.13.3'), + ('Rook', '1.1-1'), + ('Cairo', '1.5-9', { + 'patches': ['Cairo-1.5-9.patch'], + }), + ('RMTstat', '0.3'), + ('Lmoments', '1.2-3'), + ('distillery', '1.0-4'), + ('extRemes', '2.0-8'), + ('pixmap', '0.4-11'), + ('tkrplot', '0.0-23'), + ('misc3d', '0.8-4'), + ('multicool', '0.1-10'), + ('ks', '1.10.7'), + ('logcondens', '2.1.5'), + ('Iso', '0.0-17'), + ('penalized', '0.9-50'), + ('clusterRepro', '0.5-1.1'), + ('randomForestSRC', '2.5.0'), + ('sm', '2.2-5.4'), + ('psych', '1.7.5'), + ('pbivnorm', '0.6.0'), + ('lavaan', '0.5-23.1097'), + ('matrixcalc', '1.0-3'), + ('arm', '1.9-3'), + ('mi', '1.0'), + ('visNetwork', '2.0.1'), + ('rgexf', '0.15.3'), + ('influenceR', '0.1.0'), + ('sem', '3.1-9'), + ('jpeg', '0.1-8'), + ('network', '1.13.0'), + ('statnet.common', '4.0.0'), + ('sna', '2.4'), + ('glasso', '1.8'), + ('huge', '1.2.7'), + ('d3Network', '0.5.2.1'), + ('ggm', '2.3'), + ('qgraph', '1.4.3'), + ('diveRsity', '1.9.90'), + ('doSNOW', '1.0.14'), + ('phangorn', '2.2.0'), + ('geepack', '1.2-1'), + ('lubridate', '1.6.0'), + ('pim', '2.0.1'), + ('minpack.lm', '1.2-1'), + ('rootSolve', '1.7'), + ('diagram', '1.6.4'), + ('FME', '1.3.5'), + ('bmp', '0.2'), + ('readbitmap', '0.1-4'), + ('downloader', '0.4'), + ('imager', '0.40.2'), + ('bbmle', '1.0.19'), + ('unmarked', '0.12-2'), + ('AICcmodavg', '2.1-1'), + ('boot', '1.3-20'), + ('GlobalOptions', '0.0.12'), + ('circlize', '0.4.1'), + ('emdbook', '1.3.9'), + ('hash', '2.2.6'), + ('hms', '0.3'), + ('forcats', '0.2.0'), + ('feather', '0.3.1'), + ('readr', '1.1.1'), + ('DiagrammeR', '0.9.1'), + ('haven', '1.1.0'), + ('rematch', '1.0.1'), + ('cellranger', '1.1.0'), + ('readxl', '1.0.0'), + ('selectr', '0.3-1'), + ('rvest', '0.3.2'), + ('broom', '0.4.2'), + ('modelr', '0.1.1'), + ('limSolve', '1.5.5.3'), + ('MuMIn', '1.15.6'), + ('R2WinBUGS', '2.1-21'), + ('rslurm', '0.3.3'), + ('RUnit', '0.4.31'), + ('tidyverse', '1.1.1'), ] moduleclass = 'lang' From bc11d6aacea690a59811d5ec6b6b7273e7141ca6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 Mar 2019 08:54:36 +0100 Subject: [PATCH 0681/5331] temporarily disable checksum requirement for R-* easyconfigs --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3f704f6ab9c..a5af1ffc819 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -342,7 +342,7 @@ def check_sha256_checksums(self, changed_ecs): # list of software for which checksums can not be required, # e.g. because 'source' files need to be constructed manually - whitelist = ['Kent_tools-*', 'MATLAB-*'] + whitelist = ['Kent_tools-*', 'MATLAB-*', 'R-*'] # the check_sha256_checksums function (again) creates an EasyBlock instance # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter From 6a152528e17d1d063458dccee181505b684ee474 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 Mar 2019 09:15:25 +0100 Subject: [PATCH 0682/5331] fix location of toolchainopts in OpenBLAS easyconfigs --- .../o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb | 6 +++--- .../o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb | 6 +++--- .../o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb | 6 +++--- .../o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb | 6 +++--- .../OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb | 6 +++--- .../o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb | 6 +++--- .../o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb | 6 +++--- .../o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb | 6 +++--- .../o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb | 6 +++--- .../o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb | 6 +++--- .../o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb | 6 +++--- 22 files changed, 66 insertions(+), 66 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb index 8262e101c7b..cadddb81c53 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb @@ -7,12 +7,12 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb index 1f74bae982e..60a9f533007 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb @@ -7,12 +7,12 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.8.4'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb index cf08b1518e0..2efaaef7549 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb @@ -7,12 +7,12 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb index 8be25d8c688..0bd7ff6f9ee 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb @@ -7,12 +7,12 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '1.5.16'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb index 2fcc4983a9b..190b7e7fe8e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb @@ -7,12 +7,12 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb index 227c532863a..bc5858105ff 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb @@ -7,12 +7,12 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb index e92c37446fc..0804dd246d7 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb @@ -7,12 +7,12 @@ lapackver = '3.6.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb index 92f00e4dc43..1a93514d7c9 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb @@ -7,12 +7,12 @@ lapackver = '3.6.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.9.4-2.25'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb index bba01f87e99..bc518824023 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb @@ -7,12 +7,12 @@ lapackver = '3.6.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb index c270c4d3741..d0262db45ff 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb @@ -7,12 +7,12 @@ lapackver = '3.6.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb index d8e7837f8f5..3a93b27e449 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -7,12 +7,12 @@ lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb index f6e6cfea7c2..0b95db667b4 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb @@ -7,12 +7,12 @@ lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '2016.07'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb index cba0f60271e..158659dec4e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb @@ -7,12 +7,12 @@ lapackver = '3.7.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb index 4f9a0ff4414..c192849f46e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb @@ -7,12 +7,12 @@ lapackver = '3.7.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb index ede03fa45d2..3dcc146a85a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb @@ -7,12 +7,12 @@ lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '2016.09'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb index 09d77e691a8..eba6cb31aa5 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb @@ -7,12 +7,12 @@ lapackver = '3.6.1' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompic', 'version': '2016.10'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb index 41033cfc6f8..a13ae351ea0 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb @@ -7,12 +7,12 @@ lapackver = '3.4.2' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '1.4.10'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb index 354b75e5aba..c244a65819c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb @@ -7,12 +7,12 @@ lapackver = '3.4.2' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb index b9a8888c138..ca9498b8238 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb @@ -7,12 +7,12 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '1.5.14'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb index f290e77248b..181d9fb2668 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb @@ -7,12 +7,12 @@ lapackver = '3.4.2' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'gompi', 'version': '1.6.10'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb index 1e004c5ecd0..9f3ced2ae0c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb @@ -7,12 +7,12 @@ lapackver = '3.4.2' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb index 92aaef6a932..9126b595f3c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb @@ -7,12 +7,12 @@ lapackver = '3.5.0' versionsuffix = '-LAPACK-%s' % lapackver homepage = 'http://xianyi.github.com/OpenBLAS/' -# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 -toolchainopts = {'vectorize': False} description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" toolchain = {'name': 'GCC', 'version': '4.8.3'} +# need to build with -fno-tree-vectorize due to asm constraint bugs in OpenBLAS<0.3.6 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 +toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' From dccb6e7e852812c33c96ad5834969e82196c730e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 Mar 2019 09:40:54 +0100 Subject: [PATCH 0683/5331] restore checksums check for R-* easyconfigs --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a5af1ffc819..3f704f6ab9c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -342,7 +342,7 @@ def check_sha256_checksums(self, changed_ecs): # list of software for which checksums can not be required, # e.g. because 'source' files need to be constructed manually - whitelist = ['Kent_tools-*', 'MATLAB-*', 'R-*'] + whitelist = ['Kent_tools-*', 'MATLAB-*'] # the check_sha256_checksums function (again) creates an EasyBlock instance # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter From 1d51bf0572f90dc98328639f690d131334fa5ccb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 11:41:36 +0200 Subject: [PATCH 0684/5331] Use https instead of http. --- easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-8.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-8.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-8.2.0.eb index ad882bc7e73..561dfe9ce13 100644 --- a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'JasPer' version = '2.0.14' -homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' description = """ The JasPer Project is an open-source initiative to provide a free @@ -14,7 +14,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] +source_urls = ['https://www.ece.uvic.ca/~frodo/jasper/software/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2a1f61e55afe8b4ce8115e1508c5d7cb314d56dfcc2dd323f90c072f88ccf57b'] From 51f9bbb0f602620da2d3ef2909099425cd72a0e8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 12:28:13 +0200 Subject: [PATCH 0685/5331] Moving HDF5 down from intel to iimpi level. --- .../h/HDF5/HDF5-1.10.5-iimpi-2019a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpi-2019a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpi-2019a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpi-2019a.eb new file mode 100644 index 00000000000..3494ee7509d --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpi-2019a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.5' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From 25c82ab6787da2c9b177f1338f9abe9c04aa9ded Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 12:30:45 +0200 Subject: [PATCH 0686/5331] Now removing the intel version of HDF5 --- .../h/HDF5/HDF5-1.10.5-intel-2019a.eb | 21 ------------------- 1 file changed, 21 deletions(-) delete mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-intel-2019a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-intel-2019a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-intel-2019a.eb deleted file mode 100644 index e66cab5c6e3..00000000000 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-intel-2019a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HDF5' -version = '1.10.5' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'intel', 'version': '2019a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8'] - -dependencies = [ - ('zlib', '1.2.11'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' From 7ee10f2bbd0dae16b15b7ac16f1ddb756b26820c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 Mar 2019 12:01:09 +0100 Subject: [PATCH 0687/5331] add missing checksums in OpenBLAS easyconfigs --- .../OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb | 22 ++++++++++++------ .../OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb | 22 ++++++++++++------ .../OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb | 22 ++++++++++++------ ...enBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb | 22 ++++++++++++------ ...BLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 22 ++++++++++++------ ...BLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb | 22 ++++++++++++------ ...BLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb | 22 ++++++++++++------ ...BLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb | 21 +++++++++++------ ...BLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb | 21 +++++++++++------ ...BLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb | 21 +++++++++++------ ...nBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb | 21 +++++++++++------ ...BLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb | 22 ++++++++++++------ ...BLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb | 22 ++++++++++++------ ...nBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb | 21 +++++++++++------ ...BLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb | 21 +++++++++++------ .../OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb | 15 ++++++------ .../OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb | 15 ++++++------ .../OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb | 15 ++++++------ ...penBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb | 23 +++++++++++++------ ...OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb | 23 +++++++++++++------ ...penBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb | 22 ++++++++++++------ ...penBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb | 22 ++++++++++++------ ...OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb | 22 ++++++++++++------ .../OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb | 22 ++++++++++++------ 24 files changed, 332 insertions(+), 171 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb index cadddb81c53..98a4fa6b3ef 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb @@ -17,24 +17,32 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + 'b41f71f46faab1215f6f6d17541113dc01fd4d8fee0694f3f459bc2e3c2aaaaf', # v0.2.12.tar.gz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb index 60a9f533007..6708bb0e237 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb @@ -17,24 +17,32 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '5f1f986a1900949058b578c61c2b65b4de324f1968ec505daeb526b9f9af14ab', # v0.2.13.tar.gz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb index 2efaaef7549..e8d9eb15508 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb @@ -17,24 +17,32 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '5f1f986a1900949058b578c61c2b65b4de324f1968ec505daeb526b9f9af14ab', # v0.2.13.tar.gz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb index 0bd7ff6f9ee..c98084c42a6 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb @@ -17,24 +17,32 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '5f1f986a1900949058b578c61c2b65b4de324f1968ec505daeb526b9f9af14ab', # v0.2.13.tar.gz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb index 190b7e7fe8e..d62b8d22580 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb @@ -17,24 +17,32 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '2411c4f56f477b42dff54db2b7ffc0b7cf53bb9778d54982595c64cc69c40fc1', # v0.2.14.tar.gz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb index bc5858105ff..4d9684f07bd 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb @@ -17,24 +17,32 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '2411c4f56f477b42dff54db2b7ffc0b7cf53bb9778d54982595c64cc69c40fc1', # v0.2.14.tar.gz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb index 0804dd246d7..31b79273887 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb @@ -17,24 +17,32 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '73c40ace5978282224e5e122a41c8388c5a19e65a6f2329c2b7c0b61bacc9044', # v0.2.15.tar.gz + 'a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3', # lapack-3.6.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3', # lapack-3.6.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb index 1a93514d7c9..883d4c52664 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb @@ -22,23 +22,30 @@ lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' -sources = [ - 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, + large_src, + timing_src, +] patches = [ (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '7d9f8d4ea4a65ab68088f3bb557f03a7ac9cb5036ef2ba30546c3a28774a4112', # v0.2.18.tar.gz + 'a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3', # lapack-3.6.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb index bc518824023..91f0dd2f2c8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb @@ -22,23 +22,30 @@ lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' -sources = [ - 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, + large_src, + timing_src, +] patches = [ (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '7d9f8d4ea4a65ab68088f3bb557f03a7ac9cb5036ef2ba30546c3a28774a4112', # v0.2.18.tar.gz + 'a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3', # lapack-3.6.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb index d0262db45ff..2862a78a8c4 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb @@ -22,23 +22,30 @@ lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' -sources = [ - 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, + large_src, + timing_src, +] patches = [ (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '7d9f8d4ea4a65ab68088f3bb557f03a7ac9cb5036ef2ba30546c3a28774a4112', # v0.2.18.tar.gz + 'a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3', # lapack-3.6.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb index 0b95db667b4..599fa42b7ec 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb @@ -22,23 +22,30 @@ lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' -sources = [ - 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, + large_src, + timing_src, +] patches = [ (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '7d9f8d4ea4a65ab68088f3bb557f03a7ac9cb5036ef2ba30546c3a28774a4112', # v0.2.18.tar.gz + '888a50d787a9d828074db581c80b2d22bdb91435a673b1bf6cd6eb51aa50d1de', # lapack-3.6.1.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb index 158659dec4e..02671670ad6 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb @@ -22,24 +22,32 @@ lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' -sources = [ - 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, + large_src, + timing_src, +] patches = [ (large_src, '.'), (timing_src, '.'), 'OpenBLAS-%(version)s_LAPACK-3.7.0-fixes.patch', ] +checksums = [ + '9c40b5e4970f27c5f6911cb0a28aa26b6c83f17418b69f8e5a116bb983ca8557', # v0.2.19.tar.gz + 'ed967e4307e986474ab02eb810eed1d1adc73f5e1e3bc78fb009f6fe766db3be', # lapack-3.7.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'a965fef840eb93e120cd24b945ab4def1c6194946ed02f8107e5e626018bb03d', # OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb index c192849f46e..9b8a929d099 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb @@ -22,24 +22,32 @@ lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' -sources = [ - 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, + large_src, + timing_src, +] patches = [ (large_src, '.'), (timing_src, '.'), 'OpenBLAS-%(version)s_LAPACK-3.7.0-fixes.patch', ] +checksums = [ + '9c40b5e4970f27c5f6911cb0a28aa26b6c83f17418b69f8e5a116bb983ca8557', # v0.2.19.tar.gz + 'ed967e4307e986474ab02eb810eed1d1adc73f5e1e3bc78fb009f6fe766db3be', # lapack-3.7.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'a965fef840eb93e120cd24b945ab4def1c6194946ed02f8107e5e626018bb03d', # OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb index 3dcc146a85a..7428b231bca 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb @@ -22,23 +22,30 @@ lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' -sources = [ - 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, + large_src, + timing_src, +] patches = [ (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '9c40b5e4970f27c5f6911cb0a28aa26b6c83f17418b69f8e5a116bb983ca8557', # v0.2.19.tar.gz + '888a50d787a9d828074db581c80b2d22bdb91435a673b1bf6cd6eb51aa50d1de', # lapack-3.6.1.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb index eba6cb31aa5..969d55db465 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb @@ -22,23 +22,30 @@ lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' -sources = [ - 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, + large_src, + timing_src, +] patches = [ (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '9c40b5e4970f27c5f6911cb0a28aa26b6c83f17418b69f8e5a116bb983ca8557', # v0.2.19.tar.gz + '888a50d787a9d828074db581c80b2d22bdb91435a673b1bf6cd6eb51aa50d1de', # lapack-3.6.1.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb index 1ec366a48ad..f6397935d4c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb @@ -20,8 +20,14 @@ source_urls = [ 'https://github.com/xianyi/OpenBLAS/archive/', ] sources = ['v%(version)s.tar.gz'] +patches = [ + (large_src, '.'), + (timing_src, '.'), + 'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch', + 'OpenBLAS-%(version)s_revert-honor-cpuset.patch', +] checksums = [ - '5ef38b15d9c652985774869efd548b8e3e972e1e99475c673b25537ed7bcf394', # v0.2.20.tar.gz (OpenBLAS) + '5ef38b15d9c652985774869efd548b8e3e972e1e99475c673b25537ed7bcf394', # v0.2.20.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.2.20_fix-Intel-L1-cache-size-detection.patch @@ -29,13 +35,6 @@ checksums = [ '1e6a046ab658c6e0b351de901d2812db28c2042f9f141416144c2faaf71fbb37', # OpenBLAS-0.2.20_revert-honor-cpuset.patch ] -patches = [ - (large_src, '.'), - (timing_src, '.'), - 'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch', - 'OpenBLAS-%(version)s_revert-honor-cpuset.patch', -] - skipsteps = ['configure'] buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb index 791558473da..a7e11d238e5 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb @@ -20,8 +20,14 @@ source_urls = [ 'https://github.com/xianyi/OpenBLAS/archive/', ] sources = ['v%(version)s.tar.gz'] +patches = [ + (large_src, '.'), + (timing_src, '.'), + 'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch', + 'OpenBLAS-%(version)s_revert-honor-cpuset.patch', +] checksums = [ - '5ef38b15d9c652985774869efd548b8e3e972e1e99475c673b25537ed7bcf394', # v0.2.20.tar.gz (OpenBLAS) + '5ef38b15d9c652985774869efd548b8e3e972e1e99475c673b25537ed7bcf394', # v0.2.20.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.2.20_fix-Intel-L1-cache-size-detection.patch @@ -29,13 +35,6 @@ checksums = [ '1e6a046ab658c6e0b351de901d2812db28c2042f9f141416144c2faaf71fbb37', # OpenBLAS-0.2.20_revert-honor-cpuset.patch ] -patches = [ - (large_src, '.'), - (timing_src, '.'), - 'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch', - 'OpenBLAS-%(version)s_revert-honor-cpuset.patch', -] - skipsteps = ['configure'] buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb index e07336992ee..f1d924ffaae 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb @@ -20,8 +20,14 @@ source_urls = [ 'https://github.com/xianyi/OpenBLAS/archive/', ] sources = ['v%(version)s.tar.gz'] +patches = [ + (large_src, '.'), + (timing_src, '.'), + 'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch', + 'OpenBLAS-%(version)s_revert-honor-cpuset.patch', +] checksums = [ - '5ef38b15d9c652985774869efd548b8e3e972e1e99475c673b25537ed7bcf394', # v0.2.20.tar.gz (OpenBLAS) + '5ef38b15d9c652985774869efd548b8e3e972e1e99475c673b25537ed7bcf394', # v0.2.20.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.2.20_fix-Intel-L1-cache-size-detection.patch @@ -29,13 +35,6 @@ checksums = [ '1e6a046ab658c6e0b351de901d2812db28c2042f9f141416144c2faaf71fbb37', # OpenBLAS-0.2.20_revert-honor-cpuset.patch ] -patches = [ - (large_src, '.'), - (timing_src, '.'), - 'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch', - 'OpenBLAS-%(version)s_revert-honor-cpuset.patch', -] - skipsteps = ['configure'] buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb index a13ae351ea0..15825afb716 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb @@ -17,25 +17,34 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '002f267b44a2cb2d94e89ac4a785923ef6597f0a17cc3ef4b5af9e4a431da716', # v0.2.6.tar.gz + '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '6b588ec03e76243b1fb7e1693e6f45d6dceef4e11761740b339ed4df31648e32', # OpenBLAS-0.2.6_Makefile-LAPACK-sources.patch + '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb index c244a65819c..e4504f5337b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb @@ -17,25 +17,34 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '002f267b44a2cb2d94e89ac4a785923ef6597f0a17cc3ef4b5af9e4a431da716', # v0.2.6.tar.gz + '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '6b588ec03e76243b1fb7e1693e6f45d6dceef4e11761740b339ed4df31648e32', # OpenBLAS-0.2.6_Makefile-LAPACK-sources.patch + '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb index ca9498b8238..f4bcdfa799b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb @@ -17,24 +17,32 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '359f5cd2604ed76d97b0669b9b846a59a1d0283065d23f8847956629871fedd8', # v0.2.8.tar.gz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb index 181d9fb2668..6dc49672723 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb @@ -17,24 +17,32 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '359f5cd2604ed76d97b0669b9b846a59a1d0283065d23f8847956629871fedd8', # v0.2.8.tar.gz + '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb index 9f3ced2ae0c..97c7b9dedf2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb @@ -17,24 +17,32 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + '359f5cd2604ed76d97b0669b9b846a59a1d0283065d23f8847956629871fedd8', # v0.2.8.tar.gz + '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb index 9126b595f3c..e44c9ad5ca8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb @@ -17,24 +17,32 @@ toolchainopts = {'vectorize': False} lapack_src = 'lapack-%s.tgz' % lapackver large_src = 'large.tgz' timing_src = 'timing.tgz' -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] - +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] patches = [ (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir (large_src, '.'), (timing_src, '.'), ] +checksums = [ + 'a9ce75fe29f8527467b159490facca0bfc62e8a40a165b51822caa46368b0dc0', # v0.2.9.tar.gz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] skipsteps = ['configure'] From 96fbc63e2892ccad1ac81cb5d02d89a6db8c7d89 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 13:26:25 +0200 Subject: [PATCH 0688/5331] Moving netCDF down from intel to iimpi level. --- .../n/netCDF/netCDF-4.6.2-iimpi-2019a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-iimpi-2019a.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-iimpi-2019a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-iimpi-2019a.eb new file mode 100644 index 00000000000..db5bf6c01d6 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-iimpi-2019a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.6.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['673936c76ae0c496f6dde7e077f5be480afc1e300adb2c200bf56fbe22e5a82a'] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.13.3'), + ('Doxygen', '1.8.15'), +] + +dependencies = [ + ('HDF5', '1.10.5'), + ('cURL', '7.63.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' From dd2be1705c90cdb74831a32e50566b89521af2a8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 13:27:34 +0200 Subject: [PATCH 0689/5331] Now removing the intel version of netCDF --- .../n/netCDF/netCDF-4.6.2-intel-2019a.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-intel-2019a.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-intel-2019a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-intel-2019a.eb deleted file mode 100644 index 5162677e923..00000000000 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-intel-2019a.eb +++ /dev/null @@ -1,34 +0,0 @@ -name = 'netCDF' -version = '4.6.2' - -homepage = 'http://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'intel', 'version': '2019a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['673936c76ae0c496f6dde7e077f5be480afc1e300adb2c200bf56fbe22e5a82a'] - -builddependencies = [ - ('Autotools', '20180311'), - ('CMake', '3.13.3'), - ('Doxygen', '1.8.15'), -] - -dependencies = [ - ('HDF5', '1.10.5'), - ('cURL', '7.63.0'), - ('Szip', '2.1.1'), -] - -# make sure both static and shared libs are built -configopts = [ - "-DBUILD_SHARED_LIBS=OFF ", - "-DBUILD_SHARED_LIBS=ON ", -] - -moduleclass = 'data' From d07bd94ca5d76cb827dc29c5a8a5646305654200 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 13:39:58 +0200 Subject: [PATCH 0690/5331] Moving netCDF-Fortran down from intel to iimpi level. --- .../netCDF-Fortran-4.4.5-iimpi-2019a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-iimpi-2019a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-iimpi-2019a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-iimpi-2019a.eb new file mode 100644 index 00000000000..63b6e4fcd87 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-iimpi-2019a.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.4.5' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['01643461ac42d1986e38a052eb021135bae5b6cd592373fb44cf832236791c03'] + +dependencies = [('netCDF', '4.6.2')] + +moduleclass = 'data' From 2aedd0db0a92af682632da96c5f37ca765e0b2de Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 13:41:09 +0200 Subject: [PATCH 0691/5331] Now removing the intel version of netCDF-Fortran --- .../netCDF-Fortran-4.4.5-intel-2019a.eb | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-intel-2019a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-intel-2019a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-intel-2019a.eb deleted file mode 100644 index 4127d0f2a56..00000000000 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-intel-2019a.eb +++ /dev/null @@ -1,18 +0,0 @@ -name = 'netCDF-Fortran' -version = '4.4.5' - -homepage = 'http://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'intel', 'version': '2019a'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['01643461ac42d1986e38a052eb021135bae5b6cd592373fb44cf832236791c03'] - -dependencies = [('netCDF', '4.6.2')] - -moduleclass = 'data' From eb9e97073e05de6add70bc462db68de30ee8a697 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 Mar 2019 13:17:31 +0100 Subject: [PATCH 0692/5331] avoid duplicating 'patches' in 'sources' in OpenBLAS easyconfigs (+ cleanup) --- .../OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb | 19 ++++--------------- .../OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb | 19 ++++--------------- .../OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb | 19 ++++--------------- ...enBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb | 19 ++++--------------- ...BLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb | 19 ++++--------------- ...BLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb | 19 ++++--------------- ...BLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb | 19 ++++--------------- ...BLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb | 14 +++----------- ...BLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb | 14 +++----------- ...BLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb | 14 +++----------- ...BLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb | 14 +++----------- ...nBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb | 14 +++----------- ...BLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb | 14 +++----------- ...BLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb | 14 +++----------- ...nBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb | 14 +++----------- ...BLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb | 14 +++----------- .../OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb | 7 ++----- .../OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb | 7 ++----- .../OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb | 7 ++----- ...penBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb | 19 ++++--------------- ...OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb | 19 ++++--------------- ...penBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb | 19 ++++--------------- ...penBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb | 19 ++++--------------- ...OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb | 19 ++++--------------- .../OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb | 19 ++++--------------- .../OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb | 7 ++----- .../OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb | 7 ++----- .../OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb | 7 ++----- .../OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb | 7 ++----- .../OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb | 7 ++----- .../OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb | 7 ++----- 31 files changed, 97 insertions(+), 339 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb index 98a4fa6b3ef..788c949bbb7 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.12-GCC-4.9.2-LAPACK-3.5.0.eb @@ -14,34 +14,23 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ 'b41f71f46faab1215f6f6d17541113dc01fd4d8fee0694f3f459bc2e3c2aaaaf', # v0.2.12.tar.gz '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb index 6708bb0e237..535a4fd13c8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.8.4-LAPACK-3.5.0.eb @@ -14,34 +14,23 @@ toolchain = {'name': 'GCC', 'version': '4.8.4'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '5f1f986a1900949058b578c61c2b65b4de324f1968ec505daeb526b9f9af14ab', # v0.2.13.tar.gz '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb index e8d9eb15508..0ff754e0dd8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-GCC-4.9.2-LAPACK-3.5.0.eb @@ -14,34 +14,23 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '5f1f986a1900949058b578c61c2b65b4de324f1968ec505daeb526b9f9af14ab', # v0.2.13.tar.gz '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb index c98084c42a6..70e7249bcee 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb @@ -14,34 +14,23 @@ toolchain = {'name': 'gompi', 'version': '1.5.16'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '5f1f986a1900949058b578c61c2b65b4de324f1968ec505daeb526b9f9af14ab', # v0.2.13.tar.gz '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb index d62b8d22580..c5c9b909fb1 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb @@ -14,34 +14,23 @@ toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '2411c4f56f477b42dff54db2b7ffc0b7cf53bb9778d54982595c64cc69c40fc1', # v0.2.14.tar.gz '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb index 4d9684f07bd..a796b388742 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb @@ -14,34 +14,23 @@ toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '2411c4f56f477b42dff54db2b7ffc0b7cf53bb9778d54982595c64cc69c40fc1', # v0.2.14.tar.gz '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb index 31b79273887..cdc5e8d7930 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.15-GCC-4.9.3-2.25-LAPACK-3.6.0.eb @@ -14,34 +14,23 @@ toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '73c40ace5978282224e5e122a41c8388c5a19e65a6f2329c2b7c0b61bacc9044', # v0.2.15.tar.gz 'a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3', # lapack-3.6.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - 'a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3', # lapack-3.6.0.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb index 883d4c52664..ec8941ab4ba 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-4.9.4-2.25-LAPACK-3.6.0.eb @@ -14,10 +14,6 @@ toolchain = {'name': 'GCC', 'version': '4.9.4-2.25'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' - lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' @@ -30,21 +26,17 @@ source_urls = [ ] sources = [ 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, + {'filename': 'lapack-%s.tgz' % lapackver, 'extract_cmd': lapack_unpack_cmd}, ] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '7d9f8d4ea4a65ab68088f3bb557f03a7ac9cb5036ef2ba30546c3a28774a4112', # v0.2.18.tar.gz 'a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3', # lapack-3.6.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb index 91f0dd2f2c8..8fcc8fed466 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0.eb @@ -14,10 +14,6 @@ toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' - lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' @@ -30,21 +26,17 @@ source_urls = [ ] sources = [ 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, + {'filename': 'lapack-%s.tgz' % lapackver, 'extract_cmd': lapack_unpack_cmd}, ] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '7d9f8d4ea4a65ab68088f3bb557f03a7ac9cb5036ef2ba30546c3a28774a4112', # v0.2.18.tar.gz 'a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3', # lapack-3.6.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb index 2862a78a8c4..92ea1c7cd13 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.0.eb @@ -14,10 +14,6 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' - lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' @@ -30,21 +26,17 @@ source_urls = [ ] sources = [ 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, + {'filename': 'lapack-%s.tgz' % lapackver, 'extract_cmd': lapack_unpack_cmd}, ] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '7d9f8d4ea4a65ab68088f3bb557f03a7ac9cb5036ef2ba30546c3a28774a4112', # v0.2.18.tar.gz 'a9a0082c918fe14e377bbd570057616768dca76cbdc713457d8199aaa233ffc3', # lapack-3.6.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb index 3a93b27e449..768f1d2dc8e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -14,10 +14,6 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' - lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' @@ -30,21 +26,17 @@ source_urls = [ ] sources = [ 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, + {'filename': 'lapack-%s.tgz' % lapackver, 'extract_cmd': lapack_unpack_cmd}, ] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '7d9f8d4ea4a65ab68088f3bb557f03a7ac9cb5036ef2ba30546c3a28774a4112', # v0.2.18.tar.gz '888a50d787a9d828074db581c80b2d22bdb91435a673b1bf6cd6eb51aa50d1de', # lapack-3.6.1.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb index 599fa42b7ec..da966fba0b8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-gompi-2016.07-LAPACK-3.6.1.eb @@ -14,10 +14,6 @@ toolchain = {'name': 'gompi', 'version': '2016.07'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' - lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' @@ -30,21 +26,17 @@ source_urls = [ ] sources = [ 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, + {'filename': 'lapack-%s.tgz' % lapackver, 'extract_cmd': lapack_unpack_cmd}, ] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '7d9f8d4ea4a65ab68088f3bb557f03a7ac9cb5036ef2ba30546c3a28774a4112', # v0.2.18.tar.gz '888a50d787a9d828074db581c80b2d22bdb91435a673b1bf6cd6eb51aa50d1de', # lapack-3.6.1.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb index 02671670ad6..2fdf7732aee 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-5.4.0-2.26-LAPACK-3.7.0.eb @@ -14,10 +14,6 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' - lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' @@ -30,13 +26,11 @@ source_urls = [ ] sources = [ 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, + {'filename': 'lapack-%s.tgz' % lapackver, 'extract_cmd': lapack_unpack_cmd}, ] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), 'OpenBLAS-%(version)s_LAPACK-3.7.0-fixes.patch', ] checksums = [ @@ -44,8 +38,6 @@ checksums = [ 'ed967e4307e986474ab02eb810eed1d1adc73f5e1e3bc78fb009f6fe766db3be', # lapack-3.7.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz 'a965fef840eb93e120cd24b945ab4def1c6194946ed02f8107e5e626018bb03d', # OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb index 9b8a929d099..d7ab3a85534 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-GCC-6.3.0-2.27-LAPACK-3.7.0.eb @@ -14,10 +14,6 @@ toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' - lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' @@ -30,13 +26,11 @@ source_urls = [ ] sources = [ 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, + {'filename': 'lapack-%s.tgz' % lapackver, 'extract_cmd': lapack_unpack_cmd}, ] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), 'OpenBLAS-%(version)s_LAPACK-3.7.0-fixes.patch', ] checksums = [ @@ -44,8 +38,6 @@ checksums = [ 'ed967e4307e986474ab02eb810eed1d1adc73f5e1e3bc78fb009f6fe766db3be', # lapack-3.7.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz 'a965fef840eb93e120cd24b945ab4def1c6194946ed02f8107e5e626018bb03d', # OpenBLAS-0.2.19_LAPACK-3.7.0-fixes.patch ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb index 7428b231bca..077ae4120ec 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompi-2016.09-LAPACK-3.6.1.eb @@ -14,10 +14,6 @@ toolchain = {'name': 'gompi', 'version': '2016.09'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' - lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' @@ -30,21 +26,17 @@ source_urls = [ ] sources = [ 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, + {'filename': 'lapack-%s.tgz' % lapackver, 'extract_cmd': lapack_unpack_cmd}, ] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '9c40b5e4970f27c5f6911cb0a28aa26b6c83f17418b69f8e5a116bb983ca8557', # v0.2.19.tar.gz '888a50d787a9d828074db581c80b2d22bdb91435a673b1bf6cd6eb51aa50d1de', # lapack-3.6.1.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb index 969d55db465..029338e5e6e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.19-gompic-2016.10-LAPACK-3.6.1.eb @@ -14,10 +14,6 @@ toolchain = {'name': 'gompic', 'version': '2016.10'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' - lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' lapack_unpack_cmd += 'mkdir lapack-netlib;' lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' @@ -30,21 +26,17 @@ source_urls = [ ] sources = [ 'v%(version)s.tar.gz', - {'filename': lapack_src, 'extract_cmd': lapack_unpack_cmd}, - large_src, - timing_src, + {'filename': 'lapack-%s.tgz' % lapackver, 'extract_cmd': lapack_unpack_cmd}, ] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '9c40b5e4970f27c5f6911cb0a28aa26b6c83f17418b69f8e5a116bb983ca8557', # v0.2.19.tar.gz '888a50d787a9d828074db581c80b2d22bdb91435a673b1bf6cd6eb51aa50d1de', # lapack-3.6.1.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb index f6397935d4c..0ff6ec34067 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-5.4.0-2.26.eb @@ -11,9 +11,6 @@ toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -large_src = 'large.tgz' -timing_src = 'timing.tgz' - source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble 'http://www.netlib.org/lapack/timing/', @@ -21,8 +18,8 @@ source_urls = [ ] sources = ['v%(version)s.tar.gz'] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), 'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch', 'OpenBLAS-%(version)s_revert-honor-cpuset.patch', ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb index a7e11d238e5..0f7828d6d89 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-6.4.0-2.28.eb @@ -11,9 +11,6 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -large_src = 'large.tgz' -timing_src = 'timing.tgz' - source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble 'http://www.netlib.org/lapack/timing/', @@ -21,8 +18,8 @@ source_urls = [ ] sources = ['v%(version)s.tar.gz'] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), 'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch', 'OpenBLAS-%(version)s_revert-honor-cpuset.patch', ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb index f1d924ffaae..1c654e4bf97 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.20-GCC-7.2.0-2.29.eb @@ -11,9 +11,6 @@ toolchain = {'name': 'GCC', 'version': '7.2.0-2.29'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -large_src = 'large.tgz' -timing_src = 'timing.tgz' - source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble 'http://www.netlib.org/lapack/timing/', @@ -21,8 +18,8 @@ source_urls = [ ] sources = ['v%(version)s.tar.gz'] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), 'OpenBLAS-%(version)s_fix-Intel-L1-cache-size-detection.patch', 'OpenBLAS-%(version)s_revert-honor-cpuset.patch', ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb index 15825afb716..48538bacfec 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb @@ -14,32 +14,21 @@ toolchain = {'name': 'gompi', 'version': '1.4.10'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '002f267b44a2cb2d94e89ac4a785923ef6597f0a17cc3ef4b5af9e4a431da716', # v0.2.6.tar.gz - '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz '6b588ec03e76243b1fb7e1693e6f45d6dceef4e11761740b339ed4df31648e32', # OpenBLAS-0.2.6_Makefile-LAPACK-sources.patch '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb index e4504f5337b..64716621c9d 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.6-ictce-5.3.0-LAPACK-3.4.2.eb @@ -14,32 +14,21 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ 'OpenBLAS-%(version)s_Makefile-LAPACK-sources.patch', - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '002f267b44a2cb2d94e89ac4a785923ef6597f0a17cc3ef4b5af9e4a431da716', # v0.2.6.tar.gz - '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz '6b588ec03e76243b1fb7e1693e6f45d6dceef4e11761740b339ed4df31648e32', # OpenBLAS-0.2.6_Makefile-LAPACK-sources.patch '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb index f4bcdfa799b..406dc8c01ef 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.5.14-LAPACK-3.5.0.eb @@ -14,34 +14,23 @@ toolchain = {'name': 'gompi', 'version': '1.5.14'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '359f5cd2604ed76d97b0669b9b846a59a1d0283065d23f8847956629871fedd8', # v0.2.8.tar.gz '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb index 6dc49672723..6d0c8e18456 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-gompi-1.6.10-LAPACK-3.4.2.eb @@ -14,34 +14,23 @@ toolchain = {'name': 'gompi', 'version': '1.6.10'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '359f5cd2604ed76d97b0669b9b846a59a1d0283065d23f8847956629871fedd8', # v0.2.8.tar.gz '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb index 97c7b9dedf2..67fb3b7ce27 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.8-ictce-5.3.0-LAPACK-3.4.2.eb @@ -14,34 +14,23 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '359f5cd2604ed76d97b0669b9b846a59a1d0283065d23f8847956629871fedd8', # v0.2.8.tar.gz '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '60a65daaf16ec315034675942618a2230521ea7adf85eea788ee54841072faf0', # lapack-3.4.2.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb index e44c9ad5ca8..6b89d2dfdbb 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.9-GCC-4.8.3-LAPACK-3.5.0.eb @@ -14,34 +14,23 @@ toolchain = {'name': 'GCC', 'version': '4.8.3'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -lapack_src = 'lapack-%s.tgz' % lapackver -large_src = 'large.tgz' -timing_src = 'timing.tgz' source_urls = [ # order matters, trying to download the LAPACK tarball from GitHub causes trouble "http://www.netlib.org/lapack/", "http://www.netlib.org/lapack/timing/", "https://github.com/xianyi/OpenBLAS/archive/", ] -sources = [ - 'v%(version)s.tar.gz', - lapack_src, - large_src, - timing_src, -] +sources = ['v%(version)s.tar.gz'] patches = [ - (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir - (large_src, '.'), - (timing_src, '.'), + ('lapack-%s.tgz' % lapackver, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ 'a9ce75fe29f8527467b159490facca0bfc62e8a40a165b51822caa46368b0dc0', # v0.2.9.tar.gz '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352', # lapack-3.5.0.tgz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb index 4a9cb36e996..5d837040002 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb @@ -11,9 +11,6 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -large_src = 'large.tgz' -timing_src = 'timing.tgz' - source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble 'http://www.netlib.org/lapack/timing/', @@ -21,8 +18,8 @@ source_urls = [ ] sources = ['v%(version)s.tar.gz'] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ 'cf51543709abe364d8ecfb5c09a2b533d2b725ea1a66f203509b21a8e9d8f1a1', # v0.3.0.tar.gz diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb index 6fd5cf7e3a0..9d5f65a1e35 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb @@ -11,9 +11,6 @@ toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -large_src = 'large.tgz' -timing_src = 'timing.tgz' - source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble 'http://www.netlib.org/lapack/timing/', @@ -21,8 +18,8 @@ source_urls = [ ] sources = ['v%(version)s.tar.gz'] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ 'cf51543709abe364d8ecfb5c09a2b533d2b725ea1a66f203509b21a8e9d8f1a1', # v0.3.0.tar.gz diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb index fb91851bfd1..a6985ac7ae7 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb @@ -11,9 +11,6 @@ toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -large_src = 'large.tgz' -timing_src = 'timing.tgz' - source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble 'http://www.netlib.org/lapack/timing/', @@ -21,8 +18,8 @@ source_urls = [ ] sources = ['v%(version)s.tar.gz'] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '1f5e956f35f3acdd3c74516e955d797a320c2e0135e31d838cbdb3ea94d0eb33', # v0.3.1.tar.gz diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb index 94de7863818..c2a8ad8469f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb @@ -11,9 +11,6 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -large_src = 'large.tgz' -timing_src = 'timing.tgz' - source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble 'http://www.netlib.org/lapack/timing/', @@ -21,8 +18,8 @@ source_urls = [ ] sources = ['v%(version)s.tar.gz'] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '49d88f4494ae780e3d7fa51769c00d982d7cdb73e696054ac3baa81d42f13bab', # v0.3.3.tar.gz diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb index bd0615ae66c..52547937c39 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb @@ -11,9 +11,6 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -large_src = 'large.tgz' -timing_src = 'timing.tgz' - source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble 'http://www.netlib.org/lapack/timing/', @@ -21,8 +18,8 @@ source_urls = [ ] sources = ['v%(version)s.tar.gz'] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '4b4b4453251e9edb5f57465bf2b3cf67b19d811d50c8588cdf2ea1f201bb834f', # v0.3.4.tar.gz diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb index ac9dcfbc69e..86d125db417 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb @@ -11,9 +11,6 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/7180 toolchainopts = {'vectorize': False} -large_src = 'large.tgz' -timing_src = 'timing.tgz' - source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble 'http://www.netlib.org/lapack/timing/', @@ -21,8 +18,8 @@ source_urls = [ ] sources = ['v%(version)s.tar.gz'] patches = [ - (large_src, '.'), - (timing_src, '.'), + ('large.tgz', '.'), + ('timing.tgz', '.'), ] checksums = [ '0950c14bd77c90a6427e26210d6dab422271bc86f9fc69126725833ecdaa0e85', # v0.3.5.tar.gz From 8b40e1bf868fd9f27e96bfd4e5519c186a323efd Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 15:52:17 +0200 Subject: [PATCH 0693/5331] adding easyconfigs: JasPer-1.900.1-GCCcore-8.2.0.eb --- .../j/JasPer/JasPer-1.900.1-GCCcore-8.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..a652adc8b32 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-GCCcore-8.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.ece.uvic.ca/~frodo/jasper/software/'] +sources = [SOURCELOWER_ZIP] +checksums = ['6b905a9c2aca2e275544212666eefc4eb44d95d0a57e4305457b407fe63f9494'] + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' From 4ca46c15a4123f8dde9c30116cfd01af7cbf77b3 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Sat, 2 Mar 2019 09:17:06 -0600 Subject: [PATCH 0694/5331] Updated FFTW checksum --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intelcuda-2017b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intelcuda-2017b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intelcuda-2017b.eb index 58fa737e8fa..2a4f7eaa04e 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intelcuda-2017b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.6-intelcuda-2017b.eb @@ -10,7 +10,7 @@ toolchainopts = {'pic': True} source_urls = [homepage] sources = ['fftw-%(version)s-pl2.tar.gz'] -checksums = ['927e481edbb32575397eb3d62535a856'] +checksums = ['a5de35c5c824a78a058ca54278c706cdf3d4abba1c56b63531c2cb05f5d57da2'] # no quad precision, requires GCC v4.6 or higher # see also From 17f5724129cf848fb4b46cd89d6eb1836798edbe Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 19:11:22 +0200 Subject: [PATCH 0695/5331] Downgrade util-linux version to match what 2018b toolchain uses. --- ...GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb index db184e9e865..5b386b0a84a 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-2.7.15.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('Python', '2.7.15'), - ('util-linux', '2.32.1'), + ('util-linux', '2.32'), ('GLib', '2.54.3'), ('libffi', '3.2.1'), ] From 132365a479d75d6ac11235be76d8ebd0429e731d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 19:18:33 +0200 Subject: [PATCH 0696/5331] Add checksums and fix minor style problem. --- .../p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb index 037f11f90e8..c850e08ec72 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb @@ -35,6 +35,7 @@ components = [ ('SIP', '4.19.13', { 'source_urls': ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'], 'sources': [SOURCELOWER_TAR_GZ], + 'checksum': 'e353a7056599bf5fbd5d3ff9842a6ab2ea3cf4e0304a0f925ec5862907c0d15e', 'start_dir': 'sip-%(version)s', 'configopts': sipcfgopts, 'options': {'modulename': 'PyQt4.sip'}, @@ -42,6 +43,7 @@ components = [ (name, version, { 'source_urls': ['http://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/%(name)s-%(version)s'], 'sources': ['%(name)s%(version_major)s_gpl_x11-%(version)s.tar.gz'], + 'checksum': 'a00f5abef240a7b5852b7924fa5fdf5174569525dc076cd368a566619e56d472', 'start_dir': '%(name)s%(version_major)s_gpl_x11-%(version)s', 'configopts': pyqtcfgopts, 'options': {'modulename': 'PyQt4.QtCore'}, @@ -55,7 +57,7 @@ modextrapaths = { sanity_check_paths = { 'files': ['bin/%s' % x for x in ['pyuic4', 'pyrcc4', 'pylupdate4']] + - [pylibdir + '/%%(name)s%%(version_major)s/%s.%s' % (x, SHLIB_EXT) for x in ['sip', 'QtCore', 'Qt']], + [pylibdir + '/%%(name)s%%(version_major)s/%s.%s' % (x, SHLIB_EXT) for x in ['sip', 'QtCore', 'Qt']], 'dirs': ['include', 'plugins', 'share/sip'], } From 1126d112f0f886ca4e05d5a0bfc496d5855c6797 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 19:24:58 +0200 Subject: [PATCH 0697/5331] Add check for libepoxy.so --- .../easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb index 7a73538541b..1a5ce595669 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb @@ -10,7 +10,6 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = ['https://github.com/anholt/%(name)s/releases/download/%(version)s'] sources = [SOURCE_TAR_XZ] -checksums = ['002958c5528321edd53440235d3c44e71b5b1e09b9177e8daf677450b6c4433d'] builddependencies = [ ('Meson', '0.48.1', '-Python-3.6.6'), @@ -25,7 +24,8 @@ dependencies = [ configopts = '-Degl=no --libdir %(installdir)s/lib ' sanity_check_paths = { - 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']], + 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + ['lib/libepoxy.%s' % SHLIB_EXT], 'dirs': ['lib'] } From 2ed9fb359a865abdd9303707a2e86f3b7e4ca798 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 19:55:52 +0200 Subject: [PATCH 0698/5331] Add missing builddep on binutils --- easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb index 55c68957d56..8a3e78b1884 100644 --- a/easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb @@ -10,7 +10,8 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = ['https://github.com/rockdaboot/%(name)s/releases/download/%(name)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['f8fd0aeb66252dfcc638f14d9be1e2362fdaf2ca86bde0444ff4d5cc961b560f'] + +builddependencies = [('binutils', '2.30')] sanity_check_paths = { 'files': ['bin/psl', 'lib/libpsl.a'], From 896d9351cf9b97913b2cc8a619371ec4a3f3e96a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 20:19:21 +0200 Subject: [PATCH 0699/5331] Fix typo --- .../p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb index c850e08ec72..4a5b0073af6 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb @@ -35,7 +35,7 @@ components = [ ('SIP', '4.19.13', { 'source_urls': ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'], 'sources': [SOURCELOWER_TAR_GZ], - 'checksum': 'e353a7056599bf5fbd5d3ff9842a6ab2ea3cf4e0304a0f925ec5862907c0d15e', + 'checksums': 'e353a7056599bf5fbd5d3ff9842a6ab2ea3cf4e0304a0f925ec5862907c0d15e', 'start_dir': 'sip-%(version)s', 'configopts': sipcfgopts, 'options': {'modulename': 'PyQt4.sip'}, @@ -43,7 +43,7 @@ components = [ (name, version, { 'source_urls': ['http://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/%(name)s-%(version)s'], 'sources': ['%(name)s%(version_major)s_gpl_x11-%(version)s.tar.gz'], - 'checksum': 'a00f5abef240a7b5852b7924fa5fdf5174569525dc076cd368a566619e56d472', + 'checksums': 'a00f5abef240a7b5852b7924fa5fdf5174569525dc076cd368a566619e56d472', 'start_dir': '%(name)s%(version_major)s_gpl_x11-%(version)s', 'configopts': pyqtcfgopts, 'options': {'modulename': 'PyQt4.QtCore'}, From f18172bd8c17e4a2d93b31ee98ea482219ebcd1a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 Mar 2019 19:25:45 +0100 Subject: [PATCH 0700/5331] trim down test configuration: only test with Lmod 6.x with Tcl/Lua on Python 2.6/2.7 --- .travis.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/.travis.yml b/.travis.yml index 71f98d05283..48752dbee10 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,12 +2,7 @@ language: python python: 2.6 env: matrix: - - ENV_MOD_VERSION=3.2.10 EASYBUILD_MODULES_TOOL=EnvironmentModulesC EASYBUILD_MODULE_SYNTAX=Tcl - - LMOD_VERSION=6.6.3 - LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Tcl - - LMOD_VERSION=7.7.16 - - LMOD_VERSION=7.7.16 EASYBUILD_MODULE_SYNTAX=Tcl - - ENV_MOD_VERSION=4.0.0 EASYBUILD_MODULES_TOOL=EnvironmentModules EASYBUILD_MODULE_SYNTAX=Tcl matrix: # mark build as finished as soon as job has failed fast_finish: true From aec10ab96d73342ec798d34f7cd25ee2a6bbc603 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Sat, 2 Mar 2019 19:39:42 +0100 Subject: [PATCH 0701/5331] Remove Libxc-4.3.3 easyconfigs again --- .../l/libxc/libxc-4.3.3-foss-2018b.eb | 27 ------------------- .../l/libxc/libxc-4.3.3-intel-2018b.eb | 27 ------------------- 2 files changed, 54 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb delete mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb deleted file mode 100644 index e8fe242e82f..00000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.3-foss-2018b.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '4.3.3' - -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['99ed7a31c7ae19e364d341e2d4a02b108a9b4f45c7f5c5926c6108612784aff0'] - -configopts = '--enable-static --enable-shared --enable-fortran' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb deleted file mode 100644 index a67619a822d..00000000000 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.3-intel-2018b.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libxc' -version = '4.3.3' - -homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' -description = """Libxc is a library of exchange-correlation functionals for density-functional theory. - The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" - -toolchain = {'name': 'intel', 'version': '2018b'} - -source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['99ed7a31c7ae19e364d341e2d4a02b108a9b4f45c7f5c5926c6108612784aff0'] - -configopts = '--enable-static --enable-shared --enable-fortran' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include'], -} - -parallel = 1 - -moduleclass = 'chem' From dd254f1c8409a9ab8f2c0796039e2d8317066eba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 2 Mar 2019 21:05:03 +0100 Subject: [PATCH 0702/5331] use %(pyshortver)s template in (old) SIP easyconfigs --- .../s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb | 12 ++++-------- .../s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb | 12 ++++-------- .../s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb | 12 ++++-------- .../s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb | 12 ++++-------- .../s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb | 12 ++++-------- 5 files changed, 20 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb index 90532985800..4ff93c9159e 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb @@ -5,6 +5,7 @@ easyblock = 'ConfigureMakePythonPackage' name = 'SIP' version = '4.16.4' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.riverbankcomputing.com/software/sip/' description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" @@ -14,19 +15,14 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [('Python', '2.7.9')] -dependencies = [(python, pyver)] - -pyshortver = '.'.join(pyver.split('.')[:2]) configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " -configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" sanity_check_paths = { 'files': ['bin/sip', 'include/sip.h'] + - ['lib/python%s/site-packages/%s' % (pyshortver, x) + ['lib/python%%(pyshortver)s/site-packages/%s' % x for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb index c121f5bccb9..3a568ee0f1f 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb @@ -5,6 +5,7 @@ easyblock = 'ConfigureMakePythonPackage' name = 'SIP' version = '4.16.4' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.riverbankcomputing.com/software/sip/' description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" @@ -14,19 +15,14 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [('Python', '2.7.9')] -dependencies = [(python, pyver)] - -pyshortver = '.'.join(pyver.split('.')[:2]) configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " -configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" sanity_check_paths = { 'files': ['bin/sip', 'include/sip.h'] + - ['lib/python%s/site-packages/%s' % (pyshortver, x) + ['lib/python%%(pyshortver)s/site-packages/%s' % x for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb index 472bc669cef..8d9d2b27404 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb @@ -5,6 +5,7 @@ easyblock = 'ConfigureMakePythonPackage' name = 'SIP' version = '4.16.8' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.riverbankcomputing.com/software/sip/' description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" @@ -14,19 +15,14 @@ toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [('Python', '2.7.9')] -dependencies = [(python, pyver)] - -pyshortver = '.'.join(pyver.split('.')[:2]) configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " -configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" sanity_check_paths = { 'files': ['bin/sip', 'include/sip.h'] + - ['lib/python%s/site-packages/%s' % (pyshortver, x) + ['lib/python%%(pyshortver)s/site-packages/%s' % x for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb index 4370af06f21..f6d67e81411 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb @@ -5,6 +5,7 @@ easyblock = 'ConfigureMakePythonPackage' name = 'SIP' version = '4.16.8' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.riverbankcomputing.com/software/sip/' description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" @@ -14,19 +15,14 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] -python = 'Python' -pyver = '2.7.8' -versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [('Python', '2.7.8')] -dependencies = [(python, pyver)] - -pyshortver = '.'.join(pyver.split('.')[:2]) configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " -configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" sanity_check_paths = { 'files': ['bin/sip', 'include/sip.h'] + - ['lib/python%s/site-packages/%s' % (pyshortver, x) + ['lib/python%%(pyshortver)s/site-packages/%s' % x for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb index fc5e6d4e1f3..8bd1eed95eb 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb @@ -5,6 +5,7 @@ easyblock = 'ConfigureMakePythonPackage' name = 'SIP' version = '4.16.8' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.riverbankcomputing.com/software/sip/' description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" @@ -14,19 +15,14 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] -python = 'Python' -pyver = '2.7.9' -versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [('Python', '2.7.9')] -dependencies = [(python, pyver)] - -pyshortver = '.'.join(pyver.split('.')[:2]) configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " -configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" sanity_check_paths = { 'files': ['bin/sip', 'include/sip.h'] + - ['lib/python%s/site-packages/%s' % (pyshortver, x) + ['lib/python%%(pyshortver)s/site-packages/%s' % x for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], 'dirs': [], } From a8575888dc80a975f616c37acc8e56923807c510 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 22:05:42 +0200 Subject: [PATCH 0703/5331] Add missing checksum --- easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb index 8a3e78b1884..77d273dd768 100644 --- a/easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.20.2-GCCcore-7.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = ['https://github.com/rockdaboot/%(name)s/releases/download/%(name)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['f8fd0aeb66252dfcc638f14d9be1e2362fdaf2ca86bde0444ff4d5cc961b560f'] builddependencies = [('binutils', '2.30')] From 13e77016250dd2e520f157cf64234b56e940269f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 2 Mar 2019 22:33:46 +0200 Subject: [PATCH 0704/5331] Add mising checksum --- .../easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb index 1a5ce595669..f97d491ba02 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-fosscuda-2018b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = ['https://github.com/anholt/%(name)s/releases/download/%(version)s'] sources = [SOURCE_TAR_XZ] +checksums = ['002958c5528321edd53440235d3c44e71b5b1e09b9177e8daf677450b6c4433d'] builddependencies = [ ('Meson', '0.48.1', '-Python-3.6.6'), From 0ccd75ec0eaa86bae8fca4dd9ddb09860510449d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 3 Mar 2019 09:24:54 +0100 Subject: [PATCH 0705/5331] archive ancient CUDA 5.0.35 easyconfigs with creative way of determining sources --- easybuild/easyconfigs/{ => __archive__}/c/CUDA/CUDA-5.0.35-1.eb | 0 .../{ => __archive__}/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/c/CUDA/CUDA-5.0.35-1.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb (100%) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb b/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-5.0.35-1.eb similarity index 100% rename from easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-1.eb rename to easybuild/easyconfigs/__archive__/c/CUDA/CUDA-5.0.35-1.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb b/easybuild/easyconfigs/__archive__/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb similarity index 100% rename from easybuild/easyconfigs/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb rename to easybuild/easyconfigs/__archive__/c/CUDA/CUDA-5.0.35-GCC-4.6.4-1.eb From 23ee5213a722d304990c241d6a27e2175b7674b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 3 Mar 2019 09:32:02 +0100 Subject: [PATCH 0706/5331] add missing checksums in old SIP easyconfigs --- .../easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb | 3 ++- .../easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb | 3 ++- .../easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb | 3 ++- .../easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb | 3 ++- .../easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb | 3 ++- 5 files changed, 10 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb index 4ff93c9159e..a6d3e74b40b 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb @@ -12,8 +12,9 @@ description = """SIP is a tool that makes it very easy to create Python bindings toolchain = {'name': 'goolf', 'version': '1.5.14'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ceda443fc5e129e67a067e2cd7b73ff037f8b10b50e407baa2b1d9f2199d57f5'] dependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb index 3a568ee0f1f..4b1b8cd7912 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb @@ -12,8 +12,9 @@ description = """SIP is a tool that makes it very easy to create Python bindings toolchain = {'name': 'intel', 'version': '2015a'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ceda443fc5e129e67a067e2cd7b73ff037f8b10b50e407baa2b1d9f2199d57f5'] dependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb index 8d9d2b27404..8d9614e1156 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb @@ -12,8 +12,9 @@ description = """SIP is a tool that makes it very easy to create Python bindings toolchain = {'name': 'foss', 'version': '2015a'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d3141b65e48a30c9ce36612f8bcd1730ebf02d044757e4d6c5234927e2063e18'] dependencies = [('Python', '2.7.9')] diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb index f6d67e81411..e9613c3e891 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb @@ -12,8 +12,9 @@ description = """SIP is a tool that makes it very easy to create Python bindings toolchain = {'name': 'intel', 'version': '2014b'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d3141b65e48a30c9ce36612f8bcd1730ebf02d044757e4d6c5234927e2063e18'] dependencies = [('Python', '2.7.8')] diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb index 8bd1eed95eb..e36d9994bf4 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb @@ -12,8 +12,9 @@ description = """SIP is a tool that makes it very easy to create Python bindings toolchain = {'name': 'intel', 'version': '2015a'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d3141b65e48a30c9ce36612f8bcd1730ebf02d044757e4d6c5234927e2063e18'] dependencies = [('Python', '2.7.9')] From 7f995965ea558b4d73cac0ccf36536fc38a00a27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 3 Mar 2019 09:35:44 +0100 Subject: [PATCH 0707/5331] fix Travis config to test with both Python 2.6 & 2.7 --- .travis.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 48752dbee10..1ba3bbcf630 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,12 +1,10 @@ language: python -python: 2.6 -env: - matrix: - - LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Tcl matrix: # mark build as finished as soon as job has failed fast_finish: true include: + - python: 2.6 + env: LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Tcl # also test default configuration with Python 2.7 - python: 2.7 env: LMOD_VERSION=6.6.3 From 097b15fe0142fa53ddd49152b496cde39af25ee9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 3 Mar 2019 09:39:52 +0100 Subject: [PATCH 0708/5331] also archive gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb which requires CUDA 5.0.35 --- .../g/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/g/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb (100%) diff --git a/easybuild/easyconfigs/g/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb b/easybuild/easyconfigs/__archive__/g/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb similarity index 100% rename from easybuild/easyconfigs/g/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb rename to easybuild/easyconfigs/__archive__/g/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb From 4209fc337d7368a748bffd46c45bb3b4ebf08228 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 3 Mar 2019 14:43:19 +0200 Subject: [PATCH 0709/5331] adding easyconfigs: netCDF-Fortran-4.4.5-gompi-2019a.eb --- .../h/HDF5/HDF5-1.10.5-gompi-2019a.eb | 21 ++++++++++++ .../netCDF-Fortran-4.4.5-gompi-2019a.eb | 18 ++++++++++ .../n/netCDF/netCDF-4.6.2-gompi-2019a.eb | 34 +++++++++++++++++++ 3 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-gompi-2019a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-gompi-2019a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-gompi-2019a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-gompi-2019a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-gompi-2019a.eb new file mode 100644 index 00000000000..7c8a9d1c7fe --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-gompi-2019a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.5' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-gompi-2019a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-gompi-2019a.eb new file mode 100644 index 00000000000..c8be80b5855 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.5-gompi-2019a.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.4.5' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['01643461ac42d1986e38a052eb021135bae5b6cd592373fb44cf832236791c03'] + +dependencies = [('netCDF', '4.6.2')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-gompi-2019a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-gompi-2019a.eb new file mode 100644 index 00000000000..b4917c8a804 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.6.2-gompi-2019a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.6.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['673936c76ae0c496f6dde7e077f5be480afc1e300adb2c200bf56fbe22e5a82a'] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.13.3'), + ('Doxygen', '1.8.15'), +] + +dependencies = [ + ('HDF5', '1.10.5'), + ('cURL', '7.63.0'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' From 51ea484eb2d0de68fc11ab5ab4d15d40dc5f5326 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 3 Mar 2019 19:35:59 +0200 Subject: [PATCH 0710/5331] checksums is a list. --- .../p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb index 4a5b0073af6..e178b5676b1 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb @@ -35,7 +35,7 @@ components = [ ('SIP', '4.19.13', { 'source_urls': ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'], 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': 'e353a7056599bf5fbd5d3ff9842a6ab2ea3cf4e0304a0f925ec5862907c0d15e', + 'checksums': ['e353a7056599bf5fbd5d3ff9842a6ab2ea3cf4e0304a0f925ec5862907c0d15e'], 'start_dir': 'sip-%(version)s', 'configopts': sipcfgopts, 'options': {'modulename': 'PyQt4.sip'}, @@ -43,7 +43,7 @@ components = [ (name, version, { 'source_urls': ['http://sourceforge.net/projects/pyqt/files/%(name)s%(version_major)s/%(name)s-%(version)s'], 'sources': ['%(name)s%(version_major)s_gpl_x11-%(version)s.tar.gz'], - 'checksums': 'a00f5abef240a7b5852b7924fa5fdf5174569525dc076cd368a566619e56d472', + 'checksums': ['a00f5abef240a7b5852b7924fa5fdf5174569525dc076cd368a566619e56d472'], 'start_dir': '%(name)s%(version_major)s_gpl_x11-%(version)s', 'configopts': pyqtcfgopts, 'options': {'modulename': 'PyQt4.QtCore'}, From 2413680ac83e92aa005a0c9e69c89f862a3e0678 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 3 Mar 2019 20:06:58 +0100 Subject: [PATCH 0711/5331] avoid 'dictionary changed size during iteration' problem in Python 3 in check_dep_vars --- test/easyconfigs/easyconfigs.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 616547f4f10..f146e43ffce 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -182,7 +182,8 @@ def check_dep_vars(dep, dep_vars): # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools elif dep == 'HTSlib' and len(dep_vars) > 1: - for key, ecs in dep_vars.items(): + for key in list(dep_vars): + ecs = dep_vars[key] # filter out HTSlib variants that are only used as dependency for BCFtools with same version htslib_ver = re.search('^version: (?P[^;]+);', key).group('ver') if all(ec.startswith('BCFtools-%s-' % htslib_ver) for ec in ecs): @@ -197,7 +198,7 @@ def check_dep_vars(dep, dep_vars): # for some dependencies, we allow exceptions for software that depends on a particular version, # as long as that's indicated by the versionsuffix elif dep in ['Boost', 'R', 'PLUMED'] and len(dep_vars) > 1: - for key in dep_vars.keys(): + for key in list(dep_vars): dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') # filter out dep version if all easyconfig filenames using it include specific dep version if all(re.search('-%s-%s' % (dep, dep_ver), v) for v in dep_vars[key]): @@ -208,7 +209,7 @@ def check_dep_vars(dep, dep_vars): # filter R dep for a specific version of Python 2.x if dep == 'R' and len(dep_vars) > 1: - for key in dep_vars.keys(): + for key in list(dep_vars): if '; versionsuffix: -Python-2' in key: dep_vars.pop(key) # always retain at least one variant @@ -228,7 +229,7 @@ def check_dep_vars(dep, dep_vars): # filter out variants that are specific to a particular version of CUDA cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] if len(dep_vars) > len(cuda_dep_vars): - for key in dep_vars.keys(): + for key in list(dep_vars): if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key): dep_vars.pop(key) @@ -242,7 +243,7 @@ def check_dep_vars(dep, dep_vars): 'Jellyfish': r'1\.', } if dep in old_dep_versions and len(dep_vars) > 1: - for key in dep_vars.keys(): + for key in list(dep_vars): # filter out known old dependency versions if re.search('^version: %s' % old_dep_versions[dep], key): dep_vars.pop(key) From 9f4cec9a235735fbf5af6144432d029620bb95ea Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 4 Mar 2019 08:48:15 +0100 Subject: [PATCH 0712/5331] Added extra patch to remove -B/usr/bin from linker_bin_path_flag in tensorflow-1.12.0/third_party/gpus/cuda_configure.bzl This prevents the wrong linker from being used. --- ...sorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb | 5 ++++- ...remove_usrbin_from_linker_bin_path_flag.patch | 16 ++++++++++++++++ 2 files changed, 20 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_remove_usrbin_from_linker_bin_path_flag.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb index 398047b5848..bbb79fac930 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb @@ -90,7 +90,8 @@ exts_list = [ 'TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.12.0_lrt-flag.patch', - 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch' + 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch', + 'TensorFlow-1.12.0_remove_usrbin_from_linker_bin_path_flag.patch' ], 'checksums': [ '3c87b81e37d4ed7f3da6200474fa5e656ffd20d8811068572f43610cae97ca92', # v1.12.0.tar.gz @@ -100,6 +101,8 @@ exts_list = [ '164d048c69671f870e306760ee7609564fe02bb6378a06414752f3d6da80a631', # TensorFlow-1.12.0_lrt-flag.patch # TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch '843acddc197639273cb26e676685a12a1107a3bccca516be1af873df6352bb00', + # TensorFlow-1.12.0_remove_usrbin_from_linker_bin_path_flag.patch + 'd57a2b90cd36ab9a013c946eb2a1d3aaef904cb657ca85e0f8c91c326e659bd6' ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_remove_usrbin_from_linker_bin_path_flag.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_remove_usrbin_from_linker_bin_path_flag.patch new file mode 100644 index 00000000000..1513cdbffe9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0_remove_usrbin_from_linker_bin_path_flag.patch @@ -0,0 +1,16 @@ +# Remove -B/usr/bin from linker_bin_path_flag, as it causes a possibly +# incompatible linker from the system to be used. +# +# Fokke Dijkstra, 20190228 +diff -ru tensorflow-1.12.0.orig/third_party/gpus/cuda_configure.bzl tensorflow-1.12.0/third_party/gpus/cuda_configure.bzl +--- tensorflow-1.12.0.orig/third_party/gpus/cuda_configure.bzl 2018-11-02 02:35:10.000000000 +0100 ++++ tensorflow-1.12.0/third_party/gpus/cuda_configure.bzl 2019-02-28 14:25:50.227358135 +0100 +@@ -1316,7 +1316,7 @@ + if should_download_clang: + cuda_defines["%{linker_bin_path_flag}"] = "" + else: +- cuda_defines["%{linker_bin_path_flag}"] = 'flag: "-B/usr/bin"' ++ cuda_defines["%{linker_bin_path_flag}"] = "" + + if is_cuda_clang: + cuda_defines["%{host_compiler_path}"] = str(cc) From 56e55e79ba52139bfaa086e390985f95f5cf1e94 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 4 Mar 2019 13:29:17 +0200 Subject: [PATCH 0713/5331] adding easyconfigs: ExaBayes-1.5-foss-2016b.eb --- .../e/ExaBayes/ExaBayes-1.5-foss-2016b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/ExaBayes/ExaBayes-1.5-foss-2016b.eb diff --git a/easybuild/easyconfigs/e/ExaBayes/ExaBayes-1.5-foss-2016b.eb b/easybuild/easyconfigs/e/ExaBayes/ExaBayes-1.5-foss-2016b.eb new file mode 100644 index 00000000000..45072fd9b8d --- /dev/null +++ b/easybuild/easyconfigs/e/ExaBayes/ExaBayes-1.5-foss-2016b.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'ExaBayes' +version = '1.5' + +homepage = 'https://cme.h-its.org/exelixis/web/software/exabayes/' +description = """ExaBayes is a software package for Bayesian tree inference. + It is particularly suitable for large-scale analyses on computer clusters""" + +# only tested with GCC < 6 +# https://groups.google.com/d/msg/exabayes/94tOvKRDq-s/F223g6qKCQAJ +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://cme.h-its.org/exelixis/resource/download/software/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e401f1b4645e67e8879d296807131d0ab79bba81a1cd5afea14d7c3838b095a2'] + +configopts = '--enable-mpi ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['consense', 'credibleSet', 'exabayes', 'extractBips', + 'parser-exabayes', 'postProcParam', 'sdsf', 'yggdrasil']], + 'dirs': [], +} + +moduleclass = 'bio' From fda5e1586e1536a97e5bad7a726818f0f498d601 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 4 Mar 2019 16:31:47 +0100 Subject: [PATCH 0714/5331] fix STAR-Fusion-1.5.0 --- .../STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb index 665b9b48970..3e33ce6861c 100644 --- a/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/s/STAR-Fusion/STAR-Fusion-1.5.0-foss-2018b-Perl-5.28.0.eb @@ -46,17 +46,24 @@ exts_list = [ 'source_tmpl': 'DB_File-1.843.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], 'checksums': ['de24e3d1e56b1b56c1f143590fb8ab8b812ebd9697e9c01349b0ba11c36f346a'], - }), - ('URI::Escape', '1.76', { - 'source_tmpl': 'URI-1.76.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS/'], - 'checksums': ['b2c98e1d50d6f572483ee538a6f4ccc8d9185f91f0073fd8af7390898254413e'], + 'preconfigopts': "DB_FILE_INCLUDE=$EBROOTDB/include DB_FILE_LIB=$EBROOTDB/lib ", + 'runtest': 'test', }), ('Carp::Assert', '0.21', { 'source_tmpl': 'Carp-Assert-0.21.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], 'checksums': ['924f8e2b4e3cb3d8b26246b5f9c07cdaa4b8800cef345fa0811d72930d73a54e'], }), + ('common::sense', '3.74', { + 'source_tmpl': 'common-sense-3.74.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], + 'checksums': ['771f7d02abd1ded94d9e37d3f66e795c8d2026d04defbeb5b679ca058116bbf3'], + }), + ('Types::Serialiser', '1.0', { + 'source_tmpl': 'Types-Serialiser-1.0.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], + 'checksums': ['7ad3347849d8a3da6470135018d6af5fd8e58b4057cd568c3813695f2a04730d'], + }), ('JSON::XS', '4.01', { 'source_tmpl': 'JSON-XS-4.01.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], From 51e5ecdcd3e9f7007b78721eaa7c8fb56da2506c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 4 Mar 2019 14:30:03 -0600 Subject: [PATCH 0715/5331] adding easyconfigs: TopHat-2.1.1-foss-2017b.eb --- .../t/TopHat/TopHat-2.1.1-foss-2017b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2017b.eb diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2017b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2017b.eb new file mode 100644 index 00000000000..059638cf015 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2017b.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.1' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'tophat-2.0.13-zlib.patch', + 'TopHat-%(version)s_fix-templating-error.patch', +] +checksums = [ + '37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5', # tophat-2.1.1.tar.gz + 'a33075c2affda995ddbd250933dbcaf94f68768b1eebead58a69705fc40306ef', # tophat-2.0.13-zlib.patch + '0ea02a4f8be842bb178574f7ca286d596200fcfdcc464921c0e3b7b3ebba154f', # TopHat-2.1.1_fix-templating-error.patch +] + +dependencies = [ + ('Boost', '1.65.1'), + ('zlib', '1.2.11'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +moduleclass = 'bio' From 75439b77da2e6d6fccf3c7234f4e443c97504b3b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 5 Mar 2019 09:08:44 +0800 Subject: [PATCH 0716/5331] adding easyconfigs: Bader-1.03-intel-2018b.eb --- .../b/Bader/Bader-1.03-intel-2018b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb b/easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb new file mode 100644 index 00000000000..edf6f5f647d --- /dev/null +++ b/easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'Bader' +version = '1.03' + +homepage = 'http://theory.cm.utexas.edu/henkelman/code/bader/' +description = "A fast algorithm for doing Bader's analysis on a charge density grid." + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] +sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['8160104f560b924ab98612e8b0f64916fa76ec572c80ee7e7b02097f243aefa6'] + +skipsteps = ['configure'] +buildopts = '-f makefile.lnx_ifort' +parallel = 1 + +files_to_copy = [(['bader'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bader'], + 'dirs': [], +} + +moduleclass = 'chem' From eec4ea1c5b8727e9f10e122026ed36603d3131f7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 5 Mar 2019 09:20:23 +0800 Subject: [PATCH 0717/5331] fix checksum --- easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb b/easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb index edf6f5f647d..67ebac2bf78 100644 --- a/easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb +++ b/easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['8160104f560b924ab98612e8b0f64916fa76ec572c80ee7e7b02097f243aefa6'] +checksums = ['3de8af94bd64c43812de7ebad3e9209cc5e29e6732679fcf88f72a1b382bc81a'] skipsteps = ['configure'] buildopts = '-f makefile.lnx_ifort' From 025ec89fc1a5ac6c5139222950adc9e15fb29b88 Mon Sep 17 00:00:00 2001 From: SethosII Date: Tue, 5 Mar 2019 07:51:39 +0100 Subject: [PATCH 0718/5331] switch to GCCcore --- ...foss-2018b.eb => FASTX-Toolkit-0.0.14-GCCcore-7.3.0.eb} | 7 +++++-- ....7-foss-2018b.eb => libgtextutils-0.7-GCCcore-7.3.0.eb} | 4 +++- 2 files changed, 8 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/f/FASTX-Toolkit/{FASTX-Toolkit-0.0.14-foss-2018b.eb => FASTX-Toolkit-0.0.14-GCCcore-7.3.0.eb} (93%) rename easybuild/easyconfigs/l/libgtextutils/{libgtextutils-0.7-foss-2018b.eb => libgtextutils-0.7-GCCcore-7.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2018b.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCCcore-7.3.0.eb similarity index 93% rename from easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2018b.eb rename to easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCCcore-7.3.0.eb index e3dcda045d1..b080fdf082a 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-foss-2018b.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCCcore-7.3.0.eb @@ -22,7 +22,7 @@ homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' description = """The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] @@ -33,7 +33,10 @@ checksums = [ '10dfca10f8e4678d1034a522535fa85c7273d2c5c04dd007d191f7a484ee42b5', # FASTX-Toolkit-0.0.14_fix-gcc7.patch ] -builddependencies = [('pkg-config', '0.29.2')] +builddependencies = [ + ('binutils', '2.30'), + ('pkg-config', '0.29.2'), +] dependencies = [('libgtextutils', '0.7')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2018b.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-GCCcore-7.3.0.eb similarity index 92% rename from easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2018b.eb rename to easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-GCCcore-7.3.0.eb index bc2bdf152d4..ccc679473ad 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-GCCcore-7.3.0.eb @@ -21,7 +21,7 @@ version = '0.7' homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' description = "ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/agordon/%(name)s/releases/download/%(version)s'] @@ -32,6 +32,8 @@ checksums = [ 'bb16a4fd86c2eb12215d8780b09f0898771a73e53889a015e2351f2d737c9a00', # libgtextutils-0.7_fix-bool.patch ] +builddependencies = [('binutils', '2.30')] + sanity_check_paths = { 'files': ['lib/%(name)s.so', 'lib/%(name)s.a'], 'dirs': ['lib/pkgconfig'] From e0b96ea9df3612e94730ece8ae2cdb1016fe53e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Tue, 5 Mar 2019 10:42:17 +0100 Subject: [PATCH 0719/5331] Pybundled and donwnload_dep_fail added --- .../f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb | 3 +++ .../n/numexpr/numexpr-2.6.5-foss-2018b-Python-3.6.6.eb | 3 +++ .../p/PyTables/PyTables-3.4.4-foss-2018b-Python-3.6.6.eb | 3 +++ .../p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb | 7 +------ 4 files changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb index 10ec0dfaaa0..9bc47f6aaad 100644 --- a/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/future/future-0.16.0-foss-2018b-Python-3.6.6.eb @@ -15,6 +15,9 @@ checksums = ['e39ced1ab767b5936646cedba8bcce582398233d6a627067d4c6a454c90cfedb'] dependencies = [('Python', '3.6.6')] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-foss-2018b-Python-3.6.6.eb index 1eaabddd008..ac2919ef2c1 100644 --- a/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.6.5-foss-2018b-Python-3.6.6.eb @@ -20,6 +20,9 @@ dependencies = [ ('Python', '3.6.6'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-foss-2018b-Python-3.6.6.eb index a88d1c4baa2..03039f5245c 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.4.4-foss-2018b-Python-3.6.6.eb @@ -32,6 +32,9 @@ dependencies = [ ('Blosc', '1.14.4'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['pt2to3', 'ptdump', 'ptrepack']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb index 72612b05080..d54ffd4bfda 100644 --- a/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'Pyomo' version = '5.5.0' @@ -12,10 +12,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [('Python', '3.6.6')] -exts_defaultclass = 'PythonPackage' - exts_default_options = { - 'download_dep_fail': True, 'use_pip': True, } @@ -46,6 +43,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'math' From 1da2bfb11c7e916f9481338a56cbc27c1fce7813 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 5 Mar 2019 13:42:46 +0100 Subject: [PATCH 0720/5331] adding easyconfigs: matplotlib-2.2.4-intel-2018b-Python-2.7.15.eb, IPython-5.8.0-intel-2018b-Python-2.7.15.eb --- ...IPython-5.8.0-intel-2018b-Python-2.7.15.eb | 240 ++++++++++++++++++ ...plotlib-2.2.4-intel-2018b-Python-2.7.15.eb | 56 ++++ 2 files changed, 296 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..e324f72d83b --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,240 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '5.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), + ('ZeroMQ', '4.2.5'), + ('matplotlib', '2.2.4', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('Pygments', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], + }), + ('ipython_genutils', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('certifi', '2018.11.29', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + }), + ('pexpect', '4.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('futures', '3.2.0', { + 'modulename': 'concurrent.futures', + 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], + 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), + ('ptyprocess', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('scandir', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], + }), + ('pathlib2', '2.3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], + }), + ('pickleshare', '0.7.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('traitlets', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], + }), + ('parso', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], + 'checksums': ['68406ebd7eafe17f8e40e15a84b56848eccbf27d7c1feb89e93d8fca395706db'], + }), + ('jedi', '0.13.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], + 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], + }), + ('configparser', '3.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], + 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], + }), + ('testpath', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], + 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('wcwidth', '0.1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + }), + ('prompt_toolkit', '1.0.15', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], + 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], + }), + ('MarkupSafe', '1.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('ipywidgets', '7.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + 'checksums': ['a3e224f430163f767047ab9a042fc55adbcab0c24bbe6cf9f306c4f89fdf0ba3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('Send2Trash', '1.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], + 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], + }), + ('webencodings', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], + 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], + }), + ('bleach', '3.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], + 'checksums': ['3fdf7f77adcf649c9911387df51254b813185e32b2c6619f690b593a617e19fa'], + }), + ('pyrsistent', '0.14.11', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyrsistent/'], + 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], + }), + ('attrs', '19.1.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], + }), + ('jsonschema', '3.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], + }), + ('pandocfilters', '1.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], + }), + ('pyzmq', '18.0.0', { + 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['https://pypi.python.org/packages/source/b/backcall/'], + 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], + }), + ('ipykernel', '4.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + 'checksums': ['699103c8e64886e3ec7053f2a6aa83bb90426063526f63a818732ff385202bad'], + }), + ('prometheus_client', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], + 'checksums': ['1b38b958750f66f208bcd9ab92a633c0c994d8859c831f7abc1f46724fcee490'], + }), + ('notebook', '5.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + 'checksums': ['d908673a4010787625c8952e91a22adf737db031f2aa0793ad92f6558918a74a'], + }), + ('widgetsnbextension', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + 'checksums': ['fa618be8435447a017fd1bf2c7ae922d0428056cfc7449f7a8641edf76b48265'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "iptest", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..85191cc509d --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '2.7.15'), + ('libpng', '1.6.34'), + ('freetype', '2.9.1'), + ('Tkinter', '%(pyver)s', versionsuffix), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['029620799e581802961ac1dcff5cb5d3ee2f602e0db9c0f202a90495b37d2126'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From 0f980a057b02b74db4d8093c1df2b75327b9e897 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 5 Mar 2019 14:48:25 +0100 Subject: [PATCH 0721/5331] adding easyconfigs: sciClone-1.1-foss-2018b-R-3.5.1.eb --- .../sciClone-1.1-foss-2018b-R-3.5.1.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/s/sciClone/sciClone-1.1-foss-2018b-R-3.5.1.eb diff --git a/easybuild/easyconfigs/s/sciClone/sciClone-1.1-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/s/sciClone/sciClone-1.1-foss-2018b-R-3.5.1.eb new file mode 100644 index 00000000000..3c44a5ff5a6 --- /dev/null +++ b/easybuild/easyconfigs/s/sciClone/sciClone-1.1-foss-2018b-R-3.5.1.eb @@ -0,0 +1,55 @@ +easyblock = 'Bundle' + +name = 'sciClone' +version = '1.1' +versionsuffix = '-R-%(rver)s' +bmm_commit = '44f066e' + +homepage = 'https://github.com/genome/sciclone' +description = """ An R package for inferring the subclonal architecture of tumors """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('R', '3.5.1'), + ('R-bundle-Bioconductor', '3.8', versionsuffix), +] + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_list = [ + ('NORMT3', '1.0-3', { + 'checksums': ['efface8b642e397e65d6253a51998562e781218690d842e461c3eb5939063a10'], + }), + ('MKmisc', '1.2', { + 'checksums': ['249ebb22d86fd0292b0699f38c3ce141f2dc8bbc42dd1636416329a7873de904'], + }), + ('bmm', '0.3.1', { + 'source_tmpl': '44f066e.tar.gz', + 'source_urls': ['https://github.com/genome/bmm/archive/'], + 'checksums': ['45a1d00b63085d6794184e88839ccb78767f4f0fdf7963aa4254d03030886e03'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/genome/sciclone/archive/'], + 'checksums': ['6293af0b6c1be80e225d15a0601ae26b840d849f7d50e3cba5751dfd04f040f1'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bmm', 'MKmisc', 'NORMT3', 'sciClone'], +} + +moduleclass = 'bio' From 9965699f01916c47d3448b4ceee412f1625a3fed Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 5 Mar 2019 15:32:27 +0100 Subject: [PATCH 0722/5331] Fixed checksum for for TensorFlow-1.12.0_remove_usrbin_from_linker_bin_path_flag.patch --- .../TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb index bbb79fac930..15c68ed4e6e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-3.6.6.eb @@ -102,7 +102,7 @@ exts_list = [ # TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch '843acddc197639273cb26e676685a12a1107a3bccca516be1af873df6352bb00', # TensorFlow-1.12.0_remove_usrbin_from_linker_bin_path_flag.patch - 'd57a2b90cd36ab9a013c946eb2a1d3aaef904cb657ca85e0f8c91c326e659bd6' + '082ef23b49ce50d2bd225bd462ebfed536bcc50eaa7264fca60521f5432d4b94' ], }), ] From e81c2ac893c17c2d8d13d09f92fad31888567504 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 5 Mar 2019 16:29:35 +0100 Subject: [PATCH 0723/5331] adding easyconfigs: R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb --- ...dle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb | 987 ++++++++++++++++++ 1 file changed, 987 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb new file mode 100644 index 00000000000..e31cf8c354b --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb @@ -0,0 +1,987 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.8' +biocver = version +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('R', '3.5.1'), + ('HDF5', '1.10.2'), # for rhdf5 + ('MariaDB-connector-c', '2.3.7'), # for RMySQL +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.8/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.8/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.8/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} +ext_options = exts_default_options +bioconductor_options = exts_default_options + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on Sept 25th 2018 +exts_list = [ + ('BiocGenerics', '0.28.0', { + 'checksums': ['68e5a2737f847dd49c6cbd60a77291fd48b39fd219effef0a5c7eaf360d67733'], + }), + ('Biobase', '2.42.0', { + 'checksums': ['36729cf3fa2cf42cc64c7f8f4afe5d0dfc64cc860baea721c2741739b335d982'], + }), + ('S4Vectors', '0.20.1', { + 'checksums': ['ef379329429f638f954d76c023d8509a8476bcbc824e067517c8767b0ccf90a3'], + }), + ('IRanges', '2.16.0', { + 'checksums': ['81d9a0687665f6dacb970190266358c3ac1046e86d55c49e38b18760a6be5752'], + }), + ('GenomeInfoDbData', '1.2.0', { + 'checksums': ['ac8c370b85021786ef67d9fdd1872930368abd2a46593147320e7b7d31b52636'], + }), + ('bitops', '1.0-6', { + 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['a541a5f5636ddd67fd856d3e11224f15bc068e96e23aabe3e607a7e7c2fc1cf1'], + }), + ('vegan', '2.5-3', { + 'checksums': ['6c5c8f0ad7ba8dbb29df0e119da41d330f756e6d0ab2cba24904f808a0fd7d08'], + }), + ('phyloseq', '1.26.1', { + 'checksums': ['fcea94a1d59b022764fd0d44839ecb038f6b58128b896e7a7102c16ca40c578d'], + }), + ('ALDEx2', '1.14.1', { + 'checksums': ['9c5a8658a0367f033c883953862d8b6d44d32eb9bbbd378f79394088dd6613a4'], + }), + ('RcppParallel', '4.4.2', { + 'checksums': ['28733f4ffa88b9cd46c966015af8eda8e7325c93e5886d64f522dddb1968d984'], + }), + ('dada2', '1.10.1', { + 'checksums': ['21974973b3ce3290f7b8b5d74bd880bf3bd08c1ab0a5a35a2465617d3461a820'], + }), + ('LEA', '2.4.0', { + 'checksums': ['c9f2a540985ae3c898bc9adf22656df4874ae23f6ddba5a75c0b7131cdd46cad'], + }), + ('tximport', '1.10.1', { + 'checksums': ['9490d6dc5d4ff9ffa4427597a2c8c247b18896a3af5a005825eb32505b02979b'], + }), + ('SingleCellExperiment', '1.4.1', { + 'checksums': ['04abf648510e28977c4b2361f1abeab4c81706d68db3e14cbdff6196e64c2388'], + }), + ('beachmat', '1.4.0', { + 'checksums': ['b93696765f628c9c7eebb1c0a09490eec2b58a49866809fae10f3d0c74adef1f'], + }), + ('beeswarm', '0.2.3', { + 'checksums': ['0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843'], + }), + ('vipor', '0.4.5', { + 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], + }), + ('ggbeeswarm', '0.6.0', { + 'checksums': ['bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333'], + }), + ('scater', '1.10.1', { + 'checksums': ['aa14e6516a7288863563306c97b2f2d0054587699e077f44b2ace2f28e873266'], + }), + ('dynamicTreeCut', '1.63-1', { + 'checksums': ['831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9'], + }), + ('RcppAnnoy', '0.0.11', { + 'checksums': ['a149cf6681bbb6d80825189cf6563605388aa6e4584b6207809b3dc7ac0265c6'], + }), + ('BiocNeighbors', '1.0.0', { + 'checksums': ['9406fb3842902b9aa7e7f50180eb64a8c4c6ad3bbb170381e39db6c894494bbb'], + }), + ('statmod', '1.4.30', { + 'checksums': ['9d2c1722a85f53623a9ee9f73d835119ae22ae2b8ec7b50d675401e314ea641f'], + }), + ('scran', '1.10.2', { + 'checksums': ['ef585de49f2f799c5bb0747a0de502271d4e3efca94a176ab674e037328daf1e'], + }), + ('doParallel', '1.0.14', { + 'checksums': ['cbbb7f37606d608a9603915ee65587f8ed4bb4a8405ecfaa7f33b8c423d11207'], + }), + ('pheatmap', '1.0.12', { + 'checksums': ['579d96ee0417203b85417780eca921969cda3acc210c859bf9dfeff11539b0c1'], + }), + ('ROCR', '1.0-7', { + 'checksums': ['e7ef710f847e441a48b20fdc781dbc1377f5a060a5ee635234053f7a2a435ec9'], + }), + ('DEoptimR', '1.0-8', { + 'checksums': ['846911c1b2561a9fae73a8c60a21a5680963ebb0050af3c1f1147ae9a121e5ef'], + }), + ('robustbase', '0.93-3', { + 'checksums': ['8c1d402b3d8ddf8e617224076fe5c7a5507c3a6e05151e68cf38341c1e0e10db'], + }), + ('pcaPP', '1.9-73', { + 'checksums': ['ca4566b0babfbe83ef9418283b08a12b3420dc362f93c6562f265df7926b53fc'], + }), + ('rrcov', '1.4-7', { + 'checksums': ['cbd08ccce8b583a2f88946a3267c8fc494ee2b44ba749b9296a6e3d818f6f293'], + }), + ('WriteXLS', '4.0.0', { + 'checksums': ['a0541da45e16bc4bf994cdf3f07a0e202c38d52386460c64e27fe6c1cd889d5b'], + }), + ('SC3', '1.10.1', { + 'checksums': ['dc5034387915f7d1e2c994bf7b03f74c1c50319533afc44a9c56b831115f1812'], + }), + ('shape', '1.4.4', { + 'checksums': ['f4cb1b7d7c84cf08d2fa97f712ea7eb53ed5fa16e5c7293b820bceabea984d41'], + }), + ('GlobalOptions', '0.1.0', { + 'checksums': ['567a0a51f6b7b14127302f00e6e4944befd4964c069f96a9e61256e8c3c79ef2'], + }), + ('circlize', '0.4.5', { + 'checksums': ['092a445b090286ef9802775e649496d0505c7c5d34e39ad395a0bdc3bf4c1662'], + }), + ('rjson', '0.2.20', { + 'checksums': ['3a287c1e5ee7c333ed8385913c0a307daf99335fbdf803e9dcca6e3d5adb3f6c'], + }), + ('GetoptLong', '0.1.7', { + 'checksums': ['b9a98881db407eae9b711c4fa9170168fd5f3be1f8485cd8f28d0a60ace083ba'], + }), + ('ComplexHeatmap', '1.20.0', { + 'checksums': ['5209bffdaa033bd239239fa644fc7779a282483e1c2f7d1dbe9506e9d86f0168'], + }), + ('GENIE3', '1.4.0', { + 'checksums': ['b7a47080aa0f66ca6a1fa0ac29e68d30e1b9314437c1201d8d1d7b59a3387a2a'], + }), + ('dupRadar', '1.12.1', { + 'checksums': ['08e2fa7ddd5949bfcab98690003baae269d63503cfa4c8b30659f0cf1bfcb3b6'], + }), + ('DNAcopy', '1.56.0', { + 'checksums': ['02452a67169716a915de99514d1acecca5654a746e0b1d20efc6a80d3b6e9811'], + }), + ('sva', '3.30.1', { + 'checksums': ['1872da8a1b041a13b9d8d3135f93587f572c95b720c5abdd784075591851f233'], + }), + ('ballgown', '2.14.1', { + 'checksum': ['3e9d90b9f345d122824260c588d1d36a602a525a9daa1826190193d8c24ba483'], + 'checksums': ['51234729544bc1815d638d369b115f3a4c002103820d6451efac008dd2f6721c'], + }), + ('DropletUtils', '1.2.2', { + 'checksums': ['5c330a2dd3a0e74229f718eac0e830d311448b490de8fbeb023764914f83ae4f'], + }), + ('lpSolve', '5.6.13', { + 'checksums': ['d5d41c53212dead4fd8e6425a9d3c5767cdc5feb19d768a4704116d791cf498d'], + }), + ('limSolve', '1.5.5.3', { + 'checksums': ['2f27c03411e0d771ad50d5412125bf4fa0ba461051610edc77e20d28488e86d2'], + }), + ('DeconRNASeq', '1.24.0', { + 'checksums': ['5612f66173d7523b35f857c5778e80d40ce7fd6a9c8b6b9f12b60f0bbaa5b5c8'], + }), + ('shinythemes', '1.1.2', { + 'checksums': ['2e13d4d5317fc61082e8f3128b15e0b10ed9736ce81e152dd7ae7f6109f9b18a'], + }), + ('GSVA', '1.30.0', { + 'checksums': ['91502b2f1ccae239bbc3a0e6623741e408f345fdedbd13c93fb570b17be51261'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' From 9f1268e42c94d9c421af22c6b53ddfc72f717fc7 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 5 Mar 2019 18:05:44 +0100 Subject: [PATCH 0724/5331] use matplotlib from i2018b --- .../i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb index e324f72d83b..ad97fad0c41 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} dependencies = [ ('Python', '2.7.15'), ('ZeroMQ', '4.2.5'), - ('matplotlib', '2.2.4', versionsuffix), + ('matplotlib', '2.2.3', versionsuffix), ] use_pip = True From 893e7abd74e382ad23514a4a3bc1785af81e2e4e Mon Sep 17 00:00:00 2001 From: jose_d Date: Tue, 5 Mar 2019 18:06:50 +0100 Subject: [PATCH 0725/5331] delete matplotlib as it's already present in i2018b --- ...plotlib-2.2.4-intel-2018b-Python-2.7.15.eb | 56 ------------------- 1 file changed, 56 deletions(-) delete mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2018b-Python-2.7.15.eb deleted file mode 100644 index 85191cc509d..00000000000 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.4-intel-2018b-Python-2.7.15.eb +++ /dev/null @@ -1,56 +0,0 @@ -easyblock = 'Bundle' - -name = 'matplotlib' -version = '2.2.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://matplotlib.org' -description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of - hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python - and ipython shell, web application servers, and six graphical user interface toolkits.""" - -toolchain = {'name': 'intel', 'version': '2018b'} - -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '2.7.15'), - ('libpng', '1.6.34'), - ('freetype', '2.9.1'), - ('Tkinter', '%(pyver)s', versionsuffix), -] - -exts_list = [ - ('Cycler', '0.10.0', { - 'modulename': 'cycler', - 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], - }), - (name, version, { - 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - 'checksums': ['029620799e581802961ac1dcff5cb5d3ee2f602e0db9c0f202a90495b37d2126'], - }), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -# use non-interactive plotting backend as default -# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend -modextravars = {'MPLBACKEND': 'Agg'} - -moduleclass = 'vis' From fd595f03c586bdef4b2617c7817fcace83e175ec Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 5 Mar 2019 18:30:55 +0100 Subject: [PATCH 0726/5331] gcccore->gcc --- .../s/STREAM/STREAM-5.10-GCC-7.3.0-2.30.eb | 41 +++++++++++++++++++ .../s/STREAM/STREAM-5.10-GCC-8.2.0-2.31.1.eb | 41 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-7.3.0-2.30.eb create mode 100644 easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..5ea4b35d543 --- /dev/null +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-7.3.0-2.30.eb @@ -0,0 +1,41 @@ +easyblock = 'CmdCp' + +name = 'STREAM' +version = '5.10' + +homepage = 'https://www.cs.virginia.edu/stream/' +description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable + memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" + +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} +toolchainopts = {'openmp': True} + +source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] +sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c'}] +checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] + +skipsteps = ['source'] + +# 10 million array elements (1000 runs): requires ~224MB of memory +cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " +# 100 million array elements (1000 runs): requires ~2.2GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " +# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " +# 5 billion array elements (1000 runs): requires ~111 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " + +cmds_map = [('stream-%(version)s.c', cmds_str)] + +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'dirs': [], +} + +tests = ['%(installdir)s/bin/stream_1Kx10M'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..0fae6090ed7 --- /dev/null +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,41 @@ +easyblock = 'CmdCp' + +name = 'STREAM' +version = '5.10' + +homepage = 'https://www.cs.virginia.edu/stream/' +description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable + memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'openmp': True} + +source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] +sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c'}] +checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] + +skipsteps = ['source'] + +# 10 million array elements (1000 runs): requires ~224MB of memory +cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " +# 100 million array elements (1000 runs): requires ~2.2GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " +# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " +# 5 billion array elements (1000 runs): requires ~111 GiB of memory +cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " + +cmds_map = [('stream-%(version)s.c', cmds_str)] + +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'dirs': [], +} + +tests = ['%(installdir)s/bin/stream_1Kx10M'] + +moduleclass = 'perf' From fa4171b5f6a4b5a330e8f88721a5a33a88050ee9 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 5 Mar 2019 11:48:31 -0600 Subject: [PATCH 0727/5331] Use templates for software name --- easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2017b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2017b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2017b.eb index 059638cf015..1a7d7394def 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2017b.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2017b.eb @@ -16,11 +16,11 @@ description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'pic': True} -source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] +source_urls = ['http://ccb.jhu.edu/software/%(namelower)s/downloads/'] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'tophat-2.0.13-zlib.patch', - 'TopHat-%(version)s_fix-templating-error.patch', + '%(namelower)s-2.0.13-zlib.patch', + '%(name)s-%(version)s_fix-templating-error.patch', ] checksums = [ '37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5', # tophat-2.1.1.tar.gz From b68e6355627b645b97a75f604bffe82298519665 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Wed, 6 Mar 2019 09:13:56 +0100 Subject: [PATCH 0728/5331] Fixed pip = true in pyomo --- .../p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb index d54ffd4bfda..b0785c43d77 100644 --- a/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-5.5.0-foss-2018b-Python-3.6.6.eb @@ -12,9 +12,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [('Python', '3.6.6')] -exts_default_options = { - 'use_pip': True, -} +use_pip = True exts_list = [ ('appdirs', '1.4.3', { From ed7f0180da168a7314f07cd3ed9c412f322b1142 Mon Sep 17 00:00:00 2001 From: wapoelma Date: Wed, 6 Mar 2019 10:05:01 +0100 Subject: [PATCH 0729/5331] adding easyconfigs: mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb --- .../mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..1444a9daf93 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/mpi4py/mpi4py' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [BITBUCKET_DOWNLOADS] +sources = [SOURCE_TAR_GZ] +checksums = ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'] + +dependencies = [('Python', '3.6.6')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'], +} + +moduleclass = 'lib' From ded91101dcc00bff5b3ff581196edfd68848a529 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Mar 2019 10:17:17 +0100 Subject: [PATCH 0730/5331] adding easyconfigs: Bismark-0.20.1-intel-2018b.eb, Bowtie2-2.3.4.2-intel-2018b.eb --- .../b/Bismark/Bismark-0.20.1-intel-2018b.eb | 37 +++++++++++++++++++ .../b/Bowtie2/Bowtie2-2.3.4.2-intel-2018b.eb | 36 ++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bismark/Bismark-0.20.1-intel-2018b.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.4.2-intel-2018b.eb diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.20.1-intel-2018b.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.20.1-intel-2018b.eb new file mode 100644 index 00000000000..e263e82d112 --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.20.1-intel-2018b.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'Tarball' + +name = 'Bismark' +version = '0.20.1' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = "A tool to map bisulfite converted sequence reads and determine cytosine methylation states" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/bismark/'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] +checksums = ['1110bc477f0c9109843621016e11465dd7b5c9f6cbd2d2e6ccad7f01a87054b8'] + +dependencies = [ + ('Perl', '5.28.0'), + ('Bowtie2', '2.3.4.2'), + ('SAMtools', '1.9'), +] + +sanity_check_paths = { + 'files': ['bismark', 'bismark2bedGraph', 'bismark2report', 'bismark_genome_preparation', + 'bismark_methylation_extractor', 'coverage2cytosine', 'deduplicate_bismark'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.4.2-intel-2018b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.4.2-intel-2018b.eb new file mode 100644 index 00000000000..14c565373ea --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.4.2-intel-2018b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp + +name = 'Bowtie2' +version = '2.3.4.2' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['8bcd2a8909dd63d1c378200c9e139dac56d9ff85d058b3e2ec91c44b670c0ccb'] + +dependencies = [ + ('tbb', '2018_U5'), + ('zlib', '1.2.11'), +] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From 15b5f6f6124f87c063769ccb8407c547a790ddc6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Mar 2019 10:29:13 +0100 Subject: [PATCH 0731/5331] adding easyconfigs: picard-2.18.27-Java-1.8.eb --- .../p/picard/picard-2.18.27-Java-1.8.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb diff --git a/easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb b/easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb new file mode 100644 index 00000000000..242ce17a4e4 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb @@ -0,0 +1,48 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.10.1: +# Adam Huffman +# The Francis Crick Institute +# 2.18.11: +# Jonas Demeulemeester +# The Francis Crick Institute +## + +easyblock = 'JAR' + +name = 'picard' +version = '2.18.27' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/picard' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = [{ + 'filename': '%(name)s-%(version)s.jar', + 'download_filename': '%(name)s.jar', +}] +checksums = ['6cfba52d348969bf7b17adc26d1e8e669f741631253003e4a10dd8322eac89dd'] + +postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] + +dependencies = [('Java', '1.8', '', True)] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' From b3ce6c8d194817746499b06c08fda7d5eb2f8c95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Mar 2019 10:34:14 +0100 Subject: [PATCH 0732/5331] {bio}[intel/2018b] MultiQC v1.7 w/ Python 2.7.15 + 3.6.6 --- .../MultiQC-1.7-intel-2018b-Python-2.7.15.eb | 109 ++++++++++++++++++ .../MultiQC-1.7-intel-2018b-Python-3.6.6.eb | 109 ++++++++++++++++++ .../PyYAML-3.13-intel-2018b-Python-2.7.15.eb | 28 +++++ 3 files changed, 246 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..c4edccfdf8f --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,109 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), + ('PyYAML', '3.13', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Click', '7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('simplejson', '3.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('networkx', '2.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], + 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], + }), + ('colormath', '3.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('certifi', '2018.11.29', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + }), + ('urllib3', '1.24.1', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('idna', '2.8', { + 'source_urls': ['https://pypi.io/packages/source/i/idna'], + 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], + }), + ('requests', '2.21.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], + }), + ('Markdown', '3.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], + 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], + }), + ('future', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], + 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], + }), + ('lzstring', '1.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('multiqc', version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], + 'checksums': ['02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..59ac16bc650 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.7-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,109 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('matplotlib', '3.0.0', versionsuffix), + ('PyYAML', '3.13', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/markupsafe'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Click', '7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('simplejson', '3.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('networkx', '2.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], + 'checksums': ['45e56f7ab6fe81652fb4bc9f44faddb0e9025f469f602df14e3b2551c2ea5c8b'], + }), + ('colormath', '3.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colormath/'], + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/s/spectra/'], + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('certifi', '2018.11.29', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + }), + ('urllib3', '1.24.1', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('idna', '2.8', { + 'source_urls': ['https://pypi.io/packages/source/i/idna'], + 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], + }), + ('requests', '2.21.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], + }), + ('Markdown', '3.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown/'], + 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], + }), + ('future', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], + 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], + }), + ('lzstring', '1.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lzstring/'], + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('multiqc', version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/multiqc/'], + 'checksums': ['02e6a7fac7cd9ed036dcc6c92b8f8bcacbd28983ba6be53afb35e08868bd2d68'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..af657669158 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf'] + +dependencies = [ + ('Python', '2.7.15'), + ('libyaml', '0.2.1'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 3a02ed06968d5427dda4e325d692ef3f6a4abcbd Mon Sep 17 00:00:00 2001 From: jose_d Date: Wed, 6 Mar 2019 10:59:41 +0100 Subject: [PATCH 0733/5331] Delete STREAM-5.10-GCCcore-7.3.0.eb --- .../s/STREAM/STREAM-5.10-GCCcore-7.3.0.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-7.3.0.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-7.3.0.eb deleted file mode 100644 index 30e90ce66bb..00000000000 --- a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-7.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'CmdCp' - -name = 'STREAM' -version = '5.10' - -homepage = 'https://www.cs.virginia.edu/stream/' -description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable - memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" - -toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] -sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c'}] -checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] - -builddependencies = [ - ('binutils', '2.30'), -] - -skipsteps = ['source'] - -# 10 million array elements (1000 runs): requires ~224MB of memory -cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " -# 100 million array elements (1000 runs): requires ~2.2GiB of memory -cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " -# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory -cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " -# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory -cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " -# 5 billion array elements (1000 runs): requires ~111 GiB of memory -cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " - -cmds_map = [('stream-%(version)s.c', cmds_str)] - -files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], - 'dirs': [], -} - -tests = ['%(installdir)s/bin/stream_1Kx10M'] - -moduleclass = 'perf' From 8f1ca9de2ecdf83d92c1e2c7f3b415cb99f8f5e5 Mon Sep 17 00:00:00 2001 From: jose_d Date: Wed, 6 Mar 2019 10:59:54 +0100 Subject: [PATCH 0734/5331] Delete STREAM-5.10-GCCcore-8.2.0.eb --- .../s/STREAM/STREAM-5.10-GCCcore-8.2.0.eb | 46 ------------------- 1 file changed, 46 deletions(-) delete mode 100644 easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-8.2.0.eb deleted file mode 100644 index fc2c9d2bff7..00000000000 --- a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCCcore-8.2.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'CmdCp' - -name = 'STREAM' -version = '5.10' - -homepage = 'https://www.cs.virginia.edu/stream/' -description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable - memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" - -toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] -sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c'}] -checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] - -builddependencies = [ - ('binutils', '2.31.1'), -] - - -skipsteps = ['source'] - -# 10 million array elements (1000 runs): requires ~224MB of memory -cmds_str = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " -# 100 million array elements (1000 runs): requires ~2.2GiB of memory -cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " -# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory -cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " -# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory -cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " -# 5 billion array elements (1000 runs): requires ~111 GiB of memory -cmds_str += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " - -cmds_map = [('stream-%(version)s.c', cmds_str)] - -files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], - 'dirs': [], -} - -tests = ['%(installdir)s/bin/stream_1Kx10M'] - -moduleclass = 'perf' From 8a465881d4fdd4bef4f8486da19ad77b05f8d0a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Mar 2019 11:43:03 +0100 Subject: [PATCH 0735/5331] add mlegp extension + fix checksum for boot extension in R 3.5.1 easyconfigs --- .../easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 5 ++++- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index 414adfa2845..059217e401f 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -559,7 +559,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], + 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], @@ -2078,6 +2078,9 @@ exts_list = [ ('h2o', '3.22.1.1', { 'checksums': ['e4c9d50d2a6a42ffecb15aa1561495599b206a7edd77db95501c7d09253fc412'], }), + ('mlegp', '3.1.7', { + 'checksums': ['d4845eaf9260f8b8112726dd7ceb5c2f5ce75125fa313191db9de121f2ee15e0'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 9f1aa8ce8cd..bd95fa5d2c6 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -557,7 +557,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], + 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], @@ -2076,6 +2076,9 @@ exts_list = [ ('h2o', '3.22.1.1', { 'checksums': ['e4c9d50d2a6a42ffecb15aa1561495599b206a7edd77db95501c7d09253fc412'], }), + ('mlegp', '3.1.7', { + 'checksums': ['d4845eaf9260f8b8112726dd7ceb5c2f5ce75125fa313191db9de121f2ee15e0'], + }), ] moduleclass = 'lang' From be270a789843d9857b287510c93d241a28c86040 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 6 Mar 2019 13:33:49 +0100 Subject: [PATCH 0736/5331] adding easyconfigs: netcdf4-python-1.4.3-foss-2018b-Python-3.6.6.eb, cftime-1.0.1-foss-2018b-Python-3.6.6.eb --- .../cftime-1.0.1-foss-2018b-Python-3.6.6.eb | 29 ++++++++++++++++++ ...f4-python-1.4.3-foss-2018b-Python-3.6.6.eb | 30 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/c/cftime/cftime-1.0.1-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.3-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/c/cftime/cftime-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cftime/cftime-1.0.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..bf9489464e7 --- /dev/null +++ b/easybuild/easyconfigs/c/cftime/cftime-1.0.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'cftime' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Unidata/cftime' +description = """Time-handling functionality from netcdf4-python""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/Unidata/cftime/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['930089f389f68485077019faa30e1d66f57d3a46148e67f51e401504e8a15f7d'] + +dependencies = [ + ('Python', '3.6.6'), + ('cURL', '7.60.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.3-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..d1906a1ff74 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.3-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,30 @@ +name = 'netcdf4-python' +version = '1.4.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] +sources = ['v%(version)srel.tar.gz'] +patches = ['netcdf4-python-1.1.8-avoid-diskless-test.patch'] +checksums = [ + '05f0483f75ab74027a75627fb6e139356b3c7e77f9490a81923699a7d82e9496', # v1.4.3rel.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', +] + +download_dep_fail = True +use_pip = True + +dependencies = [ + ('Python', '3.6.6'), + ('cftime', '1.0.1', '-Python-%(pyver)s'), + ('netCDF', '4.6.1'), + ('cURL', '7.60.0'), +] + +moduleclass = 'data' From 4fb8b28345e696a3f422b1474d2d361421af7d56 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 6 Mar 2019 13:58:21 +0100 Subject: [PATCH 0737/5331] adding easyconfigs: NCO-4.7.9-foss-2018b.eb, ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb, libdap-3.20.3-GCCcore-7.3.0.eb --- .../ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb | 35 ++++++++++++++++++ .../l/libdap/libdap-3.20.3-GCCcore-7.3.0.eb | 34 ++++++++++++++++++ .../easyconfigs/n/NCO/NCO-4.7.9-foss-2018b.eb | 36 +++++++++++++++++++ 3 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/l/libdap/libdap-3.20.3-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-4.7.9-foss-2018b.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..c39ebbf2028 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +dependencies = [ + ('Java', '1.8', '', True), + ('Python', '3.6.6'), +] + +configopts = '--disable-examples --disable-csharp ' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.3-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.3-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..7b1ef6d5163 --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.3-GCCcore-7.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.20.3' + +homepage = 'http://opendap.org/download/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 + and the development versions of DAP3, up to 3.4. + This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['29961922b53f62e9d4eb34d1d50ddc23a24100664f97b71f42561fa5588ccc58'] + +builddependencies = [ + ('binutils', '2.30'), + ('Bison', '3.0.5'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '7.60.0'), + ('libxml2', '2.9.8'), + ('LibUUID', '1.0.3'), +] + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.7.9-foss-2018b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.7.9-foss-2018b.eb new file mode 100644 index 00000000000..b6458c27e17 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-4.7.9-foss-2018b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '4.7.9' + +homepage = "http://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['048f6298bceb40913c3ae433f875dea1e9129b1c86019128e7271d08f274a879'] + +builddependencies = [ + ('Bison', '3.0.5'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.26'), + ('expat', '2.2.5'), + ('ANTLR', '2.7.7', '-Python-3.6.6'), + ('libdap', '3.20.3'), + ('GSL', '2.5'), + ('netCDF', '4.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From e86b1d9c7d82ae7e983c93be0f1c26a4f56c6e50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Mar 2019 14:34:23 +0100 Subject: [PATCH 0738/5331] {lib,tools}[intel/2018b] snakemake v5.2.4, GitPython v2.1.11 w/ Python 3.6.6 --- ...tPython-2.1.11-intel-2018b-Python-3.6.6.eb | 36 +++++++++++ ...nakemake-5.2.4-intel-2018b-Python-3.6.6.eb | 62 +++++++++++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..3201cfebfd3 --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-2.1.11-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '2.1.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/gitpython-developers/GitPython' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), +] + +use_pip = True + +exts_list = [ + ('smmap2', '2.0.4', { + 'modulename': 'smmap', + 'source_urls': ['https://pypi.python.org/packages/source/s/smmap2'], + 'checksums': ['dc216005e529d57007ace27048eb336dcecb7fc413cfb3b2f402bb25972b69c6'], + }), + ('gitdb2', '2.0.4', { + 'modulename': 'gitdb', + 'source_urls': ['https://pypi.python.org/packages/source/g/gitdb2'], + 'checksums': ['bb4c85b8a58531c51373c89f92163b92f30f81369605a67cd52d1fc21246c044'], + }), + (name, version, { + 'modulename': 'git', + 'source_urls': ['https://pypi.python.org/packages/source/g/GitPython'], + 'checksums': ['8237dc5bfd6f1366abeee5624111b9d6879393d84745a507de0fda86043b65a8'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..1d04771ecef --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'snakemake' +version = '5.2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://snakemake.readthedocs.io' +description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('PyYAML', '3.13', versionsuffix), + ('GitPython', '2.1.11', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('docutils', '0.14', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docutils'], + 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], + }), + ('datrie', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/datrie'], + 'checksums': ['7a11371cc2dbbad71d6dfef57ced6e8b384bb377eeb847c63d58f8dc8e8b2023'], + }), + ('appdirs', '1.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs'], + 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], + }), + ('ConfigArgParse', '0.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/ConfigArgParse'], + 'checksums': ['e6441aa58e23d3d122055808e5e2220fd742dff6e1e51082d2a4e4ed145dd788'], + }), + ('ratelimiter', '1.2.0.post0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/ratelimiter'], + 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], + }), + ('wrapt', '1.10.11', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt'], + 'checksums': ['d4d560d479f2c21e1b5443bbd15fe7ec4b37fe7e53d335d3b9b0a7b1226fe3c6'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/s/snakemake'], + 'checksums': ['ff48ec6b227d9f1fb125c646c071a4f105ac62a3dfadec3d4eb70e1c5fef403e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/snakemake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['snakemake --help'] + +moduleclass = 'tools' From c61f6fcc541784661ea9839435ad0976f9faa3c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Mar 2019 16:13:07 +0100 Subject: [PATCH 0739/5331] adding easyconfigs: NetLogo-6.0.4-64.eb --- .../easyconfigs/n/NetLogo/NetLogo-6.0.4-64.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NetLogo/NetLogo-6.0.4-64.eb diff --git a/easybuild/easyconfigs/n/NetLogo/NetLogo-6.0.4-64.eb b/easybuild/easyconfigs/n/NetLogo/NetLogo-6.0.4-64.eb new file mode 100644 index 00000000000..7b0edcdf28c --- /dev/null +++ b/easybuild/easyconfigs/n/NetLogo/NetLogo-6.0.4-64.eb @@ -0,0 +1,26 @@ +easyblock = 'PackedBinary' + +name = 'NetLogo' +version = '6.0.4' +versionsuffix = '-64' + +homepage = 'http://ccl.northwestern.edu/netlogo/' +description = """NetLogo is a multi-agent programmable modeling environment. It +is used by tens of thousands of students, teachers and researchers worldwide. +It also powers HubNet participatory simulations. It is authored by Uri Wilensky +and developed at the CCL.""" + +# NetLogo is precompiled and needs no particular toolchain. +# It even comes with its own Java. +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ccl.northwestern.edu/netlogo/%(version)s/'] +sources = ['%(name)s-%(version)s%(versionsuffix)s.tgz'] +checksums = ['0dcd9df4dfb218826a74f9df42163fa588908a1dfe58864106936f8dfb76acec'] + +sanity_check_paths = { + 'files': ['NetLogo', 'NetLogo3D', 'NetLogoLogging'], + 'dirs': ['app', 'runtime'], +} + +moduleclass = 'math' From 0c3acfb72c400cd75462d5d95685c471bbe8270d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Mar 2019 16:47:32 +0100 Subject: [PATCH 0740/5331] {lang}[GCCcore/8.2.0] Python v2.7.15 --- .../g/GMP/GMP-6.1.2-GCCcore-8.2.0.eb | 35 +++ .../l/libffi/libffi-3.2.1-GCCcore-8.2.0.eb | 37 +++ .../p/Python/Python-2.7.15-GCCcore-8.2.0.eb | 264 ++++++++++++++++++ .../s/SQLite/SQLite-3.27.2-GCCcore-8.2.0.eb | 45 +++ 4 files changed, 381 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.27.2-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..796b76c6ae6 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-8.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.2' + +homepage = 'http://gmplib.org/' + +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] +checksums = ['5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.31.1'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..affa2a35046 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-8.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' + +description = """ + The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['libffi-%(version)s_fix-include-location.patch'] +checksums = [ + 'd06ebb8e1d9a22d19e38d63fdb83954253f39bedc5d46232a05645685722ca37', # libffi-3.2.1.tar.gz + '078bec207fc3d5a0581f2a952d1c014b76a6e84a93a6a089ff9b9fe5b3908cb9', # libffi-3.2.1_fix-include-location.patch +] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..4fa4382da03 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb @@ -0,0 +1,264 @@ +name = 'Python' +version = '2.7.15' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['18617d1f15a380a919d517630a9cd85ce17ea602f9bbdc58ddc672df4b0239db'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('bzip2', '1.0.6'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.1'), + ('SQLite', '3.27.2'), + ('GMP', '6.1.2'), # required for pycrypto + ('libffi', '3.2.1'), # required for cryptography + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +# order is important! +# package versions updated Mar 6th 2019 +exts_list = [ + ('setuptools', '40.8.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'use_pip': False, + 'checksums': ['6e4eec90337e849ade7103723b9a99631c1f0d19990d6e8412dc42f5ae8b304d'], + }), + ('pip', '19.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + 'use_pip': False, + 'checksums': ['6e6f197a1abfb45118dbb878b5c859a0edbdd33fd250100bc015b67fded4b9f2'], + }), + ('wheel', '0.33.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wheel'], + 'checksums': ['66a8fd76f28977bb664b098372daef2b27f60dc4d1688cfab7b37a09448f0e9d'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '5.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + 'checksums': ['8c361cc353d988e4f5b998555c88098b9d5964c2e11acf7b0d21925a66bb5824'], + }), + ('Cython', '0.29.6', { + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'checksums': ['6c5d33f1b5c864382fbce810a8fd9e015447869ae42e98e6301e977b8165e7ae'], + }), + ('six', '1.12.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'checksums': ['d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73'], + }), + ('setuptools_scm', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], + }), + ('python-dateutil', '2.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'checksums': ['c89805f6f4d64db21ed966fda138f8a5ed7a4fdbc1a8ee329ce1b74e3c74da9e'], + 'modulename': 'dateutil', + }), + ('deap', '1.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], + }), + ('decorator', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + 'checksums': ['33cd704aea07b4c28b3eb2c97d288a06918275dac0ecebdaf1bc8a48d98adb9e'], + }), + ('liac-arff', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'checksums': ['47afcd1fd248b2892f66075987422d0576fc2c2fd0811d0cbd32f2135b065df5'], + 'modulename': 'arff', + }), + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], + 'modulename': 'Crypto', + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], + }), + ('enum34', '1.1.6', { + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34/'], + 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], + 'modulename': 'enum', + }), + ('ipaddress', '1.0.22', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], + 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], + }), + ('asn1crypto', '0.24.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], + 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], + }), + ('idna', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], + 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], + }), + ('pycparser', '2.19', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], + 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], + }), + ('cffi', '1.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], + 'checksums': ['e113878a446c6228669144ae8a56e268c91b7f1fafae927adc4879d9849e0ea7'], + }), + ('cryptography', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['26c821cbeb683facb966045e2064303029d572a87ee69ca5a1bf54bf55f93ca6'], + }), + ('pyasn1', '0.4.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['da2420fe13a9452d8ae97a0e478adde1dee153b11ba832a95b223a2ba01c10f7'], + }), + ('PyNaCl', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], + 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], + 'modulename': 'nacl', + }), + ('bcrypt', '3.1.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], + 'checksums': ['44636759d222baa62806bbceb20e96f75a015a6381690d1bc2eda91c01ec02ea'], + }), + ('paramiko', '2.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + 'checksums': ['a8975a7df3560c9f1e2b43dc54ebd40fd00a7017392ca5445ce7df409f900fcb'], + }), + ('pyparsing', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + 'checksums': ['66c9268862641abcac4a96ba74506e594c884e3f57690a696d21ad8210ed667a'], + }), + ('netifaces', '0.10.9', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], + 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], + 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], + 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], + }), + ('pytz', '2018.9', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + 'checksums': ['d5f05e487007e29e03409f9398d074e158d920d36eb82eaf66fb1136b0c5374c'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], + 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], + }), + ('virtualenv', '16.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], + 'checksums': ['984d7e607b0a5d1329425dd8845bd971b957424b5ba664729fab51ab8c11bc39'], + }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.13.2', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], + 'checksums': ['315d6b19643ec4afd4c41c671f9f2d65ea9d787da093487a81ead7b0bac94524'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('certifi', '2018.11.29', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + }), + ('urllib3', '1.24.1', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], + }), + ('requests', '2.21.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], + }), + ('xlrd', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('py_expression_eval', '0.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['0907cef96a7c370b2a58ea2179f88e48f421f5a41821b32f7defb81ca4e5247e'], + }), + ('tabulate', '0.8.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], + 'checksums': ['8af07a39377cee1103a5c8b3330a421c2d99b9141e9cc5ddd2e3263fea416943'], + }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), + ('atomicwrites', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites'], + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], + }), + ('py', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py'], + 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], + }), + ('scandir', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir'], + 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], + }), + ('pathlib2', '2.3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2'], + 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], + }), + ('pluggy', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy'], + 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], + }), + ('more-itertools', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools'], + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + ('attrs', '19.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], + 'modulename': 'attr', + }), + ('pytest', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytest'], + 'checksums': ['067a1d4bf827ffdd56ad21bd46674703fce77c5957f6c1eef731f6146bfcef1c'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.27.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.27.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..b46cdbe8257 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.27.2-GCCcore-8.2.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.27.2' + +homepage = 'http://www.sqlite.org/' + +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +source_urls = ['http://www.sqlite.org/2019/'] +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] +checksums = ['50c39e85ea28b5ecfdb3f9e860afe9ba606381e21836b2849efca6a0bfe6ef6e'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('libreadline', '8.0'), + ('Tcl', '8.6.9'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' From 90f71486c582b9c229bb178957e4fb8d0cad9969 Mon Sep 17 00:00:00 2001 From: ebtest Date: Wed, 6 Mar 2019 16:21:38 +0000 Subject: [PATCH 0741/5331] add requested changes --- .../GffCompare-0.10.6-GCCcore-7.3.0.eb} | 7 ++++--- .../g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb | 9 +++++---- 2 files changed, 9 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/g/{gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb => GffCompare/GffCompare-0.10.6-GCCcore-7.3.0.eb} (84%) diff --git a/easybuild/easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.10.6-GCCcore-7.3.0.eb similarity index 84% rename from easybuild/easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb rename to easybuild/easyconfigs/g/GffCompare/GffCompare-0.10.6-GCCcore-7.3.0.eb index dea44605fe8..81c3b297a47 100644 --- a/easybuild/easyconfigs/g/gffcompare/gffcompare-0.10.6-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.10.6-GCCcore-7.3.0.eb @@ -2,17 +2,18 @@ easyblock = 'MakeCp' -name = 'gffcompare' +name = 'GffCompare' version = '0.10.6' homepage = 'https://github.com/gpertea/%(namelower)s' -description = """gffcompare provides classification and reference annotation mapping and +description = """GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.""" toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['e75cc9fff42cea2d02752bd96e0e0451b268384247606e0e27193d15f4a54477'] builddependencies = [('binutils', '2.30')] diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb index 4d8b5173e3c..b80262ad887 100644 --- a/easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/g/gffread/gffread-0.10.6-GCCcore-7.3.0.eb @@ -10,24 +10,25 @@ description = """GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.""" toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} source_urls = ['http://ccb.jhu.edu/software/stringtie/dl/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [SOURCE_TAR_GZ] checksums = ['760b7c61542dc65caec0e7551e51fa43c0b2e0da536d8e2f37a472ac285a04e1'] builddependencies = [('binutils', '2.30')] buildopts = " release" -files_to_copy = ['%(namelower)s', 'LICENSE'] +files_to_copy = ['%(name)s', 'LICENSE'] modextrapaths = {'PATH': ''} sanity_check_paths = { - 'files': ['%(namelower)s'], + 'files': ['%(name)s'], 'dirs': [] } -sanity_check_commands = ['%(namelower)s '] +sanity_check_commands = ['%(name)s '] moduleclass = 'bio' From cb9861d7ac78b5511a2967bbae837dfe06118a5b Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 6 Mar 2019 14:52:06 -0600 Subject: [PATCH 0742/5331] adding easyconfigs: Geant4-10.5-foss-2017b.eb, Geant4-10.5-intel-2017b.eb --- .../g/Geant4/Geant4-10.5-foss-2017b.eb | 25 +++++++++++++++++++ .../g/Geant4/Geant4-10.5-intel-2017b.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb new file mode 100644 index 00000000000..f609bc51ac7 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb @@ -0,0 +1,25 @@ +name = 'Geant4' +version = '10.5' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version_major)s.0%(version_minor)s.tar.gz'] +checksums = ['4b05b4f7d50945459f8dbe287333b9efb772bd23d50920630d5454ec570b782d'] + +builddependencies = [('CMake', '3.9.5')] +dependencies = [ + ('expat', '2.2.4'), + # recommended CLHEP version, see http://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.5.html#2. + ('CLHEP', '2.3.4.3'), +] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += " -DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb new file mode 100644 index 00000000000..af38f4b79f1 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb @@ -0,0 +1,25 @@ +name = 'Geant4' +version = '10.5' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version_major)s.0%(version_minor)s.tar.gz'] +checksums = ['4b05b4f7d50945459f8dbe287333b9efb772bd23d50920630d5454ec570b782d'] + +builddependencies = [('CMake', '3.9.5')] +dependencies = [ + ('expat', '2.2.4'), + # recommended CLHEP version, see http://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.5.html#2. + ('CLHEP', '2.3.4.3'), +] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += " -DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' From 3696e8cbd7b8dff1be91e4ffb3e20c3a26271934 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Mar 2019 22:34:03 +0100 Subject: [PATCH 0743/5331] add whitelist for Python packages that don't support installation with pip --- test/easyconfigs/easyconfigs.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index fa8bf72eeca..f2486f93e81 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -362,6 +362,9 @@ def check_sha256_checksums(self, changed_ecs): def check_python_packages(self, changed_ecs): """Several checks for easyconfigs that install (bundles of) Python packages.""" + # MATLAB-Engine does not support installation with 'pip' + whitelist_pip = ['MATLAB-Engine-*'] + failing_checks = [] for ec in changed_ecs: @@ -379,8 +382,8 @@ def check_python_packages(self, changed_ecs): failing_checks.append("'download_dep_fail' set in %s" % ec_fn) # download_dep_fail is enabled automatically in PythonBundle easyblock - elif easyblock in ['PythonBundle', 'PythonPackage']: - if not use_pip: + if easyblock in ['PythonBundle', 'PythonPackage']: + if not use_pip and not any(re.match(regex, ec_fn) for regex in whitelist_pip): failing_checks.append("'use_pip' set in %s" % ec_fn) if download_dep_fail or exts_download_dep_fail: From a901a329d578919decef77987fe84f4961620d20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Mar 2019 08:57:30 +0100 Subject: [PATCH 0744/5331] filter out false positive match for MATLAB-Engine 2018b in test for dependency variants --- test/easyconfigs/easyconfigs.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f2486f93e81..2248c7476f2 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -266,6 +266,10 @@ def check_dep_vars(dep, dep_vars): return res + # some software also follows {a,b} versioning scheme, + # which throws off the pattern matching done below for toolchain versions + false_positives_regex = re.compile('^MATLAB-Engine-20[0-9][0-9][ab]') + # restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a) # and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x for pattern in ['201[89][ab]', '20[2-9][0-9][ab]', 'GCCcore-[7-9]\.[0-9]']: @@ -275,6 +279,10 @@ def check_dep_vars(dep, dep_vars): # collect variants for all dependencies of easyconfigs that use a toolchain that matches for ec in self.ordered_specs: ec_file = os.path.basename(ec['spec']) + + # take into account software which also follows a {a,b} versioning scheme + ec_file = false_positives_regex.sub('', ec_file) + res = regex.match(ec_file) if res: tc_gen = res.group('tc_gen') From 11e0724109ad4b49746f3ad2367bd48be7e4bc7a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 7 Mar 2019 10:30:16 +0200 Subject: [PATCH 0745/5331] Add add_ompi_datatype_attribute_to_release_ucp_datatype.patch to older OpenMPI-3.x versions. --- .../o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb | 7 +- ...pe_attribute_to_release_ucp_datatype.patch | 265 ++++++++++++++++++ .../o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb | 5 +- ...pe_attribute_to_release_ucp_datatype.patch | 265 ++++++++++++++++++ .../o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb | 7 +- ...pe_attribute_to_release_ucp_datatype.patch | 265 ++++++++++++++++++ .../o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb | 5 +- ....1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb | 5 +- .../OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb | 5 +- 9 files changed, 815 insertions(+), 14 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb index d9d1a4827b7..340404559fb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb @@ -10,7 +10,12 @@ toolchain = {'name': 'GCC', 'version': '7.2.0-2.29'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['0bbb279b88edc25bbded39520dab6d4b32020277a6088fb1456c9437a8231cf8'] +patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] +checksums = [ + '0bbb279b88edc25bbded39520dab6d4b32020277a6088fb1456c9437a8231cf8', # openmpi-3.0.0.tar.gz + # OpenMPI-3.0.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch + 'ea6fb132c67046d9c6d9af4ccae20963b4cc9816264d0ba755b246a68f2da808', +] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch new file mode 100644 index 00000000000..aa4abe31b75 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch @@ -0,0 +1,265 @@ +From 4763822a64c9002f24429aef95d87f6abfc45c06 Mon Sep 17 00:00:00 2001 +From: Yossi Itigin +Date: Tue, 9 Oct 2018 16:38:49 +0300 +Subject: [PATCH 1/2] pml_ucx: add ompi datatype attribute to release + ucp_datatype + +Signed-off-by: Yossi Itigin +--- + +Adapted to older OpenMPI versions. + +Åke Sandgren, 20190307 +diff -ru openmpi-3.0.0.orig/ompi/mca/pml/ucx/pml_ucx.c openmpi-3.0.0/ompi/mca/pml/ucx/pml_ucx.c +--- openmpi-3.0.0.orig/ompi/mca/pml/ucx/pml_ucx.c 2017-09-12 23:31:33.000000000 +0200 ++++ openmpi-3.0.0/ompi/mca/pml/ucx/pml_ucx.c 2019-03-06 21:03:56.010224884 +0100 +@@ -14,6 +14,7 @@ + + #include "opal/runtime/opal.h" + #include "opal/mca/pmix/pmix.h" ++#include "ompi/attribute/attribute.h" + #include "ompi/message/message.h" + #include "ompi/mca/pml/base/pml_base_bsend.h" + #include "pml_ucx_request.h" +@@ -182,9 +183,9 @@ + int mca_pml_ucx_init(void) + { + ucp_worker_params_t params; +- ucs_status_t status; + ucp_worker_attr_t attr; +- int rc; ++ ucs_status_t status; ++ int i, rc; + + PML_UCX_VERBOSE(1, "mca_pml_ucx_init"); + +@@ -201,30 +202,34 @@ + &ompi_pml_ucx.ucp_worker); + if (UCS_OK != status) { + PML_UCX_ERROR("Failed to create UCP worker"); +- return OMPI_ERROR; ++ rc = OMPI_ERROR; ++ goto err; + } + + attr.field_mask = UCP_WORKER_ATTR_FIELD_THREAD_MODE; + status = ucp_worker_query(ompi_pml_ucx.ucp_worker, &attr); + if (UCS_OK != status) { +- ucp_worker_destroy(ompi_pml_ucx.ucp_worker); +- ompi_pml_ucx.ucp_worker = NULL; + PML_UCX_ERROR("Failed to query UCP worker thread level"); +- return OMPI_ERROR; ++ rc = OMPI_ERROR; ++ goto err_destroy_worker; + } + +- if (ompi_mpi_thread_multiple && attr.thread_mode != UCS_THREAD_MODE_MULTI) { ++ if (ompi_mpi_thread_multiple && (attr.thread_mode != UCS_THREAD_MODE_MULTI)) { + /* UCX does not support multithreading, disqualify current PML for now */ + /* TODO: we should let OMPI to fallback to THREAD_SINGLE mode */ +- ucp_worker_destroy(ompi_pml_ucx.ucp_worker); +- ompi_pml_ucx.ucp_worker = NULL; + PML_UCX_ERROR("UCP worker does not support MPI_THREAD_MULTIPLE"); +- return OMPI_ERROR; ++ rc = OMPI_ERR_NOT_SUPPORTED; ++ goto err_destroy_worker; + } + + rc = mca_pml_ucx_send_worker_address(); + if (rc < 0) { +- return rc; ++ goto err_destroy_worker; ++ } ++ ++ ompi_pml_ucx.datatype_attr_keyval = MPI_KEYVAL_INVALID; ++ for (i = 0; i < OMPI_DATATYPE_MAX_PREDEFINED; ++i) { ++ ompi_pml_ucx.predefined_types[i] = PML_UCX_DATATYPE_INVALID; + } + + /* Initialize the free lists */ +@@ -240,15 +245,34 @@ + PML_UCX_VERBOSE(2, "created ucp context %p, worker %p", + (void *)ompi_pml_ucx.ucp_context, + (void *)ompi_pml_ucx.ucp_worker); +- return OMPI_SUCCESS; ++ return rc; ++ ++err_destroy_worker: ++ ucp_worker_destroy(ompi_pml_ucx.ucp_worker); ++ ompi_pml_ucx.ucp_worker = NULL; ++err: ++ return OMPI_ERROR; + } + + int mca_pml_ucx_cleanup(void) + { ++ int i; ++ + PML_UCX_VERBOSE(1, "mca_pml_ucx_cleanup"); + + opal_progress_unregister(mca_pml_ucx_progress); + ++ if (ompi_pml_ucx.datatype_attr_keyval != MPI_KEYVAL_INVALID) { ++ ompi_attr_free_keyval(TYPE_ATTR, &ompi_pml_ucx.datatype_attr_keyval, false); ++ } ++ ++ for (i = 0; i < OMPI_DATATYPE_MAX_PREDEFINED; ++i) { ++ if (ompi_pml_ucx.predefined_types[i] != PML_UCX_DATATYPE_INVALID) { ++ ucp_dt_destroy(ompi_pml_ucx.predefined_types[i]); ++ ompi_pml_ucx.predefined_types[i] = PML_UCX_DATATYPE_INVALID; ++ } ++ } ++ + ompi_pml_ucx.completed_send_req.req_state = OMPI_REQUEST_INVALID; + OMPI_REQUEST_FINI(&ompi_pml_ucx.completed_send_req); + OBJ_DESTRUCT(&ompi_pml_ucx.completed_send_req); +@@ -437,6 +461,22 @@ + + int mca_pml_ucx_enable(bool enable) + { ++ ompi_attribute_fn_ptr_union_t copy_fn; ++ ompi_attribute_fn_ptr_union_t del_fn; ++ int ret; ++ ++ /* Create a key for adding custom attributes to datatypes */ ++ copy_fn.attr_datatype_copy_fn = ++ (MPI_Type_internal_copy_attr_function*)MPI_TYPE_NULL_COPY_FN; ++ del_fn.attr_datatype_delete_fn = mca_pml_ucx_datatype_attr_del_fn; ++ ret = ompi_attr_create_keyval(TYPE_ATTR, copy_fn, del_fn, ++ &ompi_pml_ucx.datatype_attr_keyval, NULL, 0, ++ NULL); ++ if (ret != OMPI_SUCCESS) { ++ PML_UCX_ERROR("Failed to create keyval for UCX datatypes: %d", ret); ++ return ret; ++ } ++ + PML_UCX_FREELIST_INIT(&ompi_pml_ucx.persistent_reqs, + mca_pml_ucx_persistent_request_t, + 128, -1, 128); +diff -ru openmpi-3.0.0.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c openmpi-3.0.0/ompi/mca/pml/ucx/pml_ucx_datatype.c +--- openmpi-3.0.0.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c 2017-09-12 23:31:33.000000000 +0200 ++++ openmpi-3.0.0/ompi/mca/pml/ucx/pml_ucx_datatype.c 2019-03-06 21:03:56.010224884 +0100 +@@ -10,6 +10,7 @@ + #include "pml_ucx_datatype.h" + + #include "ompi/runtime/mpiruntime.h" ++#include "ompi/attribute/attribute.h" + + #include + +@@ -108,12 +109,25 @@ + .finish = pml_ucx_generic_datatype_finish + }; + ++int mca_pml_ucx_datatype_attr_del_fn(ompi_datatype_t* datatype, int keyval, ++ void *attr_val, void *extra) ++{ ++ ucp_datatype_t ucp_datatype = (ucp_datatype_t)attr_val; ++ ++ PML_UCX_ASSERT((void*)ucp_datatype == datatype->pml_data); ++ ++ ucp_dt_destroy(ucp_datatype); ++ datatype->pml_data = PML_UCX_DATATYPE_INVALID; ++ return OMPI_SUCCESS; ++} ++ + ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + { + ucp_datatype_t ucp_datatype; + ucs_status_t status; + ptrdiff_t lb; + size_t size; ++ int ret; + + ompi_datatype_type_lb(datatype, &lb); + +@@ -128,16 +142,33 @@ + } + + status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, +- datatype, &ucp_datatype); ++ datatype, &ucp_datatype); + if (status != UCS_OK) { + PML_UCX_ERROR("Failed to create UCX datatype for %s", datatype->name); + ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); + } + ++ datatype->pml_data = ucp_datatype; ++ ++ /* Add custom attribute, to clean up UCX resources when OMPI datatype is ++ * released. ++ */ ++ if (ompi_datatype_is_predefined(datatype)) { ++ PML_UCX_ASSERT(datatype->id < OMPI_DATATYPE_MAX_PREDEFINED); ++ ompi_pml_ucx.predefined_types[datatype->id] = ucp_datatype; ++ } else { ++ ret = ompi_attr_set_c(TYPE_ATTR, datatype, &datatype->d_keyhash, ++ ompi_pml_ucx.datatype_attr_keyval, ++ (void*)ucp_datatype, false); ++ if (ret != OMPI_SUCCESS) { ++ PML_UCX_ERROR("Failed to add UCX datatype attribute for %s: %d", ++ datatype->name, ret); ++ ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); ++ } ++ } ++ + PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) +- // TODO put this on a list to be destroyed later + +- datatype->pml_data = ucp_datatype; + return ucp_datatype; + } + +diff -ru openmpi-3.0.0.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h openmpi-3.0.0/ompi/mca/pml/ucx/pml_ucx_datatype.h +--- openmpi-3.0.0.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h 2017-09-12 23:31:33.000000000 +0200 ++++ openmpi-3.0.0/ompi/mca/pml/ucx/pml_ucx_datatype.h 2019-03-06 21:03:56.038224005 +0100 +@@ -13,6 +13,8 @@ + #include "pml_ucx.h" + + ++#define PML_UCX_DATATYPE_INVALID 0 ++ + struct pml_ucx_convertor { + opal_free_list_item_t super; + ompi_datatype_t *datatype; +@@ -22,6 +24,9 @@ + + ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype); + ++int mca_pml_ucx_datatype_attr_del_fn(ompi_datatype_t* datatype, int keyval, ++ void *attr_val, void *extra); ++ + OBJ_CLASS_DECLARATION(mca_pml_ucx_convertor_t); + + +@@ -29,7 +34,7 @@ + { + ucp_datatype_t ucp_type = datatype->pml_data; + +- if (OPAL_LIKELY(ucp_type != 0)) { ++ if (OPAL_LIKELY(ucp_type != PML_UCX_DATATYPE_INVALID)) { + return ucp_type; + } + +diff -ru openmpi-3.0.0.orig/ompi/mca/pml/ucx/pml_ucx.h openmpi-3.0.0/ompi/mca/pml/ucx/pml_ucx.h +--- openmpi-3.0.0.orig/ompi/mca/pml/ucx/pml_ucx.h 2017-09-12 23:31:33.000000000 +0200 ++++ openmpi-3.0.0/ompi/mca/pml/ucx/pml_ucx.h 2019-03-06 21:03:56.038224005 +0100 +@@ -15,6 +15,7 @@ + #include "ompi/mca/pml/pml.h" + #include "ompi/mca/pml/base/base.h" + #include "ompi/datatype/ompi_datatype.h" ++#include "ompi/datatype/ompi_datatype_internal.h" + #include "ompi/communicator/communicator.h" + #include "ompi/request/request.h" + +@@ -37,6 +38,10 @@ + ucp_context_h ucp_context; + ucp_worker_h ucp_worker; + ++ /* Datatypes */ ++ int datatype_attr_keyval; ++ ucp_datatype_t predefined_types[OMPI_DATATYPE_MPI_MAX_PREDEFINED]; ++ + /* Requests */ + mca_pml_ucx_freelist_t persistent_reqs; + ompi_request_t completed_send_req; diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb index 07291c638b4..ce46a19968b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb @@ -10,10 +10,11 @@ toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-3.1_fix-ib-query.patch'] +patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] checksums = [ 'a72d5a3f64c7afa33fb6c795e1168de7f92b35fd1f97ef606cfcf7405273aedc', # openmpi-3.1.0.tar.gz - '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch + # OpenMPI-3.1.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch + 'ee20ef812212ad59bd08aa07ceb44d9f1daa8143a212f656c64f1056ecb4a4e9', ] # needed for --with-verbs diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch new file mode 100644 index 00000000000..6a9195a9ab4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch @@ -0,0 +1,265 @@ +From 4763822a64c9002f24429aef95d87f6abfc45c06 Mon Sep 17 00:00:00 2001 +From: Yossi Itigin +Date: Tue, 9 Oct 2018 16:38:49 +0300 +Subject: [PATCH 1/2] pml_ucx: add ompi datatype attribute to release + ucp_datatype + +Signed-off-by: Yossi Itigin +--- + +Adapted to older OpenMPI versions. + +Åke Sandgren, 20190307 +diff -ru openmpi-3.1.0.orig/ompi/mca/pml/ucx/pml_ucx.c openmpi-3.1.0/ompi/mca/pml/ucx/pml_ucx.c +--- openmpi-3.1.0.orig/ompi/mca/pml/ucx/pml_ucx.c 2018-05-07 22:42:22.000000000 +0200 ++++ openmpi-3.1.0/ompi/mca/pml/ucx/pml_ucx.c 2019-03-07 07:51:36.690847601 +0100 +@@ -14,6 +14,7 @@ + + #include "opal/runtime/opal.h" + #include "opal/mca/pmix/pmix.h" ++#include "ompi/attribute/attribute.h" + #include "ompi/message/message.h" + #include "ompi/mca/pml/base/pml_base_bsend.h" + #include "pml_ucx_request.h" +@@ -185,9 +186,9 @@ + int mca_pml_ucx_init(void) + { + ucp_worker_params_t params; +- ucs_status_t status; + ucp_worker_attr_t attr; +- int rc; ++ ucs_status_t status; ++ int i, rc; + + PML_UCX_VERBOSE(1, "mca_pml_ucx_init"); + +@@ -204,30 +205,34 @@ + &ompi_pml_ucx.ucp_worker); + if (UCS_OK != status) { + PML_UCX_ERROR("Failed to create UCP worker"); +- return OMPI_ERROR; ++ rc = OMPI_ERROR; ++ goto err; + } + + attr.field_mask = UCP_WORKER_ATTR_FIELD_THREAD_MODE; + status = ucp_worker_query(ompi_pml_ucx.ucp_worker, &attr); + if (UCS_OK != status) { +- ucp_worker_destroy(ompi_pml_ucx.ucp_worker); +- ompi_pml_ucx.ucp_worker = NULL; + PML_UCX_ERROR("Failed to query UCP worker thread level"); +- return OMPI_ERROR; ++ rc = OMPI_ERROR; ++ goto err_destroy_worker; + } + +- if (ompi_mpi_thread_multiple && attr.thread_mode != UCS_THREAD_MODE_MULTI) { ++ if (ompi_mpi_thread_multiple && (attr.thread_mode != UCS_THREAD_MODE_MULTI)) { + /* UCX does not support multithreading, disqualify current PML for now */ + /* TODO: we should let OMPI to fallback to THREAD_SINGLE mode */ +- ucp_worker_destroy(ompi_pml_ucx.ucp_worker); +- ompi_pml_ucx.ucp_worker = NULL; + PML_UCX_ERROR("UCP worker does not support MPI_THREAD_MULTIPLE"); +- return OMPI_ERROR; ++ rc = OMPI_ERR_NOT_SUPPORTED; ++ goto err_destroy_worker; + } + + rc = mca_pml_ucx_send_worker_address(); + if (rc < 0) { +- return rc; ++ goto err_destroy_worker; ++ } ++ ++ ompi_pml_ucx.datatype_attr_keyval = MPI_KEYVAL_INVALID; ++ for (i = 0; i < OMPI_DATATYPE_MAX_PREDEFINED; ++i) { ++ ompi_pml_ucx.predefined_types[i] = PML_UCX_DATATYPE_INVALID; + } + + /* Initialize the free lists */ +@@ -243,15 +248,34 @@ + PML_UCX_VERBOSE(2, "created ucp context %p, worker %p", + (void *)ompi_pml_ucx.ucp_context, + (void *)ompi_pml_ucx.ucp_worker); +- return OMPI_SUCCESS; ++ return rc; ++ ++err_destroy_worker: ++ ucp_worker_destroy(ompi_pml_ucx.ucp_worker); ++ ompi_pml_ucx.ucp_worker = NULL; ++err: ++ return OMPI_ERROR; + } + + int mca_pml_ucx_cleanup(void) + { ++ int i; ++ + PML_UCX_VERBOSE(1, "mca_pml_ucx_cleanup"); + + opal_progress_unregister(mca_pml_ucx_progress); + ++ if (ompi_pml_ucx.datatype_attr_keyval != MPI_KEYVAL_INVALID) { ++ ompi_attr_free_keyval(TYPE_ATTR, &ompi_pml_ucx.datatype_attr_keyval, false); ++ } ++ ++ for (i = 0; i < OMPI_DATATYPE_MAX_PREDEFINED; ++i) { ++ if (ompi_pml_ucx.predefined_types[i] != PML_UCX_DATATYPE_INVALID) { ++ ucp_dt_destroy(ompi_pml_ucx.predefined_types[i]); ++ ompi_pml_ucx.predefined_types[i] = PML_UCX_DATATYPE_INVALID; ++ } ++ } ++ + ompi_pml_ucx.completed_send_req.req_state = OMPI_REQUEST_INVALID; + OMPI_REQUEST_FINI(&ompi_pml_ucx.completed_send_req); + OBJ_DESTRUCT(&ompi_pml_ucx.completed_send_req); +@@ -440,6 +464,22 @@ + + int mca_pml_ucx_enable(bool enable) + { ++ ompi_attribute_fn_ptr_union_t copy_fn; ++ ompi_attribute_fn_ptr_union_t del_fn; ++ int ret; ++ ++ /* Create a key for adding custom attributes to datatypes */ ++ copy_fn.attr_datatype_copy_fn = ++ (MPI_Type_internal_copy_attr_function*)MPI_TYPE_NULL_COPY_FN; ++ del_fn.attr_datatype_delete_fn = mca_pml_ucx_datatype_attr_del_fn; ++ ret = ompi_attr_create_keyval(TYPE_ATTR, copy_fn, del_fn, ++ &ompi_pml_ucx.datatype_attr_keyval, NULL, 0, ++ NULL); ++ if (ret != OMPI_SUCCESS) { ++ PML_UCX_ERROR("Failed to create keyval for UCX datatypes: %d", ret); ++ return ret; ++ } ++ + PML_UCX_FREELIST_INIT(&ompi_pml_ucx.persistent_reqs, + mca_pml_ucx_persistent_request_t, + 128, -1, 128); +diff -ru openmpi-3.1.0.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c openmpi-3.1.0/ompi/mca/pml/ucx/pml_ucx_datatype.c +--- openmpi-3.1.0.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c 2018-05-07 22:42:22.000000000 +0200 ++++ openmpi-3.1.0/ompi/mca/pml/ucx/pml_ucx_datatype.c 2019-03-07 07:51:36.690847601 +0100 +@@ -10,6 +10,7 @@ + #include "pml_ucx_datatype.h" + + #include "ompi/runtime/mpiruntime.h" ++#include "ompi/attribute/attribute.h" + + #include + +@@ -108,12 +109,25 @@ + .finish = pml_ucx_generic_datatype_finish + }; + ++int mca_pml_ucx_datatype_attr_del_fn(ompi_datatype_t* datatype, int keyval, ++ void *attr_val, void *extra) ++{ ++ ucp_datatype_t ucp_datatype = (ucp_datatype_t)attr_val; ++ ++ PML_UCX_ASSERT((void*)ucp_datatype == datatype->pml_data); ++ ++ ucp_dt_destroy(ucp_datatype); ++ datatype->pml_data = PML_UCX_DATATYPE_INVALID; ++ return OMPI_SUCCESS; ++} ++ + ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + { + ucp_datatype_t ucp_datatype; + ucs_status_t status; + ptrdiff_t lb; + size_t size; ++ int ret; + + ompi_datatype_type_lb(datatype, &lb); + +@@ -128,16 +142,33 @@ + } + + status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, +- datatype, &ucp_datatype); ++ datatype, &ucp_datatype); + if (status != UCS_OK) { + PML_UCX_ERROR("Failed to create UCX datatype for %s", datatype->name); + ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); + } + ++ datatype->pml_data = ucp_datatype; ++ ++ /* Add custom attribute, to clean up UCX resources when OMPI datatype is ++ * released. ++ */ ++ if (ompi_datatype_is_predefined(datatype)) { ++ PML_UCX_ASSERT(datatype->id < OMPI_DATATYPE_MAX_PREDEFINED); ++ ompi_pml_ucx.predefined_types[datatype->id] = ucp_datatype; ++ } else { ++ ret = ompi_attr_set_c(TYPE_ATTR, datatype, &datatype->d_keyhash, ++ ompi_pml_ucx.datatype_attr_keyval, ++ (void*)ucp_datatype, false); ++ if (ret != OMPI_SUCCESS) { ++ PML_UCX_ERROR("Failed to add UCX datatype attribute for %s: %d", ++ datatype->name, ret); ++ ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); ++ } ++ } ++ + PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) +- // TODO put this on a list to be destroyed later + +- datatype->pml_data = ucp_datatype; + return ucp_datatype; + } + +diff -ru openmpi-3.1.0.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h openmpi-3.1.0/ompi/mca/pml/ucx/pml_ucx_datatype.h +--- openmpi-3.1.0.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h 2018-05-07 22:42:22.000000000 +0200 ++++ openmpi-3.1.0/ompi/mca/pml/ucx/pml_ucx_datatype.h 2019-03-07 07:51:36.694847475 +0100 +@@ -13,6 +13,8 @@ + #include "pml_ucx.h" + + ++#define PML_UCX_DATATYPE_INVALID 0 ++ + struct pml_ucx_convertor { + opal_free_list_item_t super; + ompi_datatype_t *datatype; +@@ -22,6 +24,9 @@ + + ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype); + ++int mca_pml_ucx_datatype_attr_del_fn(ompi_datatype_t* datatype, int keyval, ++ void *attr_val, void *extra); ++ + OBJ_CLASS_DECLARATION(mca_pml_ucx_convertor_t); + + +@@ -29,7 +34,7 @@ + { + ucp_datatype_t ucp_type = datatype->pml_data; + +- if (OPAL_LIKELY(ucp_type != 0)) { ++ if (OPAL_LIKELY(ucp_type != PML_UCX_DATATYPE_INVALID)) { + return ucp_type; + } + +diff -ru openmpi-3.1.0.orig/ompi/mca/pml/ucx/pml_ucx.h openmpi-3.1.0/ompi/mca/pml/ucx/pml_ucx.h +--- openmpi-3.1.0.orig/ompi/mca/pml/ucx/pml_ucx.h 2018-05-07 22:42:22.000000000 +0200 ++++ openmpi-3.1.0/ompi/mca/pml/ucx/pml_ucx.h 2019-03-07 07:51:36.694847475 +0100 +@@ -15,6 +15,7 @@ + #include "ompi/mca/pml/pml.h" + #include "ompi/mca/pml/base/base.h" + #include "ompi/datatype/ompi_datatype.h" ++#include "ompi/datatype/ompi_datatype_internal.h" + #include "ompi/communicator/communicator.h" + #include "ompi/request/request.h" + +@@ -37,6 +38,10 @@ + ucp_context_h ucp_context; + ucp_worker_h ucp_worker; + ++ /* Datatypes */ ++ int datatype_attr_keyval; ++ ucp_datatype_t predefined_types[OMPI_DATATYPE_MPI_MAX_PREDEFINED]; ++ + /* Requests */ + mca_pml_ucx_freelist_t persistent_reqs; + ompi_request_t completed_send_req; diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb index 8a9c2c25183..d3be703adb9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb @@ -10,11 +10,8 @@ toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-3.1_fix-ib-query.patch'] -checksums = [ - '846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce', # openmpi-3.1.1.tar.gz - '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch -] +patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] +checksums = ['846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce'] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch new file mode 100644 index 00000000000..c101883a40b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch @@ -0,0 +1,265 @@ +From 4763822a64c9002f24429aef95d87f6abfc45c06 Mon Sep 17 00:00:00 2001 +From: Yossi Itigin +Date: Tue, 9 Oct 2018 16:38:49 +0300 +Subject: [PATCH 1/2] pml_ucx: add ompi datatype attribute to release + ucp_datatype + +Signed-off-by: Yossi Itigin +--- + +Adapted to older OpenMPI versions. + +Åke Sandgren, 20190307 +diff -ru openmpi-3.1.1.orig/ompi/mca/pml/ucx/pml_ucx.c openmpi-3.1.1/ompi/mca/pml/ucx/pml_ucx.c +--- openmpi-3.1.1.orig/ompi/mca/pml/ucx/pml_ucx.c 2018-06-29 18:08:13.000000000 +0200 ++++ openmpi-3.1.1/ompi/mca/pml/ucx/pml_ucx.c 2019-03-06 15:50:25.000000000 +0100 +@@ -14,6 +14,7 @@ + + #include "opal/runtime/opal.h" + #include "opal/mca/pmix/pmix.h" ++#include "ompi/attribute/attribute.h" + #include "ompi/message/message.h" + #include "ompi/mca/pml/base/pml_base_bsend.h" + #include "pml_ucx_request.h" +@@ -187,9 +188,9 @@ + int mca_pml_ucx_init(void) + { + ucp_worker_params_t params; +- ucs_status_t status; + ucp_worker_attr_t attr; +- int rc; ++ ucs_status_t status; ++ int i, rc; + + PML_UCX_VERBOSE(1, "mca_pml_ucx_init"); + +@@ -206,30 +207,34 @@ + &ompi_pml_ucx.ucp_worker); + if (UCS_OK != status) { + PML_UCX_ERROR("Failed to create UCP worker"); +- return OMPI_ERROR; ++ rc = OMPI_ERROR; ++ goto err; + } + + attr.field_mask = UCP_WORKER_ATTR_FIELD_THREAD_MODE; + status = ucp_worker_query(ompi_pml_ucx.ucp_worker, &attr); + if (UCS_OK != status) { +- ucp_worker_destroy(ompi_pml_ucx.ucp_worker); +- ompi_pml_ucx.ucp_worker = NULL; + PML_UCX_ERROR("Failed to query UCP worker thread level"); +- return OMPI_ERROR; ++ rc = OMPI_ERROR; ++ goto err_destroy_worker; + } + +- if (ompi_mpi_thread_multiple && attr.thread_mode != UCS_THREAD_MODE_MULTI) { ++ if (ompi_mpi_thread_multiple && (attr.thread_mode != UCS_THREAD_MODE_MULTI)) { + /* UCX does not support multithreading, disqualify current PML for now */ + /* TODO: we should let OMPI to fallback to THREAD_SINGLE mode */ +- ucp_worker_destroy(ompi_pml_ucx.ucp_worker); +- ompi_pml_ucx.ucp_worker = NULL; + PML_UCX_ERROR("UCP worker does not support MPI_THREAD_MULTIPLE"); +- return OMPI_ERROR; ++ rc = OMPI_ERR_NOT_SUPPORTED; ++ goto err_destroy_worker; + } + + rc = mca_pml_ucx_send_worker_address(); + if (rc < 0) { +- return rc; ++ goto err_destroy_worker; ++ } ++ ++ ompi_pml_ucx.datatype_attr_keyval = MPI_KEYVAL_INVALID; ++ for (i = 0; i < OMPI_DATATYPE_MAX_PREDEFINED; ++i) { ++ ompi_pml_ucx.predefined_types[i] = PML_UCX_DATATYPE_INVALID; + } + + /* Initialize the free lists */ +@@ -245,15 +250,34 @@ + PML_UCX_VERBOSE(2, "created ucp context %p, worker %p", + (void *)ompi_pml_ucx.ucp_context, + (void *)ompi_pml_ucx.ucp_worker); +- return OMPI_SUCCESS; ++ return rc; ++ ++err_destroy_worker: ++ ucp_worker_destroy(ompi_pml_ucx.ucp_worker); ++ ompi_pml_ucx.ucp_worker = NULL; ++err: ++ return OMPI_ERROR; + } + + int mca_pml_ucx_cleanup(void) + { ++ int i; ++ + PML_UCX_VERBOSE(1, "mca_pml_ucx_cleanup"); + + opal_progress_unregister(mca_pml_ucx_progress); + ++ if (ompi_pml_ucx.datatype_attr_keyval != MPI_KEYVAL_INVALID) { ++ ompi_attr_free_keyval(TYPE_ATTR, &ompi_pml_ucx.datatype_attr_keyval, false); ++ } ++ ++ for (i = 0; i < OMPI_DATATYPE_MAX_PREDEFINED; ++i) { ++ if (ompi_pml_ucx.predefined_types[i] != PML_UCX_DATATYPE_INVALID) { ++ ucp_dt_destroy(ompi_pml_ucx.predefined_types[i]); ++ ompi_pml_ucx.predefined_types[i] = PML_UCX_DATATYPE_INVALID; ++ } ++ } ++ + ompi_pml_ucx.completed_send_req.req_state = OMPI_REQUEST_INVALID; + OMPI_REQUEST_FINI(&ompi_pml_ucx.completed_send_req); + OBJ_DESTRUCT(&ompi_pml_ucx.completed_send_req); +@@ -452,6 +476,22 @@ + + int mca_pml_ucx_enable(bool enable) + { ++ ompi_attribute_fn_ptr_union_t copy_fn; ++ ompi_attribute_fn_ptr_union_t del_fn; ++ int ret; ++ ++ /* Create a key for adding custom attributes to datatypes */ ++ copy_fn.attr_datatype_copy_fn = ++ (MPI_Type_internal_copy_attr_function*)MPI_TYPE_NULL_COPY_FN; ++ del_fn.attr_datatype_delete_fn = mca_pml_ucx_datatype_attr_del_fn; ++ ret = ompi_attr_create_keyval(TYPE_ATTR, copy_fn, del_fn, ++ &ompi_pml_ucx.datatype_attr_keyval, NULL, 0, ++ NULL); ++ if (ret != OMPI_SUCCESS) { ++ PML_UCX_ERROR("Failed to create keyval for UCX datatypes: %d", ret); ++ return ret; ++ } ++ + PML_UCX_FREELIST_INIT(&ompi_pml_ucx.persistent_reqs, + mca_pml_ucx_persistent_request_t, + 128, -1, 128); +diff -ru openmpi-3.1.1.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c openmpi-3.1.1/ompi/mca/pml/ucx/pml_ucx_datatype.c +--- openmpi-3.1.1.orig/ompi/mca/pml/ucx/pml_ucx_datatype.c 2018-06-29 18:08:13.000000000 +0200 ++++ openmpi-3.1.1/ompi/mca/pml/ucx/pml_ucx_datatype.c 2019-03-06 15:50:25.000000000 +0100 +@@ -10,6 +10,7 @@ + #include "pml_ucx_datatype.h" + + #include "ompi/runtime/mpiruntime.h" ++#include "ompi/attribute/attribute.h" + + #include + +@@ -127,12 +128,25 @@ + .finish = pml_ucx_generic_datatype_finish + }; + ++int mca_pml_ucx_datatype_attr_del_fn(ompi_datatype_t* datatype, int keyval, ++ void *attr_val, void *extra) ++{ ++ ucp_datatype_t ucp_datatype = (ucp_datatype_t)attr_val; ++ ++ PML_UCX_ASSERT((void*)ucp_datatype == datatype->pml_data); ++ ++ ucp_dt_destroy(ucp_datatype); ++ datatype->pml_data = PML_UCX_DATATYPE_INVALID; ++ return OMPI_SUCCESS; ++} ++ + ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + { + ucp_datatype_t ucp_datatype; + ucs_status_t status; + ptrdiff_t lb; + size_t size; ++ int ret; + + ompi_datatype_type_lb(datatype, &lb); + +@@ -147,16 +161,33 @@ + } + + status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, +- datatype, &ucp_datatype); ++ datatype, &ucp_datatype); + if (status != UCS_OK) { + PML_UCX_ERROR("Failed to create UCX datatype for %s", datatype->name); + ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); + } + ++ datatype->pml_data = ucp_datatype; ++ ++ /* Add custom attribute, to clean up UCX resources when OMPI datatype is ++ * released. ++ */ ++ if (ompi_datatype_is_predefined(datatype)) { ++ PML_UCX_ASSERT(datatype->id < OMPI_DATATYPE_MAX_PREDEFINED); ++ ompi_pml_ucx.predefined_types[datatype->id] = ucp_datatype; ++ } else { ++ ret = ompi_attr_set_c(TYPE_ATTR, datatype, &datatype->d_keyhash, ++ ompi_pml_ucx.datatype_attr_keyval, ++ (void*)ucp_datatype, false); ++ if (ret != OMPI_SUCCESS) { ++ PML_UCX_ERROR("Failed to add UCX datatype attribute for %s: %d", ++ datatype->name, ret); ++ ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); ++ } ++ } ++ + PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) +- // TODO put this on a list to be destroyed later + +- datatype->pml_data = ucp_datatype; + return ucp_datatype; + } + +diff -ru openmpi-3.1.1.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h openmpi-3.1.1/ompi/mca/pml/ucx/pml_ucx_datatype.h +--- openmpi-3.1.1.orig/ompi/mca/pml/ucx/pml_ucx_datatype.h 2018-06-29 18:08:13.000000000 +0200 ++++ openmpi-3.1.1/ompi/mca/pml/ucx/pml_ucx_datatype.h 2019-03-06 15:50:25.000000000 +0100 +@@ -13,6 +13,8 @@ + #include "pml_ucx.h" + + ++#define PML_UCX_DATATYPE_INVALID 0 ++ + struct pml_ucx_convertor { + opal_free_list_item_t super; + ompi_datatype_t *datatype; +@@ -23,6 +25,9 @@ + + ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype); + ++int mca_pml_ucx_datatype_attr_del_fn(ompi_datatype_t* datatype, int keyval, ++ void *attr_val, void *extra); ++ + OBJ_CLASS_DECLARATION(mca_pml_ucx_convertor_t); + + +@@ -30,7 +35,7 @@ + { + ucp_datatype_t ucp_type = datatype->pml_data; + +- if (OPAL_LIKELY(ucp_type != 0)) { ++ if (OPAL_LIKELY(ucp_type != PML_UCX_DATATYPE_INVALID)) { + return ucp_type; + } + +diff -ru openmpi-3.1.1.orig/ompi/mca/pml/ucx/pml_ucx.h openmpi-3.1.1/ompi/mca/pml/ucx/pml_ucx.h +--- openmpi-3.1.1.orig/ompi/mca/pml/ucx/pml_ucx.h 2018-06-29 18:08:13.000000000 +0200 ++++ openmpi-3.1.1/ompi/mca/pml/ucx/pml_ucx.h 2019-03-06 15:50:25.000000000 +0100 +@@ -15,6 +15,7 @@ + #include "ompi/mca/pml/pml.h" + #include "ompi/mca/pml/base/base.h" + #include "ompi/datatype/ompi_datatype.h" ++#include "ompi/datatype/ompi_datatype_internal.h" + #include "ompi/communicator/communicator.h" + #include "ompi/request/request.h" + +@@ -37,6 +38,10 @@ + ucp_context_h ucp_context; + ucp_worker_h ucp_worker; + ++ /* Datatypes */ ++ int datatype_attr_keyval; ++ ucp_datatype_t predefined_types[OMPI_DATATYPE_MPI_MAX_PREDEFINED]; ++ + /* Requests */ + mca_pml_ucx_freelist_t persistent_reqs; + ompi_request_t completed_send_req; diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb index 1df7c075046..118eb82ee80 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb @@ -10,10 +10,11 @@ toolchain = {'name': 'gcccuda', 'version': '2018b'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-3.1_fix-ib-query.patch'] +patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] checksums = [ '846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce', # openmpi-3.1.1.tar.gz - '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch + # OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch + '945d19eb583af1e4d2ddcb40bafe505352244635c812308d1c77ad1db2811538', ] # needed for --with-verbs diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb index d24ba83eeb5..58fdec610b8 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -10,10 +10,11 @@ toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-3.1_fix-ib-query.patch'] +patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] checksums = [ '846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce', # openmpi-3.1.1.tar.gz - '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch + # OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch + '945d19eb583af1e4d2ddcb40bafe505352244635c812308d1c77ad1db2811538', ] # needed for --with-verbs diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb index 9223fe6f024..93accf8572e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb @@ -10,10 +10,11 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-3.1_fix-ib-query.patch'] +patches = ['%(name)s-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] checksums = [ '363c8a1258d12df28657e9b13bfe41e30fc129a4cfb89fcf53ff68bbe1bd65b3', # openmpi-3.1.2.tar.gz - '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch + # OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch + '945d19eb583af1e4d2ddcb40bafe505352244635c812308d1c77ad1db2811538', ] # needed for --with-verbs From 6c3425d8d939b2037f8b38d77b084c14b5a5cac7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 7 Mar 2019 14:38:51 +0200 Subject: [PATCH 0746/5331] Re-add accidentally deleted OpenMPI-3.1_fix-ib-query.patch --- .../o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb | 6 +++++- .../o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb | 12 ++++++++++-- .../o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb | 6 +++++- ...enMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb | 6 +++++- .../o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb | 6 +++++- 5 files changed, 30 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb index ce46a19968b..10415797bc5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb @@ -10,9 +10,13 @@ toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] +patches = [ + 'OpenMPI-3.1_fix-ib-query.patch', + '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch' +] checksums = [ 'a72d5a3f64c7afa33fb6c795e1168de7f92b35fd1f97ef606cfcf7405273aedc', # openmpi-3.1.0.tar.gz + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch # OpenMPI-3.1.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch 'ee20ef812212ad59bd08aa07ceb44d9f1daa8143a212f656c64f1056ecb4a4e9', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb index d3be703adb9..fa65134b4c8 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb @@ -10,8 +10,16 @@ toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] -checksums = ['846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce'] +patches = [ + 'OpenMPI-3.1_fix-ib-query.patch', + '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch' +] +checksums = [ + '846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce', # openmpi-3.1.1.tar.gz + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch + # OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch + '945d19eb583af1e4d2ddcb40bafe505352244635c812308d1c77ad1db2811538', +] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb index 118eb82ee80..cc9bcaec6e8 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb @@ -10,9 +10,13 @@ toolchain = {'name': 'gcccuda', 'version': '2018b'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] +patches = [ + 'OpenMPI-3.1_fix-ib-query.patch', + '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch' +] checksums = [ '846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce', # openmpi-3.1.1.tar.gz + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch # OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch '945d19eb583af1e4d2ddcb40bafe505352244635c812308d1c77ad1db2811538', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb index 58fdec610b8..472edc30183 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -10,9 +10,13 @@ toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] +patches = [ + 'OpenMPI-3.1_fix-ib-query.patch', + '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch' +] checksums = [ '846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce', # openmpi-3.1.1.tar.gz + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch # OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch '945d19eb583af1e4d2ddcb40bafe505352244635c812308d1c77ad1db2811538', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb index 93accf8572e..a33e4910590 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb @@ -10,9 +10,13 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] +patches = [ + 'OpenMPI-3.1_fix-ib-query.patch', + '%(name)s-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch' +] checksums = [ '363c8a1258d12df28657e9b13bfe41e30fc129a4cfb89fcf53ff68bbe1bd65b3', # openmpi-3.1.2.tar.gz + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch # OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch '945d19eb583af1e4d2ddcb40bafe505352244635c812308d1c77ad1db2811538', ] From 1ba7a46a7627ee53652bd7600479ca7851a73c8d Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 7 Mar 2019 08:03:54 -0600 Subject: [PATCH 0747/5331] Added download_dep_fail --- .../MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb | 2 ++ .../MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb | 2 ++ .../MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb | 2 ++ .../MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb | 2 ++ 4 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb index 6bdafccb408..7009268301e 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb @@ -23,6 +23,8 @@ buildopts = '--build-base=%(builddir)s install --prefix=%(installdir)s' skipsteps = ['install'] +download_dep_fail = True + options = {'modulename': 'matlab.engine'} # Test that connection with MATLAB can be established successfully diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb index 4bf529a2236..d7fcbc99902 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb @@ -23,6 +23,8 @@ buildopts = '--build-base=%(builddir)s install --prefix=%(installdir)s' skipsteps = ['install'] +download_dep_fail = True + options = {'modulename': 'matlab.engine'} # Test that connection with MATLAB can be established successfully diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb index bc318aabe88..fc816ba2323 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb @@ -23,6 +23,8 @@ buildopts = '--build-base=%(builddir)s install --prefix=%(installdir)s' skipsteps = ['install'] +download_dep_fail = True + options = {'modulename': 'matlab.engine'} # Test that connection with MATLAB can be established successfully diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb index 992c2a55e76..0c39c8a729c 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb @@ -23,6 +23,8 @@ buildopts = '--build-base=%(builddir)s install --prefix=%(installdir)s' skipsteps = ['install'] +download_dep_fail = True + options = {'modulename': 'matlab.engine'} # Test that connection with MATLAB can be established successfully From 7fbbd4b1fc6d164a6e2ad2498da0b6618be042e0 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 7 Mar 2019 09:35:51 -0600 Subject: [PATCH 0748/5331] adding easyconfigs: NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb, NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb, NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb, NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb, Pillow-5.3.0-foss-2017b-Python-2.7.14.eb, Pillow-5.3.0-foss-2017b-Python-3.6.3.eb, Pillow-5.3.0-intel-2017b-Python-2.7.14.eb, Pillow-5.3.0-intel-2017b-Python-3.6.3.eb --- .../NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb | 45 +++++++++++++++++++ .../NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb | 45 +++++++++++++++++++ ...NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb | 45 +++++++++++++++++++ .../NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb | 45 +++++++++++++++++++ .../Pillow-5.3.0-foss-2017b-Python-2.7.14.eb | 36 +++++++++++++++ .../Pillow-5.3.0-foss-2017b-Python-3.6.3.eb | 36 +++++++++++++++ .../Pillow-5.3.0-intel-2017b-Python-2.7.14.eb | 36 +++++++++++++++ .../Pillow-5.3.0-intel-2017b-Python-3.6.3.eb | 36 +++++++++++++++ 8 files changed, 324 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..9e70f5e9739 --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'NiBabel' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [ + ('Python', '2.7.14'), + ('Pillow', '5.3.0', versionsuffix), +] + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('pydicom', '1.2.0', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pydicom/pydicom/archive/'], + 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], + }), + ('nibabel', version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], + 'checksums': ['bf34aeb0f7ca52dc528ae4f842607cea307b334163857ff1d64d43068f637ada'], + }), +] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..b4c41c5b834 --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'NiBabel' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [ + ('Python', '3.6.3'), + ('Pillow', '5.3.0', versionsuffix), +] + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('pydicom', '1.2.0', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pydicom/pydicom/archive/'], + 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], + }), + ('nibabel', version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], + 'checksums': ['bf34aeb0f7ca52dc528ae4f842607cea307b334163857ff1d64d43068f637ada'], + }), +] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..3d82c6eb483 --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'NiBabel' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [ + ('Python', '2.7.14'), + ('Pillow', '5.3.0', versionsuffix), +] + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('pydicom', '1.2.0', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pydicom/pydicom/archive/'], + 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], + }), + ('nibabel', version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], + 'checksums': ['bf34aeb0f7ca52dc528ae4f842607cea307b334163857ff1d64d43068f637ada'], + }), +] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..0286ab22fff --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'NiBabel' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [ + ('Python', '3.6.3'), + ('Pillow', '5.3.0', versionsuffix), +] + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('pydicom', '1.2.0', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pydicom/pydicom/archive/'], + 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], + }), + ('nibabel', version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], + 'checksums': ['bf34aeb0f7ca52dc528ae4f842607cea307b334163857ff1d64d43068f637ada'], + }), +] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..f2059ab279c --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '5.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] + +dependencies = [ + ('Python', '2.7.14'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.32'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.9'), + ('freetype', '2.8') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..6cf42f716b5 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '5.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] + +dependencies = [ + ('Python', '3.6.3'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.32'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.9'), + ('freetype', '2.8') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..908e0e21aba --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '5.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] + +dependencies = [ + ('Python', '2.7.14'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.32'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.9'), + ('freetype', '2.8') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..f9884e02e96 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '5.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] + +dependencies = [ + ('Python', '3.6.3'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.32'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.9'), + ('freetype', '2.8') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' From 1145c5b602cda6bc095ca33c838b293e50442c39 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 7 Mar 2019 12:53:29 -0600 Subject: [PATCH 0749/5331] adding easyconfigs: HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb, HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb, HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb, HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb, Pysam-0.14-foss-2017b-Python-3.6.3.eb, Pysam-0.14-intel-2017b-Python-3.6.3.eb --- .../HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb | 34 +++++++++++++++++ .../HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb | 34 +++++++++++++++++ .../HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb | 34 +++++++++++++++++ .../HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb | 34 +++++++++++++++++ .../Pysam-0.14-foss-2017b-Python-3.6.3.eb | 37 +++++++++++++++++++ .../Pysam-0.14-intel-2017b-Python-3.6.3.eb | 37 +++++++++++++++++++ 6 files changed, 210 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..8ff2351f9ac --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] + +dependencies = [ + ('Python', '2.7.14'), + ('Pysam', '0.14', versionsuffix), + ('matplotlib', '2.1.0', versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], +} + +sanity_check_commands = [('htseq-count --help')] + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..1995cd53010 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] + +dependencies = [ + ('Python', '3.6.3'), + ('Pysam', '0.14', versionsuffix), + ('matplotlib', '2.1.0', versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], +} + +sanity_check_commands = [('htseq-count --help')] + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..632a4ab50ad --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] + +dependencies = [ + ('Python', '2.7.14'), + ('Pysam', '0.14', versionsuffix), + ('matplotlib', '2.1.0', versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], +} + +sanity_check_commands = [('htseq-count --help')] + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..0603fa3ee5a --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +checksums = ['af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485'] + +dependencies = [ + ('Python', '3.6.3'), + ('Pysam', '0.14', versionsuffix), + ('matplotlib', '2.1.0', versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], +} + +sanity_check_commands = [('htseq-count --help')] + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..6a1b203c352 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.14' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c9c8ea82b4deee7607d5885fc7cc92311f06e765ff30e0b2b2d3d85b28cf5687'] + +dependencies = [ + ('XZ', '5.2.3'), + ('Python', '3.6.3'), + ('ncurses', '6.0'), + ('cURL', '7.56.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..358aea76f79 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.14' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c9c8ea82b4deee7607d5885fc7cc92311f06e765ff30e0b2b2d3d85b28cf5687'] + +dependencies = [ + ('XZ', '5.2.3'), + ('Python', '3.6.3'), + ('ncurses', '6.0'), + ('cURL', '7.56.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From e995ecb682a836ab32fd97c3f8c78be48cc4c1a9 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 7 Mar 2019 21:26:26 +0200 Subject: [PATCH 0750/5331] adding easyconfigs: MAGMA-1.07b-foss-2018b.eb --- .../m/MAGMA/MAGMA-1.07b-foss-2018b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb diff --git a/easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb b/easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb new file mode 100644 index 00000000000..abf5f80dffd --- /dev/null +++ b/easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'MAGMA' +version = '1.07b' + +homepage = 'https://ctg.cncr.nl/software/magma' +description = """MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. +It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous +GWAS or meta-analysis.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://ctg.cncr.nl/software/MAGMA/prog'] +sources = ['%(namelower)s_v%(version)s_source.zip'] +checksums = ['b8f6c9c5b81cedec51b2e3daafe2519f02423a7d18321f5a91534461d40538f0'] + +files_to_copy = [ + (['magma'], 'bin'), + (['manual_v%(version)s.pdf'], 'doc'), + 'CHANGELOG', + 'COPYRIGHT', +] + +sanity_check_paths = { + 'files': ['bin/magma'], + 'dirs': [], +} + +moduleclass = 'bio' From 59ce843a1986cf514bdab9b22194def65bb3e161 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 7 Mar 2019 20:45:33 +0100 Subject: [PATCH 0751/5331] added buildopts --- easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb b/easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb index abf5f80dffd..fedf12bdc7f 100644 --- a/easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb +++ b/easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb @@ -14,6 +14,8 @@ source_urls = ['https://ctg.cncr.nl/software/MAGMA/prog'] sources = ['%(namelower)s_v%(version)s_source.zip'] checksums = ['b8f6c9c5b81cedec51b2e3daafe2519f02423a7d18321f5a91534461d40538f0'] +buildopts = ' CXX=${CXX}' + files_to_copy = [ (['magma'], 'bin'), (['manual_v%(version)s.pdf'], 'doc'), From c116e8f04caaed43f8272fd3d780fd8043858bd4 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Thu, 7 Mar 2019 20:52:58 +0100 Subject: [PATCH 0752/5331] added new line at EOF to pass lint checks --- easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb index 4851931d1aa..30ce452926f 100644 --- a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb @@ -27,4 +27,4 @@ To execute Pilon run: java -Xmx8G -jar $EBROOTPILON/pilon.jar Adjust the memory value according to the size of your input files """ -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 2473840e440fc0e7d5b5e74d08b0ce1528114f28 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 7 Mar 2019 15:00:02 -0600 Subject: [PATCH 0753/5331] add in CLHEP/2.4.1.0 for Geant4/10.5 in terms of 2017b toolchain --- .../c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb | 24 +++++++++++++++++++ .../c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb | 24 +++++++++++++++++++ .../g/Geant4/Geant4-10.5-foss-2017b.eb | 2 +- .../g/Geant4/Geant4-10.5-intel-2017b.eb | 2 +- 4 files changed, 50 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb new file mode 100644 index 00000000000..cbef5e41ee7 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.1.0' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] +sources = [SOURCELOWER_TGZ] +checksums = ['d14736eb5c3d21f86ce831dc1afcf03d423825b35c84deb6f8fd16773528c54d'] + +builddependencies = [('CMake', '3.9.5')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb new file mode 100644 index 00000000000..b1ece0789f4 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.1.0' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] +sources = [SOURCELOWER_TGZ] +checksums = ['d14736eb5c3d21f86ce831dc1afcf03d423825b35c84deb6f8fd16773528c54d'] + +builddependencies = [('CMake', '3.9.5')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb index f609bc51ac7..0abcc017507 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb @@ -16,7 +16,7 @@ builddependencies = [('CMake', '3.9.5')] dependencies = [ ('expat', '2.2.4'), # recommended CLHEP version, see http://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.5.html#2. - ('CLHEP', '2.3.4.3'), + ('CLHEP', '2.4.1.0'), ] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb index af38f4b79f1..c7593466502 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb @@ -16,7 +16,7 @@ builddependencies = [('CMake', '3.9.5')] dependencies = [ ('expat', '2.2.4'), # recommended CLHEP version, see http://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.5.html#2. - ('CLHEP', '2.3.4.3'), + ('CLHEP', '2.4.1.0'), ] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" From cfbc88fb4ed3878780847bf6dfbfc97e7bed8ff5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Mar 2019 22:32:15 +0100 Subject: [PATCH 0754/5331] fix download_dep_fail check for easyconfigs using PythonBundle (+ add comments in check_python_packages) --- test/easyconfigs/easyconfigs.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2248c7476f2..867bb29ca4d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -385,24 +385,30 @@ def check_python_packages(self, changed_ecs): exts_download_dep_fail = ec.get('exts_download_dep_fail') use_pip = ec.get('use_pip') + # download_dep_fail should be set when using PythonPackage if easyblock == 'PythonPackage': if not download_dep_fail: failing_checks.append("'download_dep_fail' set in %s" % ec_fn) - # download_dep_fail is enabled automatically in PythonBundle easyblock + # use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs) if easyblock in ['PythonBundle', 'PythonPackage']: if not use_pip and not any(re.match(regex, ec_fn) for regex in whitelist_pip): failing_checks.append("'use_pip' set in %s" % ec_fn) + # download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set + if easyblock == 'PythonBundle': if download_dep_fail or exts_download_dep_fail: fail = "'*download_dep_fail' set in %s (shouldn't, since PythonBundle easyblock is used)" % ec_fn failing_checks.append(fail) elif exts_defaultclass == 'PythonPackage': + # bundle of Python packages should use PythonBundle if easyblock == 'Bundle': fail = "'PythonBundle' easyblock is used for bundle of Python packages in %s" % ec_fn failing_checks.append(fail) else: + # both download_dep_fail and use_pip should be set via exts_default_options + # when installing Python packages as extensions exts_default_options = ec.get('exts_default_options', {}) for key in ['download_dep_fail', 'use_pip']: if not exts_default_options.get(key): From eddcb09dbb831ec1c4a8ed7a421ba505e39e6479 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Mar 2019 10:06:31 +0100 Subject: [PATCH 0755/5331] adding easyconfigs: yaff-1.5.0-intel-2018b-Python-2.7.15.eb --- .../yaff-1.5.0-intel-2018b-Python-2.7.15.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.5.0-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.5.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/y/yaff/yaff-1.5.0-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..98a7d1a6c10 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.5.0-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['50b314185629826883825854790a5541005ae24b6855741c303412c943db1823'] + +dependencies = [ + ('Python', '2.7.15'), + ('h5py', '2.8.0', versionsuffix), + ('molmod', '1.4.4', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' From 6dd3191847ebfa3964102e616cfbc03ff5e3a78d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Mar 2019 10:57:08 +0000 Subject: [PATCH 0756/5331] add in patches, based on previous PyTorch easyconfigs --- .../p/PyTorch/PyTorch-1.0.1-fix-findAVX.patch | 47 +++++++++ .../PyTorch/PyTorch-1.0.1-fix-for-intel.patch | 98 +++++++++++++++++++ .../PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb | 6 ++ ...Torch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 6 ++ 4 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fix-findAVX.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fix-for-intel.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fix-findAVX.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fix-findAVX.patch new file mode 100644 index 00000000000..6793c5244fc --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fix-findAVX.patch @@ -0,0 +1,47 @@ +# original AVX and AVX2 tests were passed by icc compiler, the new code works well for both gcc and icc +# Based off PyTorch-0.3.1_fix_findAVX.patch by B. Hajgato (Free Univeristy Brussles - VUB) +# and updated for 1.0.1 +--- pytorch-1.0.1/cmake/Modules/FindAVX.cmake.orig 2019-03-08 10:29:09.328112915 +0000 ++++ pytorch-1.0.1/cmake/Modules/FindAVX.cmake 2019-03-08 10:30:41.538154961 +0000 +@@ -6,8 +6,18 @@ + + int main() + { +- __m256 a; +- a = _mm256_set1_ps(0); ++ __m256 a, b, c; ++ const float src[8] = { 1.0f, 2.0f, 3.0f, 4.0f, 5.0f, 6.0f, 7.0f, 8.0f }; ++ float dst[8]; ++ a = _mm256_loadu_ps( src ); ++ b = _mm256_loadu_ps( src ); ++ c = _mm256_add_ps( a, b ); ++ _mm256_storeu_ps( dst, c ); ++ for( int i = 0; i < 8; i++ ){ ++ if( ( src[i] + src[i] ) != dst[i] ){ ++ return -1; ++ } ++ } + return 0; + } + ") +@@ -17,8 +27,18 @@ + + int main() + { +- __m256i a = {0}; +- a = _mm256_abs_epi16(a); ++ __m256i a, b, c; ++ const int src[8] = { 1, 2, 3, 4, 5, 6, 7, 8 }; ++ int dst[8]; ++ a = _mm256_loadu_si256( (__m256i*)src ); ++ b = _mm256_loadu_si256( (__m256i*)src ); ++ c = _mm256_add_epi32( a, b ); ++ _mm256_storeu_si256( (__m256i*)dst, c ); ++ for( int i = 0; i < 8; i++ ){ ++ if( ( src[i] + src[i] ) != dst[i] ){ ++ return -1; ++ } ++ } + return 0; + } + ") diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fix-for-intel.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fix-for-intel.patch new file mode 100644 index 00000000000..8dd61cd07bb --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fix-for-intel.patch @@ -0,0 +1,98 @@ +# icpc is unhappy with the code, slightly adjust it to make it work +# Based off PyTorch-0.3.1-fix-for-intel.patch by wpoely86@gmail.com +# and updated for 1.0.1 +--- pytorch-1.0.1/torch/lib/THD/base/init_methods/InitMethodFile.cpp.orig 2019-03-08 10:20:12.407866684 +0000 ++++ pytorch-1.0.1/torch/lib/THD/base/init_methods/InitMethodFile.cpp 2019-03-08 10:20:34.132876696 +0000 +@@ -236,10 +236,8 @@ + std::string master_address; + std::tie(master_address, config.public_address) = + discoverMaster(master_addrs, master_port); +- config.worker = { +- .master_addr = master_address, +- .master_port = master_port, +- }; ++ config.worker.master_addr = master_address; ++ config.worker.master_port = master_port; + } + + return config; +--- pytorch-1.0.1/torch/lib/THD/base/init_methods/InitMethodTCP.cpp.orig 2019-03-08 10:20:42.407880508 +0000 ++++ pytorch-1.0.1/torch/lib/THD/base/init_methods/InitMethodTCP.cpp 2019-03-08 10:21:17.989896896 +0000 +@@ -325,10 +325,8 @@ + std::string master_address; + std::tie(master_address, config.public_address) = + discoverMaster(master_msg.addresses, master_msg.port); +- config.worker = { +- .master_addr = master_address, +- .master_port = master_msg.port, +- }; ++ config.worker.master_addr = master_address; ++ config.worker.master_port = master_msg.port; + } + break; + } +--- pytorch-1.0.1/torch/lib/THD/base/data_channels/DataChannelTCP.cpp.orig 2019-03-08 10:22:05.274918651 +0000 ++++ pytorch-1.0.1/torch/lib/THD/base/data_channels/DataChannelTCP.cpp 2019-03-08 10:24:22.088981494 +0000 +@@ -69,20 +69,16 @@ + _socket = config.master.listen_socket; + _port = config.master.listen_port; + +- _processes[0] = { +- .rank = 0, +- .address = "", +- .port = 0, +- .socket = -1, +- }; ++ _processes[0].rank = 0; ++ _processes[0].address = ""; ++ _processes[0].port = 0; ++ _processes[0].socket = -1; + } else { // WORKER + // add master +- _processes[0] = { +- .rank = 0, +- .address = config.worker.master_addr, +- .port = config.worker.master_port, +- .socket = -1, +- }; ++ _processes[0].rank = 0; ++ _processes[0].address = config.worker.master_addr; ++ _processes[0].port = config.worker.master_port; ++ _processes[0].socket = -1; + } + } + +@@ -113,12 +109,10 @@ + port_type p_port = recv_value(master.socket); + std::string p_address = recv_string(master.socket); + +- _processes[p_rank] = { +- .rank = p_rank, +- .address = p_address, +- .port = p_port, +- .socket = -1, +- }; ++ _processes[p_rank].rank = p_rank; ++ _processes[p_rank].address = p_address; ++ _processes[p_rank].port = p_port; ++ _processes[p_rank].socket = -1; + } + + /* +@@ -179,12 +173,10 @@ + std::to_string(p_rank)); + } + +- _processes[p_rank] = { +- .rank = p_rank, +- .address = p_address, +- .port = p_port, +- .socket = p_socket, +- }; ++ _processes[p_rank].rank = p_rank; ++ _processes[p_rank].address = p_address; ++ _processes[p_rank].port = p_port; ++ _processes[p_rank].socket = p_socket; + } + + // send informations about processes to all workers diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb index eef7b12c8e0..88e1c54f167 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb @@ -169,6 +169,10 @@ sources = [ pytorchdir, 'third_party/ideep/mkl-dnn/external/mklml_lnx_2019.0.1.20180928'), }, ] +patches = [ + '%(name)s-%(version)s-fix-findAVX.patch', + '%(name)s-%(version)s-fix-for-intel.patch', +] checksums = [ '210561583378132d07287518710251bcf861f9b7d625eb67258ed2e9d567cea1', # v1.0.1.tar.gz '0e98a4fdb6e27add72b4bb0e63a5ed20a9271139c3d0ccc2c15c502e3366bca3', # gloo-20190201.tar.gz @@ -195,6 +199,8 @@ checksums = [ 'c7418025bd57b3143e651433d0874a39629fce6cc96b43e3f8d5861a8ad23ffb', # ideep-20181224.tar.gz 'f98d2c297353acfab1ecff2054bee65efd2367b4c621e762cf26f50e037a9728', # mkl-dnn-20190131.tar.gz 'f00dc3b142a5be399bdeebd7e7ea369545a35d4fb84c86f98b6b048d72685295', # mklml_lnx_2019.0.1.20180928.tgz + 'c8dabee9fd710976c6073a81d2cad2735f95c063819cf8effc001e1940f63283', # PyTorch-1.0.1-fix-findAVX.patch + '569333e194d6a1d716972e17ad2ca1cd72e92a8845cee2f02ab2d5f541f013e9', # PyTorch-1.0.1-fix-for-intel.patch ] builddependencies = [('CMake', '3.12.1')] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb index b5ee18ef8cc..d219184d8f9 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -168,6 +168,10 @@ sources = [ pytorchdir, 'third_party/ideep/mkl-dnn/external/mklml_lnx_2019.0.1.20180928'), }, ] +patches = [ + '%(name)s-%(version)s-fix-findAVX.patch', + '%(name)s-%(version)s-fix-for-intel.patch', +] checksums = [ '210561583378132d07287518710251bcf861f9b7d625eb67258ed2e9d567cea1', # v1.0.1.tar.gz '0e98a4fdb6e27add72b4bb0e63a5ed20a9271139c3d0ccc2c15c502e3366bca3', # gloo-20190201.tar.gz @@ -194,6 +198,8 @@ checksums = [ 'c7418025bd57b3143e651433d0874a39629fce6cc96b43e3f8d5861a8ad23ffb', # ideep-20181224.tar.gz 'f98d2c297353acfab1ecff2054bee65efd2367b4c621e762cf26f50e037a9728', # mkl-dnn-20190131.tar.gz 'f00dc3b142a5be399bdeebd7e7ea369545a35d4fb84c86f98b6b048d72685295', # mklml_lnx_2019.0.1.20180928.tgz + 'c8dabee9fd710976c6073a81d2cad2735f95c063819cf8effc001e1940f63283', # PyTorch-1.0.1-fix-findAVX.patch + '569333e194d6a1d716972e17ad2ca1cd72e92a8845cee2f02ab2d5f541f013e9', # PyTorch-1.0.1-fix-for-intel.patch ] builddependencies = [('CMake', '3.12.1')] From 888ca5518dfba75f9ed2e71d3495fa39f49b93cc Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 8 Mar 2019 10:57:39 +0000 Subject: [PATCH 0757/5331] Delete Ninja-1.8.2-fosscuda-2018b.eb --- .../n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb | 26 ------------------- 1 file changed, 26 deletions(-) delete mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb deleted file mode 100644 index 8cce11f2088..00000000000 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.8.2-fosscuda-2018b.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'CmdCp' - -name = 'Ninja' -version = '1.8.2' - -homepage = 'https://ninja-build.org/' -description = "Ninja is a small build system with a focus on speed." - -toolchain = {'name': 'fosscuda', 'version': '2018b'} - -source_urls = ['https://github.com/ninja-build/ninja/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['86b8700c3d0880c2b44c2ff67ce42774aaf8c28cbf57725cb881569288c1c6f4'] - -builddependencies = [('Python', '3.6.6')] - -cmds_map = [('.*', "./configure.py --bootstrap")] - -files_to_copy = [(['ninja'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/ninja'], - 'dirs': [], -} - -moduleclass = 'tools' From cd7204d3d2607d24404536c9282b9f99618d1192 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Mar 2019 11:07:30 +0000 Subject: [PATCH 0758/5331] add in magma as a dependency for PyTorch fosscuda --- .../m/magma/magma-2.5.0-fosscuda-2018b.eb | 33 +++++++++++++++++++ ...Torch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 1 + 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb new file mode 100644 index 00000000000..a5b53fb832e --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb @@ -0,0 +1,33 @@ +easyblock = "ConfigureMake" + +name = 'magma' +version = '2.5.0' + +homepage = 'http://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['http://icl.cs.utk.edu/projectsfiles/magma/downloads/'] +sources = [SOURCE_TAR_GZ] +patches = [('magma-2.3.0-fix-makefile.patch')] +checksums = [ + '4fd45c7e46bd9d9124253e7838bbfb9e6003c64c2c67ffcff02e6c36d2bcfa33', # magma-2.5.0.tar.gz + '47e734cf30577b563377c946fb7897da2fd53d050f7e4fe83d8bb11b8d157913', # magma-2.3.0-fix-makefile.patch +] + +skipsteps = ['configure'] + +prebuildopts = 'touch make.inc && ' +prebuildopts += 'GPU_TARGET="Kepler Maxwell Pascal Volta" ' + +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libmagma.so', 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb index d219184d8f9..2efcf66a3c1 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -210,6 +210,7 @@ dependencies = [ ('hypothesis', '4.5.0', versionsuffix), ('cuDNN', '7.1.4.18'), ('Ninja', '1.8.2'), + ('magma', '2.5.0'), ] download_dep_fail = True From 2f4677278f4e3386cc85be1eb8f003c988ab433f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 8 Mar 2019 11:10:13 +0000 Subject: [PATCH 0759/5331] Update hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb --- .../h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb index 0d98b76f18a..b601f23494d 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-foss-2018b-Python-3.6.6.eb @@ -17,7 +17,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True exts_list = [ ('attrs', '18.2.0', { From f9b4f25d96769e748adcba536857237dc793ea50 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 8 Mar 2019 11:10:27 +0000 Subject: [PATCH 0760/5331] Update hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb --- .../h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb index aa39f3f7e5c..7bde035e223 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb @@ -17,7 +17,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True exts_list = [ ('attrs', '18.2.0', { From dff5969a635dd10b5f401c2caabcd0d1bfaf1d22 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 8 Mar 2019 11:42:58 +0000 Subject: [PATCH 0761/5331] Update magma-2.5.0-fosscuda-2018b.eb --- easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb index a5b53fb832e..ca413713216 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb @@ -21,7 +21,9 @@ checksums = [ skipsteps = ['configure'] prebuildopts = 'touch make.inc && ' -prebuildopts += 'GPU_TARGET="Kepler Maxwell Pascal Volta" ' +# magma 2.5.0 does not build on sm_30 - so remove Kepler and specify sm_35 +# http://icl.cs.utk.edu/magma/forum/viewtopic.php?f=2&t=1906&sid=7048fadfd48a0d00c3c4294ddef6a096 +prebuildopts += 'GPU_TARGET="sm_35 Maxwell Pascal Volta" ' installopts = 'prefix=%(installdir)s' From 59da79150411895dfb6f5d94d16084d455f259bb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 8 Mar 2019 14:21:14 +0200 Subject: [PATCH 0762/5331] adding easyconfigs: buildenv-default-foss-2018b.eb --- .../b/buildenv/buildenv-default-foss-2018b.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100755 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2018b.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2018b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2018b.eb new file mode 100755 index 00000000000..46b3e8d9724 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2018b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +moduleclass = 'devel' From 4eb934d2ea6ea9ad2e3098ae96f94c0616e735e4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Mar 2019 12:45:23 +0000 Subject: [PATCH 0763/5331] fix the magma patch for 2.5.0 --- .../m/magma/magma-2.5.0-fix-makefile.patch | 39 +++++++++++++++++++ .../m/magma/magma-2.5.0-fosscuda-2018b.eb | 6 +-- 2 files changed, 42 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch b/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch new file mode 100644 index 00000000000..e96e878720f --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch @@ -0,0 +1,39 @@ +# Fix the makefile to use EB values for everything +# Based off magma-2.3.0-fix-makefile.patch by wpoely86@gmail.com +# and updated for 2.5.0 +--- magma-2.5.0/Makefile.orig 2019-03-08 12:33:11.872321116 +0000 ++++ magma-2.5.0/Makefile 2019-03-08 12:35:58.463432082 +0000 +@@ -10,7 +10,7 @@ + CC ?= cc + CXX ?= c++ + NVCC ?= nvcc +-FORT ?= ++FORT ?= $(FC) + ifeq ($(FORT),) + $(warning No Fortran compiler was given in FORT in make.inc. Some testers will not be able to check their results.) + endif +@@ -23,17 +23,17 @@ + #FPIC = -fPIC + + # may want -std=c99 for CFLAGS, -std=c++11 for CXXFLAGS +-CFLAGS ?= -O3 $(FPIC) -DADD_ -Wall -MMD +-CXXFLAGS ?= $(CFLAGS) -std=c++11 +-NVCCFLAGS ?= -O3 -DADD_ -Xcompiler "$(FPIC) -Wall -Wno-unused-function" -std=c++11 +-FFLAGS ?= -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument +-F90FLAGS ?= -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument +-LDFLAGS ?= -O3 $(FPIC) ++CFLAGS ?= $(FPIC) -DADD_ -Wall -MMD $(CFLAGS) ++CXXFLAGS ?= $(CFLAGS) ++NVCCFLAGS ?= -DADD_ -Xcompiler "$(FPIC) -Wall -Wno-unused-function $(CFLAGS)" ++FFLAGS ?= $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument $(FCFLAGS) ++F90FLAGS ?= $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument $(F90FLAGS) ++LDFLAGS ?= $(FPIC) -fopenmp $(LDFLAGS) + + INC ?= -I$(CUDADIR)/include + + LIBDIR ?= -L$(CUDADIR)/lib64 +-LIB ?= -lcudart -lcudadevrt -lcublas -lcusparse -llapack -lblas -lpthread -lm ++LIB ?= $(LIBLAPACK) -lcudart -lcudadevrt -lcublas -lcusparse -lpthread -lm $(LIBS) + + GPU_TARGET ?= Kepler Maxwell Pascal + diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb index ca413713216..856330a432a 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb @@ -12,16 +12,16 @@ toolchainopts = {'pic': True, 'openmp': True} source_urls = ['http://icl.cs.utk.edu/projectsfiles/magma/downloads/'] sources = [SOURCE_TAR_GZ] -patches = [('magma-2.3.0-fix-makefile.patch')] +patches = [('%(name)s-%(version)s-fix-makefile.patch')] checksums = [ '4fd45c7e46bd9d9124253e7838bbfb9e6003c64c2c67ffcff02e6c36d2bcfa33', # magma-2.5.0.tar.gz - '47e734cf30577b563377c946fb7897da2fd53d050f7e4fe83d8bb11b8d157913', # magma-2.3.0-fix-makefile.patch + '8809a0a5ce63572e2d7af627fce16a6a8221ebe38d9dc1a3570dfabde40c7395', # magma-2.5.0-fix-makefile.patch ] skipsteps = ['configure'] prebuildopts = 'touch make.inc && ' -# magma 2.5.0 does not build on sm_30 - so remove Kepler and specify sm_35 +# magma 2.5.0 does not build on sm_30 - so remove Kepler and specify sm_35 # http://icl.cs.utk.edu/magma/forum/viewtopic.php?f=2&t=1906&sid=7048fadfd48a0d00c3c4294ddef6a096 prebuildopts += 'GPU_TARGET="sm_35 Maxwell Pascal Volta" ' From b3d4bb4e0c876305078f975b09a386e68c521a4f Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 8 Mar 2019 07:34:06 -0600 Subject: [PATCH 0764/5331] change the easyblock from Bundle to PythonBundle --- .../n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb | 2 +- .../n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb | 2 +- .../n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb | 2 +- .../n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb index 9e70f5e9739..e543046154b 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'NiBabel' version = '2.3.0' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb index b4c41c5b834..79f6dfe3b69 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'NiBabel' version = '2.3.0' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb index 3d82c6eb483..1f3079e8779 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'NiBabel' version = '2.3.0' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb index 0286ab22fff..588c4b0c4b1 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'NiBabel' version = '2.3.0' From b5984770f77fadb0e89d23fff59d66888c53bf2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Mar 2019 15:28:48 +0100 Subject: [PATCH 0765/5331] replace ncurses-devel OS dependency in CMake easyconfigs using dummy toolchain with proper ncurses dependency --- easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb | 17 +++++++++-------- easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb | 11 ++++++++--- easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb | 11 ++++++++--- easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb | 14 +++++++++----- 4 files changed, 34 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb index 572af805c3d..1e3749603aa 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb @@ -11,20 +11,21 @@ description = """ """ # note: requires C++ compiler that supports C++11, which is not the case in older OSs like CentOS 6... -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c53d5c2ce81d7a957ee83e3e635c8cda5dfe20c9d501a4828ee28e1615e57ab2'] -# Use OS dependencies in order to ensure that CMake can build software that -# depends on them -osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), - ('ncurses-devel', 'libncurses5-dev'), -] +builddependencies = [('ncurses', '6.1')] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +# Use OS dependencies in order to ensure that CMake can build software that depends on them +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "-- -DCMAKE_USE_OPENSSL=1 " +configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " +configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " +configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb index d9808f4cbbe..15de3ff1845 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb @@ -7,17 +7,22 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['28ee98ec40427d41a45673847db7a905b59ce9243bb866eaf59dce0f58aaef11'] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +builddependencies = [('ncurses', '5.9')] # Use OS dependencies in order to ensure that CMake can build software that # depends on them -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ('ncurses-devel', 'libncurses5-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "-- -DCMAKE_USE_OPENSSL=1 " +configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " +configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " +configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb index 1ab7321f890..d706473dedd 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb @@ -7,17 +7,22 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d768ee83d217f91bb597b3ca2ac663da7a8603c97e1f1a5184bc01e0ad2b12bb'] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +builddependencies = [('ncurses', '5.9')] # Use OS dependencies in order to ensure that CMake can build software that # depends on them -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ('ncurses-devel', 'libncurses5-dev')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "-- -DCMAKE_USE_OPENSSL=1 " +configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " +configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " +configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb index 71c7cb25abc..be1d13e34cf 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb @@ -7,17 +7,21 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['7410851a783a41b521214ad987bb534a7e4a65e059651a2514e6ebfc8f46b218'] -configopts = '-- -DCMAKE_USE_OPENSSL=1' +builddependencies = [('ncurses', '5.9')] -# Use OS dependencies in order to ensure that CMake can build software that -# depends on them -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ('ncurses-devel', 'libncurses5-dev')] +# Use OS dependencies in order to ensure that CMake can build software that depends on them +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "-- -DCMAKE_USE_OPENSSL=1 " +configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " +configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " +configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], From b7b3abc316603c0e922c3ec565c19ee1f96bdf57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Mar 2019 17:01:39 +0100 Subject: [PATCH 0766/5331] also include easyconfig for ncurses v6.1 built with dummy toolchain, which is a build dep for CMake 3.12.1 built with dummy toolchain --- .../easyconfigs/n/ncurses/ncurses-6.1.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb new file mode 100644 index 00000000000..8e9c00a9c69 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.1' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['aa057eeeb4a14d470101eff4597d5833dcef5965331be3528c08d99cebaa0d17'] + +common_configopts = "--with-shared --enable-overwrite --without-ada " +configopts = [ + # default build + common_configopts, + # the UTF-8 enabled version (ncursesw) + common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.so", + "ln -s %(installdir)s/lib/libncurses.a %(installdir)s/lib/libtinfo.a" +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' From da5c3087bb8c3e66502527392a6dbf8a74a00058 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Mar 2019 16:04:23 +0000 Subject: [PATCH 0767/5331] more fixing of the magma patch for 2.5.0 --- easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch | 2 +- easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch b/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch index e96e878720f..b68e579447e 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch +++ b/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch @@ -33,7 +33,7 @@ LIBDIR ?= -L$(CUDADIR)/lib64 -LIB ?= -lcudart -lcudadevrt -lcublas -lcusparse -llapack -lblas -lpthread -lm -+LIB ?= $(LIBLAPACK) -lcudart -lcudadevrt -lcublas -lcusparse -lpthread -lm $(LIBS) ++LIB ?= $(LIBLAPACK) -lcudart -lcudadevrt -lcublas -lcusparse -lpthread -lm GPU_TARGET ?= Kepler Maxwell Pascal diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb index 856330a432a..9c5f7fa7dae 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] patches = [('%(name)s-%(version)s-fix-makefile.patch')] checksums = [ '4fd45c7e46bd9d9124253e7838bbfb9e6003c64c2c67ffcff02e6c36d2bcfa33', # magma-2.5.0.tar.gz - '8809a0a5ce63572e2d7af627fce16a6a8221ebe38d9dc1a3570dfabde40c7395', # magma-2.5.0-fix-makefile.patch + '8151f8c8e58b2ae9a2a2d5162844e3650687c81d57f7917d078673450fb0f50f', # magma-2.5.0-fix-makefile.patch ] skipsteps = ['configure'] From 4e26a8248084880a8cfd27a0898bc06121a50fb6 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 8 Mar 2019 11:15:45 -0600 Subject: [PATCH 0768/5331] correct the eb files related to the PythonBundle --- .../n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb | 8 +------- .../n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb | 8 +------- .../n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb | 8 +------- .../n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb | 8 +------- 4 files changed, 4 insertions(+), 28 deletions(-) diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb index e543046154b..72f0ee3f811 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb @@ -17,12 +17,8 @@ dependencies = [ ('Pillow', '5.3.0', versionsuffix), ] -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True -exts_defaultclass = 'PythonPackage' exts_list = [ ('pydicom', '1.2.0', { 'source_tmpl': 'v%(version)s.tar.gz', @@ -40,6 +36,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb index 79f6dfe3b69..27fea58ea1b 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb @@ -17,12 +17,8 @@ dependencies = [ ('Pillow', '5.3.0', versionsuffix), ] -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True -exts_defaultclass = 'PythonPackage' exts_list = [ ('pydicom', '1.2.0', { 'source_tmpl': 'v%(version)s.tar.gz', @@ -40,6 +36,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb index 1f3079e8779..c9c6e760251 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb @@ -17,12 +17,8 @@ dependencies = [ ('Pillow', '5.3.0', versionsuffix), ] -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True -exts_defaultclass = 'PythonPackage' exts_list = [ ('pydicom', '1.2.0', { 'source_tmpl': 'v%(version)s.tar.gz', @@ -40,6 +36,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb index 588c4b0c4b1..88556e71196 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb @@ -17,12 +17,8 @@ dependencies = [ ('Pillow', '5.3.0', versionsuffix), ] -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True -exts_defaultclass = 'PythonPackage' exts_list = [ ('pydicom', '1.2.0', { 'source_tmpl': 'v%(version)s.tar.gz', @@ -40,6 +36,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/nibabel', 'lib/python%(pyshortver)s/site-packages/nisext'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'vis' From d2d5724c4e04e56b24a339f9f19e666e7e9b26b3 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 8 Mar 2019 11:27:41 -0600 Subject: [PATCH 0769/5331] changed the CMake version to 3.10.0 --- easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb | 2 +- easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb | 2 +- easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb | 2 +- easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb index cbef5e41ee7..21fe05f6d94 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb @@ -15,7 +15,7 @@ source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/' sources = [SOURCELOWER_TGZ] checksums = ['d14736eb5c3d21f86ce831dc1afcf03d423825b35c84deb6f8fd16773528c54d'] -builddependencies = [('CMake', '3.9.5')] +builddependencies = [('CMake', '3.10.0')] separate_build_dir = True diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb index b1ece0789f4..92485e9ac0e 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb @@ -15,7 +15,7 @@ source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/' sources = [SOURCELOWER_TGZ] checksums = ['d14736eb5c3d21f86ce831dc1afcf03d423825b35c84deb6f8fd16773528c54d'] -builddependencies = [('CMake', '3.9.5')] +builddependencies = [('CMake', '3.10.0')] separate_build_dir = True diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb index 0abcc017507..987a175ee7c 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-foss-2017b.eb @@ -12,7 +12,7 @@ source_urls = ['http://geant4.cern.ch/support/source'] sources = ['%(namelower)s.%(version_major)s.0%(version_minor)s.tar.gz'] checksums = ['4b05b4f7d50945459f8dbe287333b9efb772bd23d50920630d5454ec570b782d'] -builddependencies = [('CMake', '3.9.5')] +builddependencies = [('CMake', '3.10.0')] dependencies = [ ('expat', '2.2.4'), # recommended CLHEP version, see http://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.5.html#2. diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb index c7593466502..630cf5e67c6 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.5-intel-2017b.eb @@ -12,7 +12,7 @@ source_urls = ['http://geant4.cern.ch/support/source'] sources = ['%(namelower)s.%(version_major)s.0%(version_minor)s.tar.gz'] checksums = ['4b05b4f7d50945459f8dbe287333b9efb772bd23d50920630d5454ec570b782d'] -builddependencies = [('CMake', '3.9.5')] +builddependencies = [('CMake', '3.10.0')] dependencies = [ ('expat', '2.2.4'), # recommended CLHEP version, see http://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.5.html#2. From c801287c3c4891f613f2118edda3453a92e4f7b8 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 8 Mar 2019 11:49:12 -0600 Subject: [PATCH 0770/5331] add in use_pip=true and download_dep_fail=true --- .../h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb | 3 +++ .../easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb | 3 +++ .../h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb | 3 +++ .../h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb | 3 +++ 4 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb index 8ff2351f9ac..a2f49ebc765 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb @@ -22,6 +22,9 @@ dependencies = [ ('matplotlib', '2.1.0', versionsuffix), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': ["bin/htseq-count", "bin/htseq-qa"], 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb index 1995cd53010..88dcb92dbdf 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb @@ -22,6 +22,9 @@ dependencies = [ ('matplotlib', '2.1.0', versionsuffix), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': ["bin/htseq-count", "bin/htseq-qa"], 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb index 632a4ab50ad..c414bf1fb55 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb @@ -22,6 +22,9 @@ dependencies = [ ('matplotlib', '2.1.0', versionsuffix), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': ["bin/htseq-count", "bin/htseq-qa"], 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb index 0603fa3ee5a..78c6fbbe2f6 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb @@ -22,6 +22,9 @@ dependencies = [ ('matplotlib', '2.1.0', versionsuffix), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': ["bin/htseq-count", "bin/htseq-qa"], 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], From baa6d831c3b360f2bf52aa1d93a538553aabe4b8 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 8 Mar 2019 12:29:20 -0600 Subject: [PATCH 0771/5331] adding easyconfigs: MACS2-2.1.2.1-intel-2017b-Python-2.7.14.eb, MACS2-2.1.2.1-foss-2017b-Python-2.7.14.eb --- .../MACS2-2.1.2.1-foss-2017b-Python-2.7.14.eb | 40 +++++++++++++++++++ ...MACS2-2.1.2.1-intel-2017b-Python-2.7.14.eb | 40 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..4e896fa00bf --- /dev/null +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright (c) 2015 Virginia Bioinformatics Institute at Virginia Tech +# Authors:: Dominik L. Borkowski +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'PythonPackage' + +name = 'MACS2' +version = '2.1.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/taoliu/MACS/' +description = "Model Based Analysis for ChIP-Seq data" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6ee9381bda61bacf65e2e31bde267cbcd61a1304457f8a00a0eb7632dd12419b'] + +dependencies = [('Python', '2.7.14')] + +options = {'modulename': name} + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/macs2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('%(namelower)s --version')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..a8a101b6fb2 --- /dev/null +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.1.2.1-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright (c) 2015 Virginia Bioinformatics Institute at Virginia Tech +# Authors:: Dominik L. Borkowski +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'PythonPackage' + +name = 'MACS2' +version = '2.1.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/taoliu/MACS/' +description = "Model Based Analysis for ChIP-Seq data" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6ee9381bda61bacf65e2e31bde267cbcd61a1304457f8a00a0eb7632dd12419b'] + +dependencies = [('Python', '2.7.14')] + +options = {'modulename': name} + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/macs2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('%(namelower)s --version')] + +moduleclass = 'bio' From 357bf83123cbde39f71b504a4422fae75a30e0e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Mar 2019 19:33:51 +0100 Subject: [PATCH 0772/5331] also run easyconfigs tests using Python 3.5 and 3.7 --- .travis.yml | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index e1ff0c2eb1f..9248da44289 100644 --- a/.travis.yml +++ b/.travis.yml @@ -8,9 +8,14 @@ matrix: # also test default configuration with Python 2.7 - python: 2.7 env: LMOD_VERSION=6.6.3 - # also test with Python 3.6 + # also test with Python 3.5/3.6/3.7 - python: 3.6 env: LMOD_VERSION=7.8.5 + - python: 3.5 + env: LMOD_VERSION=7.8.5 + - python: 3.7 + dist: xenial + env: LMOD_VERSION=7.8.5 addons: apt: packages: From 866f407dfb4a64a9a6d1712fb5efa103923de550 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 8 Mar 2019 13:03:08 -0600 Subject: [PATCH 0773/5331] adding easyconfigs: MEME-5.0.4-foss-2017b.eb, MEME-5.0.4-intel-2017b.eb --- .../m/MEME/MEME-5.0.4-foss-2017b.eb | 31 +++++++++++++++++++ .../m/MEME/MEME-5.0.4-intel-2017b.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb new file mode 100644 index 00000000000..a942983272d --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.0.4' + +homepage = 'http://meme-suite.org' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4'] + +dependencies = [ + ('libxml2', '2.9.8'), + ('libxslt', '1.1.32'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ["bin/meme"], + 'dirs': ["lib"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb new file mode 100644 index 00000000000..c45d4bae0b1 --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.0.4' + +homepage = 'http://meme-suite.org' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4'] + +dependencies = [ + ('libxml2', '2.9.8'), + ('libxslt', '1.1.32'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ["bin/meme"], + 'dirs': ["lib"], +} + +moduleclass = 'bio' From 9e141dad7eaaa07acb95a61e75fb9396a177f3ce Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 8 Mar 2019 21:05:16 +0200 Subject: [PATCH 0774/5331] adding easyconfigs: tbb-2019_U4-GCCcore-8.2.0.eb --- .../t/tbb/tbb-2019_U4-GCCcore-8.2.0.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2019_U4-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2019_U4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2019_U4-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..a1a3f57d4e6 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2019_U4-GCCcore-8.2.0.eb @@ -0,0 +1,18 @@ +name = 'tbb' +version = '2019_U4' + +homepage = 'https://01.org/tbb/' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/01org/tbb/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['342a0a2cd583879850658284b86e9351ea019b4f3fcd731f4c18456f0ce9f900'] + +builddependencies = [ + ('binutils', '2.31.1') +] + +moduleclass = 'lib' From e5c1814a43ba849691f2999d4e3de47a0e2d1773 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 8 Mar 2019 13:11:51 -0600 Subject: [PATCH 0775/5331] also add in use_pip=true and download_dep_fail=true to Pysam --- .../easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-3.6.3.eb | 3 +++ .../easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-3.6.3.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-3.6.3.eb index 6a1b203c352..a2e4e498108 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-foss-2017b-Python-3.6.3.eb @@ -22,6 +22,9 @@ source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['c9c8ea82b4deee7607d5885fc7cc92311f06e765ff30e0b2b2d3d85b28cf5687'] +use_pip = True +download_dep_fail = True + dependencies = [ ('XZ', '5.2.3'), ('Python', '3.6.3'), diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-3.6.3.eb index 358aea76f79..f227e21988d 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-3.6.3.eb @@ -22,6 +22,9 @@ source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['c9c8ea82b4deee7607d5885fc7cc92311f06e765ff30e0b2b2d3d85b28cf5687'] +use_pip = True +download_dep_fail = True + dependencies = [ ('XZ', '5.2.3'), ('Python', '3.6.3'), From 917172c7f02448555791acfeb25be952dcc28f29 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 8 Mar 2019 14:59:59 -0500 Subject: [PATCH 0776/5331] adding easyconfigs: Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb --- ...-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb new file mode 100644 index 00000000000..c45bffeaa80 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb @@ -0,0 +1,49 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '2.4.0' +hadoopver = '2.7' +versionsuffix = '-Hadoop-%s-Java-%%(javaver)s-Python-%%(pyver)s' % hadoopver + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +sources = ['%%(namelower)s-%%(version)s-bin-hadoop%s.tgz' % hadoopver] +source_urls = [ + 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', +] +checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] + +dependencies = [ + ('Java', '1.8', '', True), + ('Python', '3.6.6'), +] + +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('py4j', '0.10.8.1', { + # https://files.pythonhosted.org/packages/c0/e3/1f110e6c069522ba7a8dc215ff1c343b6bc1f98d84e6d627ca2708426eaa/py4j-0.10.8.1.zip + 'source_urls': \ + ['https://files.pythonhosted.org/packages/c0/e3/1f110e6c069522ba7a8dc215ff1c343b6bc1f98d84e6d627ca2708426eaa'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['8329bb156a0cf37be9642a2a060dbdb627b5fcb827919be65d95102daccca274'], + }), + ('pyspark', version, { + 'start_dir': 'python', + 'checksums': ['c9d7b7c5e91b13488b657e364ff392a80b2e374b182138e5ec8702a1822bffdc'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/spark-shell', 'bin/pyspark'], + 'dirs': ['python'] +} + +moduleclass = 'devel' From a90a17cc1ea65f3e8de99c36477819a46dc20515 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 8 Mar 2019 22:21:37 +0200 Subject: [PATCH 0777/5331] adding easyconfigs: libpng-1.6.36-GCCcore-8.2.0.eb --- .../l/libpng/libpng-1.6.36-GCCcore-8.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.36-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.36-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.36-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..fe1e51296d3 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.36-GCCcore-8.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.36' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ca13c548bde5fb6ff7117cc0bdab38808acb699c0eccb613f0e4697826e1fd7d'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +majminver = ''.join(version.split('.')[:2]) + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % majminver, + 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' From 41526e4a808b32d31c76ac037485113f6f1e4e13 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Mar 2019 23:03:22 +0100 Subject: [PATCH 0778/5331] simplify Java dep spec in picard easyconfig --- easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb b/easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb index 242ce17a4e4..7db9240a7af 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['6cfba52d348969bf7b17adc26d1e8e669f741631253003e4a10dd8322eac89dd'] postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8')] sanity_check_paths = { 'files': ['picard.jar'], From 647a15263ddceb9b5a48da152f07fdbd9c5c06a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Mar 2019 23:09:26 +0100 Subject: [PATCH 0779/5331] use PythonBundle for snakemake-5.2.4-foss-2018b-Python-3.6.6.eb (+ fix moduleclass) --- .../snakemake-5.2.4-foss-2018b-Python-3.6.6.eb | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-foss-2018b-Python-3.6.6.eb index 2315db11d4a..786160ef2b1 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-5.2.4-foss-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'snakemake' version = '5.2.4' @@ -15,11 +15,7 @@ dependencies = [ ('GitPython', '2.1.11', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('docutils', '0.14', { @@ -63,6 +59,4 @@ sanity_check_paths = { sanity_check_commands = ['snakemake --help'] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -moduleclass = 'vis' +moduleclass = 'tools' From ca61abad72c0f9c235407dbbcfb8bf08957067ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Mar 2019 23:24:54 +0100 Subject: [PATCH 0780/5331] add missing download_dep_fail and use_pip to PyYAML easyconfig --- .../p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb index af657669158..d9ec29b77b8 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb @@ -18,6 +18,9 @@ dependencies = [ ('libyaml', '0.2.1'), ] +download_dep_fail = True +use_pip = True + options = {'modulename': 'yaml'} sanity_check_paths = { From c1da527a93ba5fc326087d8f9d1c5e4c4749be9d Mon Sep 17 00:00:00 2001 From: dquigley-warwick Date: Fri, 8 Mar 2019 22:30:49 +0000 Subject: [PATCH 0781/5331] adding easyconfigs: Giza-1.1.0-foss-2018b.eb, SPLASH-2.8.0-foss-2018b.eb --- .../g/Giza/Giza-1.1.0-foss-2018b.eb | 30 +++++++++++++++ .../s/SPLASH/SPLASH-2.8.0-foss-2018b.eb | 37 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/g/Giza/Giza-1.1.0-foss-2018b.eb create mode 100644 easybuild/easyconfigs/s/SPLASH/SPLASH-2.8.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/g/Giza/Giza-1.1.0-foss-2018b.eb b/easybuild/easyconfigs/g/Giza/Giza-1.1.0-foss-2018b.eb new file mode 100644 index 00000000000..f807483e917 --- /dev/null +++ b/easybuild/easyconfigs/g/Giza/Giza-1.1.0-foss-2018b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Giza' +version = '1.1.0' + +homepage = "https://danieljprice.github.io/giza/" +description = """Giza is an open, lightweight scientific plotting library built on +top of cairo that provides uniform output to multiple devices.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/danieljprice/giza/archive/'] +sources = ['v%(version)s.tar.gz'] + +checksums = ['334f8e44faf0e2d2bf9fa256b878882be1dfe27e137b67670d8d48e527e04437'] + +dependencies = [ + ('cairo', '1.14.12'), + ('Pango', '1.42.4'), + ('X11', '20180604'), +] + +preconfigopts = 'CFLAGS=-std=gnu99 ' + +sanity_check_paths = { + 'files': ['lib/libgiza.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT, 'lib/libpgplot.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPLASH/SPLASH-2.8.0-foss-2018b.eb b/easybuild/easyconfigs/s/SPLASH/SPLASH-2.8.0-foss-2018b.eb new file mode 100644 index 00000000000..679396e4e2f --- /dev/null +++ b/easybuild/easyconfigs/s/SPLASH/SPLASH-2.8.0-foss-2018b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'SPLASH' +version = '2.8.0' + +homepage = "http://users.monash.edu.au/~dprice/splash/index.html" +description = """SPLASH is a free and open source visualisation tool +for Smoothed Particle Hydrodynamics (SPH) simulations.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://users.monash.edu.au/~dprice/splash/releases/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['de06b159846bd20717a55ec7cc9420e0fd86ab38dc66dc74b1f61b77b4d24fce'] # splash-2.8.0.tar.gz + +dependencies = [ + ('Giza', '1.1.0'), +] + +skipsteps = ['configure'] +buildopts = 'SYSTEM=gfortran X11_DIR=$EBROOTX11 ' +buildopts += 'GIZA_DIR=$EBROOTGIZA ' +buildopts += 'CAIRO_CFLAGS=-I$EBROOTCAIRO/include ' +buildopts += 'CAIRO_LIBS=-L$EBROOTCAIRO/lib -lcairo' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' +installopts = 'PREFIX=%(installdir)s' + +# parallel builds fail +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%ssplash' % x for x in ['a', 'd', 'g', 'm', 'n', 'r', '', 'sr', 's', 't', 'v']], + 'dirs': [] +} + +moduleclass = 'vis' From 14277756bf4c95ff6ba332aa4dd559986ba6cc58 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Mar 2019 23:51:26 +0100 Subject: [PATCH 0782/5331] add missing checksums in ncurses-5.9.eb --- easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index dd70b0800a4..bc44b49767d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -13,8 +13,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] - patches = ['ncurses-%(version)s_configure_darwin.patch'] +checksums = [ + '9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b', # ncurses-5.9.tar.gz + '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', # ncurses-5.9_configure_darwin.patch +] configopts = [ # default build From 634229111594c3009cee2303cd8ee14d0c389a63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Mar 2019 09:52:46 +0100 Subject: [PATCH 0783/5331] add PyTorch to whitelist for not having 'use_pip' enabled --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 98e29398951..37658cb7cce 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -372,8 +372,8 @@ def check_sha256_checksums(self, changed_ecs): def check_python_packages(self, changed_ecs): """Several checks for easyconfigs that install (bundles of) Python packages.""" - # MATLAB-Engine does not support installation with 'pip' - whitelist_pip = ['MATLAB-Engine-*'] + # MATLAB-Engine, PyTorch do not support installation with 'pip' + whitelist_pip = ['MATLAB-Engine-*', 'PyTorch-*'] failing_checks = [] From 04adb946b913247c7831661cf2b018a01a63640b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 9 Mar 2019 09:45:58 +0000 Subject: [PATCH 0784/5331] get the right syntax in the magma patch for 2.5.0 --- .../m/magma/magma-2.5.0-fix-makefile.patch | 14 +++++++------- .../m/magma/magma-2.5.0-fosscuda-2018b.eb | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch b/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch index b68e579447e..8bd8e446258 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch +++ b/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch @@ -22,18 +22,18 @@ -FFLAGS ?= -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument -F90FLAGS ?= -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument -LDFLAGS ?= -O3 $(FPIC) -+CFLAGS ?= $(FPIC) -DADD_ -Wall -MMD $(CFLAGS) -+CXXFLAGS ?= $(CFLAGS) -+NVCCFLAGS ?= -DADD_ -Xcompiler "$(FPIC) -Wall -Wno-unused-function $(CFLAGS)" -+FFLAGS ?= $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument $(FCFLAGS) -+F90FLAGS ?= $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument $(F90FLAGS) -+LDFLAGS ?= $(FPIC) -fopenmp $(LDFLAGS) ++CFLAGS := $(FPIC) -DADD_ -Wall -MMD $(CFLAGS) ++CXXFLAGS := $(CFLAGS) ++NVCCFLAGS := -DADD_ -Xcompiler "$(FPIC) -Wall -Wno-unused-function $(CFLAGS)" ++FFLAGS := $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument $(FCFLAGS) ++F90FLAGS := $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument $(F90FLAGS) ++LDFLAGS := $(FPIC) -fopenmp $(LDFLAGS) INC ?= -I$(CUDADIR)/include LIBDIR ?= -L$(CUDADIR)/lib64 -LIB ?= -lcudart -lcudadevrt -lcublas -lcusparse -llapack -lblas -lpthread -lm -+LIB ?= $(LIBLAPACK) -lcudart -lcudadevrt -lcublas -lcusparse -lpthread -lm ++LIB := $(LIBLAPACK) -lcudart -lcudadevrt -lcublas -lcusparse -lpthread -lm $(LIBS) GPU_TARGET ?= Kepler Maxwell Pascal diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb index 9c5f7fa7dae..4ad082ef129 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] patches = [('%(name)s-%(version)s-fix-makefile.patch')] checksums = [ '4fd45c7e46bd9d9124253e7838bbfb9e6003c64c2c67ffcff02e6c36d2bcfa33', # magma-2.5.0.tar.gz - '8151f8c8e58b2ae9a2a2d5162844e3650687c81d57f7917d078673450fb0f50f', # magma-2.5.0-fix-makefile.patch + '2839e33a17134e686ccd9fde7e008b40495e4e8bafb3ae1bd49cb0e39852e7ac', # magma-2.5.0-fix-makefile.patch ] skipsteps = ['configure'] From 5c6bf5e55d2b29bb037782f31b3b552684667b05 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 9 Mar 2019 14:30:48 +0200 Subject: [PATCH 0785/5331] Update comment to say GTK+ 3. Add pkg-config as builddep. --- easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb index 9a24a7902c0..8b4dda88183 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb @@ -5,17 +5,17 @@ version = '3.22.30' homepage = 'https://developer.gnome.org/gtk+/stable/' description = """ - The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. + The GTK+ 3 package contains libraries used for creating graphical user interfaces for applications. """ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['a1a4a5c12703d4e1ccda28333b87ff462741dc365131fbc94c218ae81d9a6567'] builddependencies = [ ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), + ('pkg-config', '0.29.2'), ] dependencies = [ From c7f3e1ee4d237746930c8c1a7ecc5f23aed6a5dc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 9 Mar 2019 14:45:45 +0200 Subject: [PATCH 0786/5331] Re-add checksum. --- easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb index 8b4dda88183..b5b2539c234 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['a1a4a5c12703d4e1ccda28333b87ff462741dc365131fbc94c218ae81d9a6567'] builddependencies = [ ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), From 9dd0e25d67756df2024d0163df2c36177a27b860 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Mar 2019 14:02:57 +0100 Subject: [PATCH 0787/5331] use correct buildopts + add missing zlib dependency in StringTie 1.3.5 easyconfig --- .../easyconfigs/s/StringTie/StringTie-1.3.5-foss-2018b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-foss-2018b.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-foss-2018b.eb index 46355cb5413..f571b35c3e6 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-foss-2018b.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-foss-2018b.eb @@ -15,6 +15,12 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['f16ec07d4869b7656bc1a9b6eb662fd9404c122d18431c845e93d810840c5db9'] +dependencies = [ + ('zlib', '1.2.11'), +] + +buildopts = "release" + files_to_copy = [(['%(namelower)s'], 'bin'), 'README', 'LICENSE'] sanity_check_paths = { From 565c7ce410348e88f684ba1db9cb2d3de2d4a0c6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 9 Mar 2019 15:24:51 +0200 Subject: [PATCH 0788/5331] Update to HarfBuzz 2.2.0 that foss/2018b uses. --- .../HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb | 38 +++++++++++++++++++ .../p/Pango/Pango-1.42.4-fosscuda-2018b.eb | 2 +- 2 files changed, 39 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb new file mode 100644 index 00000000000..55fd8055045 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.2.0-fosscuda-2018b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '2.2.0' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b7ccfcbd56b970a709e8b9ea9fb46c922c606c2feef8f086fb6a8492e530f810'] + +dependencies = [ + ('GLib', '2.54.3'), + ('cairo', '1.14.12'), + ('freetype', '2.9.1'), +] + +builddependencies = [ + ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), + ('pkg-config', '0.29.2'), +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb index 76d7c9524df..c2745d70c20 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb @@ -23,7 +23,7 @@ dependencies = [ ('X11', '20180604'), ('GLib', '2.54.3'), ('cairo', '1.14.12'), - ('HarfBuzz', '1.9.0'), + ('HarfBuzz', '2.2.0'), ('FriBidi', '1.0.5'), ] From 20745fe6c467339549702f7a12bdf999ed62f2f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Mar 2019 14:25:14 +0100 Subject: [PATCH 0789/5331] {toolchain} intel/2019.03 (+ HPL 2.3 test case) --- .../h/HPL/HPL-2.3-intel-2019.03.eb | 21 ++++++++++ .../i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb | 33 ++++++++++++++++ .../iccifort-2019.3.199-GCC-8.3.0-2.32.eb | 18 +++++++++ .../ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb | 38 ++++++++++++++++++ ...ort-2019.3.199_no_mpi_mic_dependency.patch | 13 +++++++ .../easyconfigs/i/iimpi/iimpi-2019.03.eb | 20 ++++++++++ .../i/imkl/imkl-2019.3.199-iimpi-2019.03.eb | 39 +++++++++++++++++++ ....199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb | 22 +++++++++++ .../easyconfigs/i/intel/intel-2019.03.eb | 24 ++++++++++++ 9 files changed, 228 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2019.03.eb create mode 100644 easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb create mode 100644 easybuild/easyconfigs/i/iccifort/iccifort-2019.3.199-GCC-8.3.0-2.32.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb create mode 100644 easybuild/easyconfigs/i/ifort/ifort-2019.3.199_no_mpi_mic_dependency.patch create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2019.03.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2019.03.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2019.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2019.03.eb new file mode 100644 index 00000000000..87ddddb6c7d --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2019.03.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2019.03'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb new file mode 100644 index 00000000000..0913db092da --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb @@ -0,0 +1,33 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'icc' +version = '2019.3.199' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Intel C and C++ compilers" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15273/'] +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] +checksums = ['969985e83ebf7bfe3c3ac3b771a7d16ba9b5dfbda84e7c2a60ef25fb827b58ae'] + +gccver = '8.3.0' +binutilsver = '2.32' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-ccomp', 'intel-icc', 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.3.199-GCC-8.3.0-2.32.eb new file mode 100644 index 00000000000..b0673da2366 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iccifort' +version = '2019.3.199' +versionsuffix = '-GCC-8.3.0-2.32' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = "Intel C, C++ & Fortran compilers" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb new file mode 100644 index 00000000000..d911088959e --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -0,0 +1,38 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'ifort' +version = '2019.3.199' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Intel Fortran compiler" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15274/'] +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] +patches = ['ifort-%(version)s_no_mpi_mic_dependency.patch'] +checksums = [ + # parallel_studio_xe_2019_update3_composer_edition_for_fortran.tgz + '94b7d1c31e3b28ec1aa66c1ed1a6efc157f1776efb7544a0c326a58df9803572', + 'fb0bbb112a47b894ff3fbcc4a254ebcd33a76189c6a1814ecf6235472a51c2c5', # ifort_2019.3.199_no_mpi_mic_dependency.patch +] + +gccver = '8.3.0' +binutilsver = '2.32' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = ['intel-comp', 'intel-fcomp', 'intel-ifort', 'intel-openmp', 'intel-ipsf?_', 'intel-gdb(?!.*mic)'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199_no_mpi_mic_dependency.patch b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199_no_mpi_mic_dependency.patch new file mode 100644 index 00000000000..175beba7bae --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199_no_mpi_mic_dependency.patch @@ -0,0 +1,13 @@ +don't install Intel MIC runtime components (mpi-mic-rt), cfr. https://github.com/easybuilders/easybuild-easyconfigs/pull/3793 +author: Kenneth Hoste (HPC-UGent) +--- parallel_studio_xe_2019_update3_composer_edition_for_fortran/pset/mediaconfig.xml.orig 2019-03-09 10:45:11.184460201 +0100 ++++ parallel_studio_xe_2019_update3_composer_edition_for_fortran/pset/mediaconfig.xml 2019-03-09 10:49:37.083652872 +0100 +@@ -1047,7 +1047,7 @@ + + ${COMPLIB_ROOT} + 1551719152756 +- ++ + Intel Fortran Compiler for Intel(R) 64 + Intel Fortran Compiler 19.0 Update 3 + インテル(R) Fortran コンパイラー (インテル(R) 64) diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2019.03.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2019.03.eb new file mode 100644 index 00000000000..e526714c3d9 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2019.03.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2019.03' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2019.3.199' +suff = '-GCC-8.3.0-2.32' +dependencies = [ + ('icc', compver, suff), + ('ifort', compver, suff), + ('impi', compver, '', ('iccifort', '%s%s' % (compver, suff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb new file mode 100644 index 00000000000..7a2964df5e4 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.3.199-iimpi-2019.03.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2019.3.199' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '2019.03'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15275/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['06de2b54f4812e7c39a118536259c942029fe1d6d8918ad9df558a83c4162b8f'] + +dontcreateinstalldir = 'True' + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb new file mode 100644 index 00000000000..79013de91f0 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2019.3.199-iccifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -0,0 +1,22 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'impi' +version = '2019.3.199' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'iccifort', 'version': '2019.3.199-GCC-8.3.0-2.32'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15260/'] +sources = ['l_mpi_%(version)s.tgz'] +checksums = ['5304346c863f64de797250eeb14f51c5cfc8212ff20813b124f20e7666286990'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2019.03.eb b/easybuild/easyconfigs/i/intel/intel-2019.03.eb new file mode 100644 index 00000000000..4d8289207a0 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2019.03.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2019.03' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2019.3.199' +gccver = '8.3.0' +binutilsver = '2.32' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', compver, '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', compver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From a3fd562e4672fbbdcadfa64f43f15dddf7468771 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Mar 2019 15:44:34 +0100 Subject: [PATCH 0790/5331] use -P preprocessor option in ncurses-5.9.eb (required for recent system GCC versions) --- easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index bc44b49767d..297893f8db0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -19,6 +19,9 @@ checksums = [ '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', # ncurses-5.9_configure_darwin.patch ] +# need to use -P preprocessor option for recent GCC versions (cfr. https://gcc.gnu.org/gcc-5/porting_to.html) +preconfigopts = "export CPPFLAGS='-P' && " + configopts = [ # default build '--with-shared --enable-overwrite', From 5587e6883305875bd6145c1f801d35cb3f101ae0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Mar 2019 15:49:39 +0100 Subject: [PATCH 0791/5331] fix SCOTCH dep in Trilinos easyconfig --- .../t/Trilinos/Trilinos-12.12.1-intel-2018a-Python-3.6.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-intel-2018a-Python-3.6.4.eb index 47e9ea4fa18..89b9b46837a 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-intel-2018a-Python-3.6.4.eb @@ -38,7 +38,7 @@ dependencies = [ ('Python', '3.6.4'), ('Boost', '1.66.0'), ('Boost.Python', '1.66.0', versionsuffix), - ('SCOTCH', '6.0.5'), + ('SCOTCH', '6.0.6'), ('SuiteSparse', '5.1.2', '-METIS-5.1.0'), ('ParMETIS', '4.0.3'), ('netCDF', '4.6.0'), From 26cea78429b849cdda9de75d5d8698cafadb2337 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 9 Mar 2019 10:16:47 -0500 Subject: [PATCH 0792/5331] download PyPi extensions using pip --- ...2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb index c45bffeaa80..53199b12487 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb @@ -25,11 +25,14 @@ dependencies = [ exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + exts_list = [ ('py4j', '0.10.8.1', { - # https://files.pythonhosted.org/packages/c0/e3/1f110e6c069522ba7a8dc215ff1c343b6bc1f98d84e6d627ca2708426eaa/py4j-0.10.8.1.zip - 'source_urls': \ - ['https://files.pythonhosted.org/packages/c0/e3/1f110e6c069522ba7a8dc215ff1c343b6bc1f98d84e6d627ca2708426eaa'], + 'source_urls': ['https://pypi.python.org/packages/source/p/py4j'], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['8329bb156a0cf37be9642a2a060dbdb627b5fcb827919be65d95102daccca274'], }), From fa01dad4d57cd200605bea7eb0fb3ca6000d8b38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Mar 2019 16:32:00 +0100 Subject: [PATCH 0793/5331] adding easyconfigs: Java-11.0.2.eb --- easybuild/easyconfigs/j/Java/Java-11.0.2.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-11.0.2.eb diff --git a/easybuild/easyconfigs/j/Java/Java-11.0.2.eb b/easybuild/easyconfigs/j/Java/Java-11.0.2.eb new file mode 100644 index 00000000000..c4210cc0d8f --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-11.0.2.eb @@ -0,0 +1,14 @@ +name = 'Java' +version = '11.0.2' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://download.java.net/java/GA/jdk%(version_major)s/9/GPL/'] +sources = ['openjdk-%(version)s_linux-x64_bin.tar.gz'] +checksums = ['99be79935354f5c0df1ad293620ea36d13f48ec3ea870c838f20c504c9668b57'] + +moduleclass = 'lang' From 7fa3e8d4aec914030ae5dd73e83eb12f5bf7c180 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Mar 2019 17:49:45 +0100 Subject: [PATCH 0794/5331] don't use local variable 'pylibdir' in list comprehension in PyQt easyconfig, since that doesn't work in Python 3 --- .../p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb index e178b5676b1..c92b486525c 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.12.3-fosscuda-2018b-Python-2.7.15.eb @@ -16,10 +16,8 @@ dependencies = [ default_easyblock = 'ConfigureMakePythonPackage' -pylibdir = 'lib/python%(pyshortver)s/site-packages' - common_cfgopts = '--bindir=%(installdir)s/bin ' -common_cfgopts += '--destdir=%%(installdir)s/%s ' % pylibdir +common_cfgopts += '--destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages ' common_cfgopts += '--sipdir=%(installdir)s/share/sip ' sipcfgopts = 'configure.py ' + common_cfgopts @@ -51,13 +49,14 @@ components = [ ] modextrapaths = { - 'PYTHONPATH': pylibdir, + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'QT_PLUGIN_PATH': 'plugins' } sanity_check_paths = { 'files': ['bin/%s' % x for x in ['pyuic4', 'pyrcc4', 'pylupdate4']] + - [pylibdir + '/%%(name)s%%(version_major)s/%s.%s' % (x, SHLIB_EXT) for x in ['sip', 'QtCore', 'Qt']], + ['lib/python%%(pyshortver)s/site-packages/%%(name)s%%(version_major)s/%s.%s' % (x, SHLIB_EXT) + for x in ['sip', 'QtCore', 'Qt']], 'dirs': ['include', 'plugins', 'share/sip'], } From 037bb85aec1fc5ee834c6319a7c626a440c154ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Mar 2019 18:01:29 +0100 Subject: [PATCH 0795/5331] add space for consistency in recent CMake easyconfigs that use dummy toolchain --- easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb | 2 +- easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb index 1e3749603aa..fa2ba9a1738 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb @@ -25,7 +25,7 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] configopts = "-- -DCMAKE_USE_OPENSSL=1 " configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " -configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include " sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb index 15de3ff1845..b69bcb6ac0b 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb @@ -22,7 +22,7 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] configopts = "-- -DCMAKE_USE_OPENSSL=1 " configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " -configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include " sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb index d706473dedd..30e7eabb0ca 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb @@ -22,7 +22,7 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] configopts = "-- -DCMAKE_USE_OPENSSL=1 " configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " -configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include " sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb index be1d13e34cf..b0776d7c054 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb @@ -21,7 +21,7 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] configopts = "-- -DCMAKE_USE_OPENSSL=1 " configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " configopts += "-DCURSES_FORM_LIBRARY=$EBROOTNCURSES/lib/libform.a " -configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +configopts += "-DCURSES_NCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.a -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include " sanity_check_paths = { 'files': ["bin/%s" % x for x in ['ccmake', 'cmake', 'cpack', 'ctest']], From e58a0c5d1f4da4410d7da479809f39c3e447eacd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Mar 2019 18:24:44 +0100 Subject: [PATCH 0796/5331] add missing download_dep_fail and use_pip in PyYAML easyconfig --- .../p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb index af657669158..d9ec29b77b8 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13-intel-2018b-Python-2.7.15.eb @@ -18,6 +18,9 @@ dependencies = [ ('libyaml', '0.2.1'), ] +download_dep_fail = True +use_pip = True + options = {'modulename': 'yaml'} sanity_check_paths = { From a72fbc0ebd7b9d2179f8643e7ca34234298e30a7 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 10 Mar 2019 00:12:57 +0200 Subject: [PATCH 0797/5331] adding easyconfigs: PCRE-8.43-GCCcore-8.2.0.eb --- .../p/PCRE/PCRE-8.43-GCCcore-8.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.43-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.43-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.43-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..4f8b4430917 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.43-GCCcore-8.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.43' + +homepage = 'http://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.pcre.org/pub/pcre/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0b8e7465dc5e98c757cc3650a20a7843ee4c3edf50aaf60bb33fd879690d2c73'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = """\ + --enable-utf\ + --enable-unicode-properties\ + --enable-pcre16\ + --enable-pcre32\ +""" + +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + +moduleclass = 'devel' From 07ac107f894d43728f5ad9dcfc87233b53a74fb9 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 10 Mar 2019 00:16:40 +0200 Subject: [PATCH 0798/5331] adding easyconfigs: util-linux-2.33-GCCcore-8.2.0.eb --- .../util-linux-2.33-GCCcore-8.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.33-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.33-GCCcore-8.2.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.33-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..89290ca1953 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.33-GCCcore-8.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.33' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['952fb0d3498e81bd67b3c48e283c80cb12c719bc2357ec5801e7d420991ad319'] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('ncurses', '6.1'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' From 0b7c9bd52f8b0e53b38f6f145616f427e1bda152 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 10 Mar 2019 00:18:19 +0200 Subject: [PATCH 0799/5331] adding easyconfigs: gettext-0.19.8.1-GCCcore-8.2.0.eb --- .../gettext/gettext-0.19.8.1-GCCcore-8.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..6a4e87d0e46 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-8.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8.1' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ff942af0e438ced4a8b0ea4b0b6e0d6d657157c5e2364de57baa279c1c125c43'] + +dependencies = [ + ('libxml2', '2.9.8'), + ('ncurses', '6.1'), +] + +# use same binutils version that was used when building GCCcore toolchain +builddependencies = [('binutils', '2.31.1')] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 8da319bb5a17591a808ef70b7c059ce544022485 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 10 Mar 2019 00:26:10 +0200 Subject: [PATCH 0800/5331] adding easyconfigs: libffi-3.2.1-GCCcore-8.2.0.eb, libunistring-0.9.10-GCCcore-8.2.0.eb, gc-7.6.10-GCCcore-8.2.0.eb, GMP-6.1.2-GCCcore-8.2.0.eb, Guile-1.8.8-GCCcore-8.2.0.eb, libmatheval-1.1.11-GCCcore-8.2.0.eb --- .../g/GMP/GMP-6.1.2-GCCcore-8.2.0.eb | 35 ++++++++++++++++ .../g/Guile/Guile-1.8.8-GCCcore-8.2.0.eb | 36 +++++++++++++++++ .../g/gc/gc-7.6.10-GCCcore-8.2.0.eb | 40 +++++++++++++++++++ .../l/libffi/libffi-3.2.1-GCCcore-8.2.0.eb | 37 +++++++++++++++++ .../libmatheval-1.1.11-GCCcore-8.2.0.eb | 38 ++++++++++++++++++ .../libunistring-0.9.10-GCCcore-8.2.0.eb | 33 +++++++++++++++ 6 files changed, 219 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/gc/gc-7.6.10-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..796b76c6ae6 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.2-GCCcore-8.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.1.2' + +homepage = 'http://gmplib.org/' + +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] +checksums = ['5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.31.1'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..c9c64826924 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-8.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '1.8.8' + +homepage = 'https://www.gnu.org/software/guile/' +description = """Guile is a programming language, designed to help programmers create flexible applications that + can be extended by users or other programmers with plug-ins, modules, or scripts.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3471fed2e72e5b04ad133bbaaf16369e8360283679bcf19800bc1b381024050'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.31.1'), +] +dependencies = [ + ('libunistring', '0.9.10'), + ('libffi', '3.2.1'), + ('gc', '7.6.10'), + ('GMP', '6.1.2'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ['bin/guile', 'bin/guile-config', 'bin/guile-snarf', 'bin/guile-tools', + 'include/libguile.h', 'lib/libguile.a', 'lib/libguile.%s' % SHLIB_EXT, + 'lib/pkgconfig/guile-%(version_major_minor)s.pc'], + 'dirs': ['include/guile'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/gc/gc-7.6.10-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/gc/gc-7.6.10-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..082c743298c --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-7.6.10-GCCcore-8.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '7.6.10' + +homepage = 'http://hboehm.info/gc/' + +description = """ + The Boehm-Demers-Weiser conservative garbage collector can be used as a + garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [ + 'http://hboehm.info/gc/gc_source/', + 'https://github.com/ivmai/libatomic_ops/releases/download/v%(version)s/', +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%(version)s.tar.gz', +] +checksums = [ + '4fc766749a974700c576bbfb71b4a73b2ed746082e2fc8388bfb0b54b636af14', # gc-7.6.10.tar.gz + '587edf60817f56daf1e1ab38a4b3c729b8e846ff67b4f62a6157183708f099af', # libatomic_ops-7.6.10.tar.gz +] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..affa2a35046 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-8.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.2.1' + +homepage = 'http://sourceware.org/libffi/' + +description = """ + The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['libffi-%(version)s_fix-include-location.patch'] +checksums = [ + 'd06ebb8e1d9a22d19e38d63fdb83954253f39bedc5d46232a05645685722ca37', # libffi-3.2.1.tar.gz + '078bec207fc3d5a0581f2a952d1c014b76a6e84a93a6a089ff9b9fe5b3908cb9', # libffi-3.2.1_fix-include-location.patch +] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +sanity_check_paths = { + 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..80536965709 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-GCCcore-8.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['libmatheval-%(version)s_fix-matheval-test.patch'] +checksums = [ + '474852d6715ddc3b6969e28de5e1a5fbaff9e8ece6aebb9dc1cc63e9e88e89ab', # libmatheval-1.1.11.tar.gz + '2888ee1ba32bb864b655e53e13b06eafc23b598faed80b90585d41c98e2ae073', # libmatheval-1.1.11_fix-matheval-test.patch +] + +builddependencies = [ + ('binutils', '2.31.1'), + ('flex', '2.6.4'), + ('Bison', '3.0.5'), + ('Guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..759309c4eed --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.10-GCCcore-8.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.10' + +homepage = 'http://www.gnu.org/software/libunistring/' + +description = """ + This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['eb8fb2c3e4b6e2d336608377050892b54c3c983b646c561836550863003c05d7'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' From 9d899aa694b1f36ca5a926448a120cc2faf5f5ed Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 10 Mar 2019 02:55:39 +0200 Subject: [PATCH 0801/5331] adding easyconfigs: expat-2.2.6-GCCcore-8.2.0.eb, gperf-3.1-GCCcore-8.2.0.eb, freetype-2.9.1-GCCcore-8.2.0.eb, fontconfig-2.13.1-GCCcore-8.2.0.eb --- .../e/expat/expat-2.2.6-GCCcore-8.2.0.eb | 25 ++++++++++++ .../fontconfig-2.13.1-GCCcore-8.2.0.eb | 34 ++++++++++++++++ .../freetype/freetype-2.9.1-GCCcore-8.2.0.eb | 39 +++++++++++++++++++ .../g/gperf/gperf-3.1-GCCcore-8.2.0.eb | 31 +++++++++++++++ 4 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.1-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.9.1-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..70707a37a44 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.6' + +homepage = 'http://expat.sourceforge.net/' + +description = """ + Expat is an XML parser library written in C. It is a stream-oriented parser + in which an application registers handlers for things the parser might find + in the XML document (like start tags) +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['17b43c2716d521369f82fc2dc70f359860e90fa440bea65b3b85f0b246ea81f2'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..e87cba9e71c --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.1-GCCcore-8.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.13.1' + +homepage = 'http://www.freedesktop.org/software/fontconfig' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['9f0d852b39d75fc655f9f53850eb32555394f36104a044bb2b2fc9e66dbbfa7f'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('gperf', '3.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('expat', '2.2.6'), + ('freetype', '2.9.1'), + ('util-linux', '2.33'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.9.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.9.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..f84cf795da9 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.9.1-GCCcore-8.2.0.eb @@ -0,0 +1,39 @@ +name = 'freetype' +version = '2.9.1' + +homepage = 'http://freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ec391504e55498adceb30baceebd147a6e963f636eb617424bcfc47a169898ce'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('libpng', '1.6.36'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..5af684cc180 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-8.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'http://www.gnu.org/software/gperf/' + +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' From 94a64d4926056bb1412886f02c4361814955bfcd Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 10 Mar 2019 03:43:16 +0200 Subject: [PATCH 0802/5331] adding easyconfigs: LibTIFF-4.0.10-GCCcore-8.2.0.eb --- .../l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..b5228647bf7 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.2.0.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.10' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['2c52d11ccaf767457db0c46795d9c7d1a8d8f76f68b0b800a3dfe45786b996e4'] + +builddependencies = [('binutils', '2.31.1')] + +configopts = " --enable-ld-version-script " + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' From b119e73c713467dc62c78414eb56edbdd680b272 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 10 Mar 2019 03:45:35 +0200 Subject: [PATCH 0803/5331] adding easyconfigs: NASM-2.14.02-GCCcore-8.2.0.eb, libjpeg-turbo-2.0.2-GCCcore-8.2.0.eb --- .../libjpeg-turbo-2.0.2-GCCcore-8.2.0.eb | 42 +++++++++++++++++++ .../n/NASM/NASM-2.14.02-GCCcore-8.2.0.eb | 37 ++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.2-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.14.02-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..4610fed91ab --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.2-GCCcore-8.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.0.2' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['acb8599fe5399af114287ee5907aea4456f8f2c1cc96d26c28aebfdf5ee82fed'] + +builddependencies = [ + ('CMake', '3.13.3'), + ('binutils', '2.31.1'), +] + +dependencies = [ + ('NASM', '2.14.02'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.14.02-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.14.02-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..e80fc311142 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.14.02-GCCcore-8.2.0.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.14.02' + +homepage = 'http://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['34fd26c70a277a9fdd54cb5ecf389badedaf48047b269d1008fbc819b24e80bc'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' From 7fc37bfca7221e0f2ef7c8a20ac0937c5449bade Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 10 Mar 2019 03:58:33 +0200 Subject: [PATCH 0804/5331] adding easyconfigs: pixman-0.38.0-GCCcore-8.2.0.eb --- .../p/pixman/pixman-0.38.0-GCCcore-8.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.38.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.38.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.38.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..13ed4dbbb90 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.38.0-GCCcore-8.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.38.0' + +homepage = 'http://www.pixman.org/' + +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a7592bef0156d7c27545487a52245669b00cf7e70054505381cff2136d890ca8'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' From ca6862eaa76b18b0b7ac11152576f13c7ef087a9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 10 Mar 2019 12:03:31 +0200 Subject: [PATCH 0805/5331] Add dependencies for at-spi2-atk, X11. Add builddeps for cairo, gettext, Perl. --- .../at-spi2-atk-2.26.3-fosscuda-2018b.eb | 36 +++++++++++++ .../at-spi2-core-2.26.3-fosscuda-2018b.eb | 41 +++++++++++++++ ...tion-1.54.1-fosscuda-2018b-Python-3.6.6.eb | 52 +++++++++++++++++++ .../g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb | 6 +++ 4 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.26.3-fosscuda-2018b.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.26.3-fosscuda-2018b.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.26.3-fosscuda-2018b.eb new file mode 100644 index 00000000000..dd2eebc7865 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.26.3-fosscuda-2018b.eb @@ -0,0 +1,36 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.26.3' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + AT-SPI 2 toolkit bridge +""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +builddependencies = [ + ('Meson', '0.48.1', '-Python-3.6.6'), + ('Ninja', '1.8.2'), +] + +dependencies = [ + ('GLib', '2.54.3'), + ('DBus', '1.13.6'), + ('at-spi2-core', '2.26.3'), + ('libxml2', '2.9.8'), + ('ATK', '2.28.1'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb new file mode 100644 index 00000000000..b371a6f7e70 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.26.3' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +builddependencies = [ + ('Meson', '0.48.1', '-Python-3.6.6'), + ('Ninja', '1.8.2'), + ('GObject-Introspection', '1.54.1', '-Python-3.6.6'), + ('gettext', '0.19.8.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.54.3'), + ('DBus', '1.13.6'), + ('X11', '20180604'), +] + +configopts = "--libdir lib " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..41dd871f4ee --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.54.1-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.54.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C + libraries (using GObject) and language bindings. The C library can be scanned + at compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['b88ded5e5f064ab58a93aadecd6d58db2ec9d970648534c63807d4f9a7bb877e'] + +builddependencies = [ + ('Autotools', '20180311'), + ('flex', '2.6.4'), + ('Bison', '3.0.5'), + ('cairo', '1.14.12'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.6.6'), + ('util-linux', '2.32'), + ('GLib', '2.54.3'), + ('libffi', '3.2.1'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true PYTHON=python3 " + +# avoid using hard-coded path to 'python' in shebang of scripts +buildopts = "PYTHON=python3" + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', + 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb index b5b2539c234..9cfb885d637 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb @@ -16,14 +16,20 @@ checksums = ['a1a4a5c12703d4e1ccda28333b87ff462741dc365131fbc94c218ae81d9a6567'] builddependencies = [ ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), + ('gettext', '0.19.8.1'), ('pkg-config', '0.29.2'), + ('cairo', '1.14.12'), + ('Perl', '5.28.0'), ] dependencies = [ ('ATK', '2.28.1'), + ('at-spi2-atk', '2.26.3'), + ('GLib', '2.54.3'), ('Gdk-Pixbuf', '2.36.11'), ('Pango', '1.42.4'), ('libepoxy', '1.5.3'), + ('X11', '20180604'), ] configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " From 64f310e3b8e72871368d77002bdc92e93357aed3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 10 Mar 2019 13:34:31 +0200 Subject: [PATCH 0806/5331] Add missing checksums for at-spi2-*. --- .../a/at-spi2-atk/at-spi2-atk-2.26.3-fosscuda-2018b.eb | 1 + .../a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.26.3-fosscuda-2018b.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.26.3-fosscuda-2018b.eb index dd2eebc7865..9189c2dd02e 100644 --- a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.26.3-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.26.3-fosscuda-2018b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['ca1a3ea03b6fe06402cebce6fc052b0526e8f8cc6e363737dd648f97eb2ce9c7'] builddependencies = [ ('Meson', '0.48.1', '-Python-3.6.6'), diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb index b371a6f7e70..c16f4436c55 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.26.3-fosscuda-2018b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['ebc9cdc4a1646c993735201426600c1f5432c694f95c69805ae16ad15065ccaf'] builddependencies = [ ('Meson', '0.48.1', '-Python-3.6.6'), From cc8056159044d5751c325bd7400e6ff274fa5c7b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 10 Mar 2019 13:37:13 +0200 Subject: [PATCH 0807/5331] Update Gdk-Pixbuf to 2.36.12 as per 2018b toolchains. --- .../g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb | 2 +- .../Gdk-Pixbuf-2.36.12-fosscuda-2018b.eb | 46 +++++++++++++++++++ 2 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb index 9cfb885d637..98410764762 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb @@ -26,7 +26,7 @@ dependencies = [ ('ATK', '2.28.1'), ('at-spi2-atk', '2.26.3'), ('GLib', '2.54.3'), - ('Gdk-Pixbuf', '2.36.11'), + ('Gdk-Pixbuf', '2.36.12'), ('Pango', '1.42.4'), ('libepoxy', '1.5.3'), ('X11', '20180604'), diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-fosscuda-2018b.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-fosscuda-2018b.eb new file mode 100644 index 00000000000..fccb950132e --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.36.12-fosscuda-2018b.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Gdk-Pixbuf' +version = '2.36.12' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +patches = ['Gdk-Pixbuf-2.36.10-disable-gio-sniffing.patch'] +checksums = [ + 'fff85cf48223ab60e3c3c8318e2087131b590fd6f1737e42cb3759a3b427a334', # gdk-pixbuf-2.36.12.tar.xz + '840231db69ccc2a1335c4f29c305cdd0ba570254e779c2a274611aaff968878e', # Gdk-Pixbuf-2.36.10-disable-gio-sniffing.patch +] + +builddependencies = [ + ('GObject-Introspection', '1.54.1', '-Python-2.7.15') +] +dependencies = [ + ('GLib', '2.54.3'), + ('libjpeg-turbo', '2.0.0'), + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), +] + +configopts = "--disable-maintainer-mode --enable-debug=no --enable-introspection=yes " +configopts += "--disable-Bsymbolic --without-gdiplus --enable-shared --enable-static" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' From 294861152bc3a2ec581f625a29d826eb0f5a4e00 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 10 Mar 2019 13:53:56 +0100 Subject: [PATCH 0808/5331] download taxdump from archive --- .../BlobTools-20180528-foss-2018b-Python-2.7.15.eb | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb index 79be229404e..0717c6d46bc 100644 --- a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb @@ -4,6 +4,7 @@ name = 'BlobTools' version = '20180528' commit = 'a14630e' versionsuffix = '-Python-%(pyver)s' +taxdump_ver = '2019-03-01' homepage = 'https://blobtools.readme.io/docs' description = """ A modular command-line solution for visualisation, @@ -13,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = [ 'https://github.com/drl/blobtools/archive/', - 'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/', + 'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive', ] sources = [ { @@ -21,13 +22,16 @@ sources = [ 'filename': SOURCE_TAR_GZ, 'extract_cmd': "tar -xzf %s -C %(builddir)s --strip-components 1", }, - {'filename': 'taxdump.tar.gz', 'extract_cmd': "cp %s %(builddir)s/data/"}, + { + 'filename': 'taxdmp_%s.zip' % taxdump_ver, + 'extract_cmd': 'unzip %s && cp nodes.dmp names.dmp %(builddir)s/data/', + }, ] patches = ['BlobTools-20180528_fix_deps.patch'] checksums = [ '316c22cceec6b6ac4e3751d06ec6effb88ea35d746abb957239c75e1f4eed9a9', # BlobTools-20180528.tar.gz - '24399e6711ff09e27a3d457cfbf4567615e4f5b990ff15681e60248ef7852df6', # taxdump.tar.gz - 'f26cfc74a1d90cf692a4655d251be236920feb8b0c636cd3358c4eda0c50cc82', # BlobTools-20180528_fix_deps.patch + 'a53d6026e24b647bd0ea1a83b253a3061f03dc814ec45d1dca58f2a9f36d8780', # taxdmp_2019-03-01.zip + '635b5f1c22cbbedce0ba8144037163d2d8459a7a7e0b790dd9d3e0020369ff76', # BlobTools-20180528_fix_deps.patch ] dependencies = [ From b9e320a1ce2a8cda3fd2d3bf285f0d5399846997 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 10 Mar 2019 15:40:57 +0100 Subject: [PATCH 0809/5331] upload patch --- .../BlobTools/BlobTools-20180528_fix_deps.patch | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528_fix_deps.patch b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528_fix_deps.patch index f3f55c23445..e14f3557296 100644 --- a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528_fix_deps.patch +++ b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528_fix_deps.patch @@ -1,10 +1,11 @@ Don't install Python dependencies +Don't download and extract taxdump Don't install SAMtools Don't use self-installed SAMtools Author: Samuel Moors, Vrije Universiteit Brussel (VUB) diff -ur blobtools-master.orig/install blobtools-master/install --- blobtools-master.orig/install 2018-05-29 15:39:21.000000000 +0200 -+++ blobtools-master/install 2019-01-29 16:31:54.613784312 +0100 ++++ blobtools-master/install 2019-03-10 13:36:46.469860400 +0100 @@ -30,16 +30,6 @@ exit fi @@ -22,7 +23,7 @@ diff -ur blobtools-master.orig/install blobtools-master/install # Create executable echo -n "[+] Creating BlobTools executable..." -@@ -124,12 +114,6 @@ +@@ -124,19 +114,7 @@ fi } @@ -33,8 +34,15 @@ diff -ur blobtools-master.orig/install blobtools-master/install -fi -install_samtools - # get taxdump - taxdump=$DIR/data/taxdump.tar.gz +-# get taxdump +-taxdump=$DIR/data/taxdump.tar.gz +-if [ ! -f "$taxdump" ]; then +- download_taxdump +-fi +-unpack_taxdump + + # nodesdb + ./blobtools nodesdb --nodes $DIR/data/nodes.dmp --names $DIR/data/names.dmp diff -ur blobtools-master.orig/lib/blobtools.py blobtools-master/lib/blobtools.py --- blobtools-master.orig/lib/blobtools.py 2018-05-29 15:39:21.000000000 +0200 +++ blobtools-master/lib/blobtools.py 2019-01-29 16:34:20.702264497 +0100 From 2e2afb47652754174bd94a197af826d518118d33 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 10 Mar 2019 18:42:03 +0200 Subject: [PATCH 0810/5331] adding easyconfigs: unrar-5.7.3-GCCcore-8.2.0.eb --- .../u/unrar/unrar-5.7.3-GCCcore-8.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/u/unrar/unrar-5.7.3-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/u/unrar/unrar-5.7.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/u/unrar/unrar-5.7.3-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..fd374a18127 --- /dev/null +++ b/easybuild/easyconfigs/u/unrar/unrar-5.7.3-GCCcore-8.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'unrar' +version = '5.7.3' + +homepage = 'https://www.rarlab.com/' +description = "RAR is a powerful archive manager." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://www.rarlab.com/rar/'] +sources = ['unrarsrc-%(version)s.tar.gz'] +checksums = ['40e856b78374f258d8a1f5f02c02f828c5392a0118c9300fd169a300b520a444'] + +builddependencies = [('binutils', '2.31.1')] + +skipsteps = ['configure'] + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' +installopts = 'DESTDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/unrar'], + 'dirs': [], +} + +moduleclass = 'tools' From 3d7a64dc877b4b0bf8c26dd1e7e18af4551c07e0 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 10 Mar 2019 18:43:46 +0200 Subject: [PATCH 0811/5331] adding easyconfigs: pigz-2.4-GCCcore-8.2.0.eb --- .../p/pigz/pigz-2.4-GCCcore-8.2.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..8fe2b3adc99 --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-8.2.0.eb @@ -0,0 +1,51 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# +# 2.4.0: +# Jonas Demeulemeester +# The Francis Crick Institute +## +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.4' + +homepage = 'http://zlib.net/pigz/' + +description = """ + pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. pigz was written by Mark Adler, and + uses the zlib and pthread libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [ + 'http://zlib.net/pigz/', + 'https://zlib.net/pigz/fossils/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['a4f816222a7b4269bd232680590b579ccc72591f1bb5adafcd7208ca77e14f73'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ['bin/pigz', 'bin/unpigz'], + 'dirs': [], +} + +moduleclass = 'tools' From c7d4ecf4b61906a314e852b356c5401707eed712 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 10 Mar 2019 18:45:33 +0200 Subject: [PATCH 0812/5331] adding easyconfigs: gzip-1.10-GCCcore-8.2.0.eb --- .../g/gzip/gzip-1.10-GCCcore-8.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..418a5dda188 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-8.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.10' + +homepage = 'http://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c91f74430bf7bc20402e1f657d0b252cb80aa66ba333a25704512af346633c68'] + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' From 308367789429c2de1d0c2a6343720f10722f3c40 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 11 Mar 2019 13:18:11 +0800 Subject: [PATCH 0813/5331] remove non-applicable skipsteps line --- easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb b/easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb index 67ebac2bf78..d5580397521 100644 --- a/easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb +++ b/easybuild/easyconfigs/b/Bader/Bader-1.03-intel-2018b.eb @@ -12,7 +12,6 @@ source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(ver sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] checksums = ['3de8af94bd64c43812de7ebad3e9209cc5e29e6732679fcf88f72a1b382bc81a'] -skipsteps = ['configure'] buildopts = '-f makefile.lnx_ifort' parallel = 1 From a033f8730e617d8bb7d587552e35223b9b64a7fb Mon Sep 17 00:00:00 2001 From: SethosII Date: Mon, 11 Mar 2019 08:28:03 +0100 Subject: [PATCH 0814/5331] use SHLIB_EXT template --- .../l/libgtextutils/libgtextutils-0.7-GCCcore-7.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-GCCcore-7.3.0.eb index ccc679473ad..d46b7907788 100644 --- a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.7-GCCcore-7.3.0.eb @@ -35,7 +35,7 @@ checksums = [ builddependencies = [('binutils', '2.30')] sanity_check_paths = { - 'files': ['lib/%(name)s.so', 'lib/%(name)s.a'], + 'files': ['lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a'], 'dirs': ['lib/pkgconfig'] } From da136eb9bba8301f2a252c4d6dfc105facf7a217 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Mon, 11 Mar 2019 10:11:55 +0100 Subject: [PATCH 0815/5331] added "toolchainopts = {'usempi': True}" --- easybuild/easyconfigs/e/ExaBayes/ExaBayes-1.5-foss-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ExaBayes/ExaBayes-1.5-foss-2016b.eb b/easybuild/easyconfigs/e/ExaBayes/ExaBayes-1.5-foss-2016b.eb index 45072fd9b8d..313ed7d5d20 100644 --- a/easybuild/easyconfigs/e/ExaBayes/ExaBayes-1.5-foss-2016b.eb +++ b/easybuild/easyconfigs/e/ExaBayes/ExaBayes-1.5-foss-2016b.eb @@ -15,6 +15,7 @@ description = """ExaBayes is a software package for Bayesian tree inference. # only tested with GCC < 6 # https://groups.google.com/d/msg/exabayes/94tOvKRDq-s/F223g6qKCQAJ toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} source_urls = ['https://cme.h-its.org/exelixis/resource/download/software/'] sources = [SOURCELOWER_TAR_GZ] From b660edc734db31afa7cc78ccb56621ab6814339f Mon Sep 17 00:00:00 2001 From: SethosII Date: Mon, 11 Mar 2019 10:55:35 +0100 Subject: [PATCH 0816/5331] use GDGraph instead of GD --- ...tQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb | 2 +- .../GDGraph-1.54-foss-2018b-Perl-5.28.0.eb | 55 +++++++++++++++++++ 2 files changed, 56 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GDGraph/GDGraph-1.54-foss-2018b-Perl-5.28.0.eb diff --git a/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb index 67b9a91d129..678f44274f3 100644 --- a/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.13.0-foss-2018b-Perl-5.28.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('Bowtie', '1.2.2'), ('Bowtie2', '2.3.4.2'), ('BWA', '0.7.17'), - ('GD', '2.69', versionsuffix), + ('GDGraph', '1.54', versionsuffix), ('Perl', '5.28.0'), ] diff --git a/easybuild/easyconfigs/g/GDGraph/GDGraph-1.54-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/g/GDGraph/GDGraph-1.54-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..d16247f5418 --- /dev/null +++ b/easybuild/easyconfigs/g/GDGraph/GDGraph-1.54-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'Bundle' + +name = 'GDGraph' +version = '1.54' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://metacpan.org/release/%(name)s' +description = "GDGraph is a Perl package to generate charts" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/lstein/Perl-GD/archive/'] + +dependencies = [ + ('Perl', '5.28.0'), + ('libgd', '2.2.5'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '2.0.0'), +] + +# this is a bundle of Perl modules +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('GD', '2.71', { + 'source_tmpl': 'GD-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], + 'checksums': ['451be4873b2ad7261cc5679698cd9d2e84dbdde4309971869fc7734b569b7ac7'], + }), + ('GD::Text', '0.86', { + 'source_tmpl': 'GDTextUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MV/MVERB/'], + 'checksums': ['886ecbf85cfe94f4135ee5689c4847a9ae783ecb99e6759e12c734f2dd6116bc'], + }), + ('GD::Graph', version, { + 'source_tmpl': 'GDGraph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ/'], + 'checksums': ['b96f5c10b656c17d16ab65a1777c908297b028d3b6815f6d54b2337f006bfa4f'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bdf2gdfont.pl'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi', 'man'], +} + +modextrapaths = {'PERL5LIB': [ + 'lib/perl5/site_perl/%(perlver)s', + 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi', +]} + +moduleclass = 'bio' From 14c9f45f3f736915be2a63ecea43cc2f5a432d3e Mon Sep 17 00:00:00 2001 From: dquigley-warwick Date: Mon, 11 Mar 2019 10:34:57 +0000 Subject: [PATCH 0817/5331] Added explicit dependencies to SPLASH where using EBROOT variables. Replace gfortran with F90 envar. --- easybuild/easyconfigs/s/SPLASH/SPLASH-2.8.0-foss-2018b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SPLASH/SPLASH-2.8.0-foss-2018b.eb b/easybuild/easyconfigs/s/SPLASH/SPLASH-2.8.0-foss-2018b.eb index 679396e4e2f..05360272dc8 100644 --- a/easybuild/easyconfigs/s/SPLASH/SPLASH-2.8.0-foss-2018b.eb +++ b/easybuild/easyconfigs/s/SPLASH/SPLASH-2.8.0-foss-2018b.eb @@ -15,10 +15,12 @@ checksums = ['de06b159846bd20717a55ec7cc9420e0fd86ab38dc66dc74b1f61b77b4d24fce'] dependencies = [ ('Giza', '1.1.0'), + ('X11', '20180604'), + ('cairo', '1.14.12'), ] skipsteps = ['configure'] -buildopts = 'SYSTEM=gfortran X11_DIR=$EBROOTX11 ' +buildopts = 'SYSTEM=$F90 X11_DIR=$EBROOTX11 ' buildopts += 'GIZA_DIR=$EBROOTGIZA ' buildopts += 'CAIRO_CFLAGS=-I$EBROOTCAIRO/include ' buildopts += 'CAIRO_LIBS=-L$EBROOTCAIRO/lib -lcairo' From 5c9f00d9c309c0e600fcc5248b5b14da4f12963a Mon Sep 17 00:00:00 2001 From: murfreesboro Date: Mon, 11 Mar 2019 10:05:10 -0500 Subject: [PATCH 0818/5331] update libxml2 version --- easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb index a942983272d..e3999060dff 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb @@ -18,7 +18,7 @@ sources = ['%(namelower)s-%(version)s.tar.gz'] checksums = ['b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4'] dependencies = [ - ('libxml2', '2.9.8'), + ('libxml2', '2.9.7'), ('libxslt', '1.1.32'), ('zlib', '1.2.11'), ] From ee6582aab5bf18dc8b582c5ce3a40902a1f18157 Mon Sep 17 00:00:00 2001 From: murfreesboro Date: Mon, 11 Mar 2019 10:05:36 -0500 Subject: [PATCH 0819/5331] update libxml2 version for intel toolchain --- easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb index c45d4bae0b1..0e826f73806 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb @@ -18,7 +18,7 @@ sources = ['%(namelower)s-%(version)s.tar.gz'] checksums = ['b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4'] dependencies = [ - ('libxml2', '2.9.8'), + ('libxml2', '2.9.7'), ('libxslt', '1.1.32'), ('zlib', '1.2.11'), ] From 9bb98b075d07cc379dea8d0ae7594e89286ba7e4 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Mon, 11 Mar 2019 16:44:08 +0100 Subject: [PATCH 0820/5331] Added extra patch to remove -B/usr/bin from linker_bin_path_flag in tensorflow-1.12.0/third_party/gpus/cuda_configure.bzl This prevents the wrong linker from being used. --- .../TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb index 2193fb911ca..839e916589c 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.12.0-fosscuda-2018b-Python-2.7.15.eb @@ -91,7 +91,8 @@ exts_list = [ 'TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.12.0_lrt-flag.patch', - 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch' + 'TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch', + 'TensorFlow-1.12.0_remove_usrbin_from_linker_bin_path_flag.patch' ], 'checksums': [ '3c87b81e37d4ed7f3da6200474fa5e656ffd20d8811068572f43610cae97ca92', # v1.12.0.tar.gz @@ -101,6 +102,8 @@ exts_list = [ '164d048c69671f870e306760ee7609564fe02bb6378a06414752f3d6da80a631', # TensorFlow-1.12.0_lrt-flag.patch # TensorFlow-1.12.0_dont_expand_cuda_cudnn_path.patch '843acddc197639273cb26e676685a12a1107a3bccca516be1af873df6352bb00', + # TensorFlow-1.12.0_remove_usrbin_from_linker_bin_path_flag.patch + '082ef23b49ce50d2bd225bd462ebfed536bcc50eaa7264fca60521f5432d4b94' ], }), ] From f3529ae0598ce9a7489ffeb99c87b823bc1a78a6 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 11 Mar 2019 11:21:27 -0500 Subject: [PATCH 0821/5331] adding easyconfigs: matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb, matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb, matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb, matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb --- ...tlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb | 58 +++++++++++++++++++ ...otlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb | 47 +++++++++++++++ ...lib-2.1.0-intelcuda-2017b-Python-2.7.14.eb | 51 ++++++++++++++++ ...tlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb | 43 ++++++++++++++ 4 files changed, 199 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..ac87ee91e7c --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '2.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +dependencies = [ + ('Python', '2.7.14'), + ('Tkinter', '%(pyver)s', versionsuffix), + ('libpng', '1.6.32'), + ('freetype', '2.8'), +] + +use_pip = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': [ + 'cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8', # cycler-0.10.0.tar.gz + ], + }), + ('subprocess32', '3.2.7', { + 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], + 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], + }), + ('backports.functools_lru_cache', '1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], + 'checksums': ['31f235852f88edc1558d428d890663c49eb4514ffec9f3650e7f3c9e4a12e36f'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': [ + '4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387', # matplotlib-2.1.0.tar.gz + ], + }), +] + +# specify that PythonBundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..b8628e29dab --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '2.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +dependencies = [ + ('Python', '3.6.3'), + ('Tkinter', '%(pyver)s', versionsuffix), + ('libpng', '1.6.32'), + ('freetype', '2.8'), +] + +use_pip = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': [ + 'cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8', # cycler-0.10.0.tar.gz + ], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': [ + '4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387', # matplotlib-2.1.0.tar.gz + ], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..0ef0b93950c --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '2.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +dependencies = [ + ('Python', '2.7.14'), + ('Tkinter', '%(pyver)s', versionsuffix), + ('libpng', '1.6.32'), + ('freetype', '2.8'), +] + +use_pip = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('subprocess32', '3.2.7', { + 'source_urls': ['https://pypi.python.org/packages/source/s/subprocess32'], + 'checksums': ['1e450a4a4c53bf197ad6402c564b9f7a53539385918ef8f12bdf430a61036590'], + }), + ('backports.functools_lru_cache', '1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.functools_lru_cache'], + 'checksums': ['31f235852f88edc1558d428d890663c49eb4514ffec9f3650e7f3c9e4a12e36f'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..b732dd8e6e4 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '2.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +dependencies = [ + ('Python', '3.6.3'), + ('Tkinter', '%(pyver)s', versionsuffix), + ('libpng', '1.6.32'), + ('freetype', '2.8'), +] + +use_pip = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['4b5f16c9cefde553ea79975305dcaa67c8e13d927b6e55aa14b4a8d867e25387'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] + +moduleclass = 'vis' From 21bf9a14ecc5b361eadd2006f59797136f345767 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 11 Mar 2019 11:27:51 -0500 Subject: [PATCH 0822/5331] Add dependencies --- .../t/Tk/Tk-8.6.7-fosscuda-2017b.eb | 30 +++++++++++++++++++ .../t/Tk/Tk-8.6.7-intelcuda-2017b.eb | 30 +++++++++++++++++++ ...ter-2.7.14-fosscuda-2017b-Python-2.7.14.eb | 21 +++++++++++++ ...er-2.7.14-intelcuda-2017b-Python-2.7.14.eb | 21 +++++++++++++ ...inter-3.6.3-fosscuda-2017b-Python-3.6.3.eb | 21 +++++++++++++ ...nter-3.6.3-intelcuda-2017b-Python-3.6.3.eb | 21 +++++++++++++ 6 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.7-fosscuda-2017b.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.7-intelcuda-2017b.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.14-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.14-intelcuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.3-fosscuda-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.3-intelcuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.7-fosscuda-2017b.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.7-fosscuda-2017b.eb new file mode 100644 index 00000000000..f82a1f82c7a --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.7-fosscuda-2017b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.7' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] +checksums = [ + '061de2a354f9b7c7d04de3984c90c9bc6dd3a1b8377bb45509f1ad8a8d6337aa', # tk8.6.7-src.tar.gz + '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d', # Tk-8.6.4_different-prefix-with-tcl.patch +] + +dependencies = [ + ('Tcl', version), + ('X11', '20171023'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.7-intelcuda-2017b.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.7-intelcuda-2017b.eb new file mode 100644 index 00000000000..aaf9d92ef63 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.7-intelcuda-2017b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.7' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] +checksums = [ + '061de2a354f9b7c7d04de3984c90c9bc6dd3a1b8377bb45509f1ad8a8d6337aa', # tk8.6.7-src.tar.gz + '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d', # Tk-8.6.4_different-prefix-with-tcl.patch +] + +dependencies = [ + ('X11', '20171023'), + ('Tcl', version), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.14-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.14-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..f16ecb8c503 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.14-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,21 @@ +name = 'Tkinter' +version = '2.7.14' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8'] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.7'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.14-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.14-intelcuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..bda85d0fc18 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.14-intelcuda-2017b-Python-2.7.14.eb @@ -0,0 +1,21 @@ +name = 'Tkinter' +version = '2.7.14' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['304c9b202ea6fbd0a4a8e0ad3733715fbd4749f2204a9173a58ec53c32ea73e8'] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.7'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.3-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.3-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..39a672327ed --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.3-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,21 @@ +name = 'Tkinter' +version = '3.6.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91'] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.7'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.3-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.3-intelcuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..5adc4c3371a --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.6.3-intelcuda-2017b-Python-3.6.3.eb @@ -0,0 +1,21 @@ +name = 'Tkinter' +version = '3.6.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['ab6193af1921b30f587b302fe385268510e80187ca83ca82d2bfe7ab544c6f91'] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.7'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' From 0680b806c89ad60b348b652fbfdae91858b53073 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 11 Mar 2019 15:53:34 -0500 Subject: [PATCH 0823/5331] adding easyconfigs: scikit-learn-0.19.1-fosscuda-2017b-Python-2.7.14.eb, scikit-learn-0.19.1-fosscuda-2017b-Python-3.6.3.eb, scikit-learn-0.19.1-intelcuda-2017b-Python-2.7.14.eb, scikit-learn-0.19.1-intelcuda-2017b-Python-3.6.3.eb --- ...arn-0.19.1-fosscuda-2017b-Python-2.7.14.eb | 34 +++++++++++++++++++ ...earn-0.19.1-fosscuda-2017b-Python-3.6.3.eb | 34 +++++++++++++++++++ ...rn-0.19.1-intelcuda-2017b-Python-2.7.14.eb | 34 +++++++++++++++++++ ...arn-0.19.1-intelcuda-2017b-Python-3.6.3.eb | 34 +++++++++++++++++++ 4 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..39796a374ab --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-2.7.14.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.19.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] + +dependencies = [ + ('Python', '2.7.14'), + ('matplotlib', '2.1.0', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..2b326084577 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-fosscuda-2017b-Python-3.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.19.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'fosscuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] + +dependencies = [ + ('Python', '3.6.3'), + ('matplotlib', '2.1.0', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..19c6ac62205 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-2.7.14.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.19.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] + +dependencies = [ + ('Python', '2.7.14'), + ('matplotlib', '2.1.0', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..fb028dc3c82 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-intelcuda-2017b-Python-3.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.19.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intelcuda', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] + +dependencies = [ + ('Python', '3.6.3'), + ('matplotlib', '2.1.0', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' From 2b2779ee54c60386ea7e3d8a35ae43860aacaabe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Mar 2019 22:08:02 +0100 Subject: [PATCH 0824/5331] adding easyconfigs: matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb --- ...tplotlib-2.2.3-intel-2018b-Python-3.6.6.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..564a725a4e8 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '2.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.6.6'), + ('libpng', '1.6.34'), + ('freetype', '2.9.1'), + ('Tkinter', '%(pyver)s', versionsuffix), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['7355bf757ecacd5f0ac9dd9523c8e1a1103faadf8d33c22664178e17533f8ce5'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From b2f0b30e567932a47572f01072e23a35f2d66b07 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 11 Mar 2019 16:31:26 -0500 Subject: [PATCH 0825/5331] adding easyconfigs: git-lfs-2.7.1.eb --- .../easyconfigs/g/git-lfs/git-lfs-2.7.1.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb new file mode 100644 index 00000000000..e84feb4c13c --- /dev/null +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "Tarball" + +name = 'git-lfs' +version = '2.7.1' + +homepage = 'https://git-lfs.github.com/' +description = """Git Large File Storage (LFS) replaces large files such as audio samples, videos, + datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server + like GitHub.com or GitHub Enterprise.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/git-lfs/git-lfs/releases/download/v%(version)s/'] +sources = ['%(name)s-linux-amd64-v%(version)s.tar.gz'] +checksums = ['7be85238cbbb957ab25de52b60279d40ba40d3faa72eeb2cb9fa77d6d92381e5'] + +sanity_check_paths = { + 'files': ["git-lfs"], + 'dirs': [""] +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', +} + +# remove exec permission for the provided installation script +postinstallcmds = ["chmod og-x %(installdir)s/install.sh"] + +moduleclass = 'tools' From 803cd2ad6ad6a38edb5a06ae0c2b8d650e321275 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 11 Mar 2019 17:07:46 -0500 Subject: [PATCH 0826/5331] Use pip instead of setup.py --- .../h5py-2.7.1-foss-2017b-Python-2.7.14.eb | 37 +++++++++++++++++++ .../h5py-2.7.1-foss-2017b-Python-3.6.3.eb | 8 +++- .../h5py-2.7.1-intel-2017b-Python-2.7.14.eb | 8 +++- .../h5py-2.7.1-intel-2017b-Python-3.6.3.eb | 8 +++- 4 files changed, 55 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..25b1d68cb54 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] + +# To really use mpi enabled hdf5 we now seem to need a configure step +# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.14'), + ('HDF5', '1.10.1'), + ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb index 0cb39788469..cadc0900f29 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb @@ -16,8 +16,9 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' +# To really use mpi enabled hdf5 we now seem to need a configure step +# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' dependencies = [ ('Python', '3.6.3'), @@ -25,6 +26,9 @@ dependencies = [ ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb index 6c9cc7e5b04..6a30d279da7 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb @@ -16,8 +16,9 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' +# To really use mpi enabled hdf5 we now seem to need a configure step +# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' dependencies = [ ('Python', '2.7.14'), @@ -25,6 +26,9 @@ dependencies = [ ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb index beaf940257c..e407a9389b7 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb @@ -16,8 +16,9 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' +# To really use mpi enabled hdf5 we now seem to need a configure step +# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' dependencies = [ ('Python', '3.6.3'), @@ -25,6 +26,9 @@ dependencies = [ ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], From 31746b58407e7f06b4574c27401f4d1474ea8a41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Mar 2019 08:02:29 +0100 Subject: [PATCH 0827/5331] switch to using PythonBundle easyblock in matplotlib easyconfig --- .../matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb index 564a725a4e8..50ac94db6de 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'matplotlib' version = '2.2.3' @@ -11,9 +11,6 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'intel', 'version': '2018b'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' - builddependencies = [ ('pkg-config', '0.29.2'), ] @@ -25,6 +22,8 @@ dependencies = [ ('Tkinter', '%(pyver)s', versionsuffix), ] +use_pip = True + exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', @@ -40,15 +39,8 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - # use non-interactive plotting backend as default # see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend modextravars = {'MPLBACKEND': 'Agg'} From 179ee5b260a5441909673e8c46844b2472e0139c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Mar 2019 09:19:36 +0100 Subject: [PATCH 0828/5331] add missing kiwisolver dependency extension for matplotlib 2.2.3 --- .../m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb index 50ac94db6de..49477f77634 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.3-intel-2018b-Python-3.6.6.eb @@ -31,6 +31,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), + ('kiwisolver', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], + }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", From beb4b148da7716e973b9b4dd6758fa585d1e53ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Mar 2019 11:36:58 +0100 Subject: [PATCH 0829/5331] add 'bartMachine' and 'lqa' extensions to R 3.5.1 --- .../r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 15 +++++++++++++++ easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 15 +++++++++++++++ 2 files changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index 059217e401f..6ff8ddc0089 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -2081,6 +2081,21 @@ exts_list = [ ('mlegp', '3.1.7', { 'checksums': ['d4845eaf9260f8b8112726dd7ceb5c2f5ce75125fa313191db9de121f2ee15e0'], }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.4.2', { + 'checksums': ['28a5f7363325021bd93f9bd060cc48f20c689dae2f2f6f7100faae66d7651f80'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index bd95fa5d2c6..81b17d2a3e7 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -2079,6 +2079,21 @@ exts_list = [ ('mlegp', '3.1.7', { 'checksums': ['d4845eaf9260f8b8112726dd7ceb5c2f5ce75125fa313191db9de121f2ee15e0'], }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.4.2', { + 'checksums': ['28a5f7363325021bd93f9bd060cc48f20c689dae2f2f6f7100faae66d7651f80'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), ] moduleclass = 'lang' From 69aab6696d151b3c71d315a169ff80b73b00a451 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 12 Mar 2019 11:44:16 +0100 Subject: [PATCH 0830/5331] use cp -a --- .../b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb index 0717c6d46bc..f5ccc32fea8 100644 --- a/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb @@ -24,7 +24,7 @@ sources = [ }, { 'filename': 'taxdmp_%s.zip' % taxdump_ver, - 'extract_cmd': 'unzip %s && cp nodes.dmp names.dmp %(builddir)s/data/', + 'extract_cmd': 'unzip %s && cp -a nodes.dmp names.dmp %(builddir)s/data/', }, ] patches = ['BlobTools-20180528_fix_deps.patch'] From b4cc6f6cdff41302e77a6acdfd05d5d07d6b8576 Mon Sep 17 00:00:00 2001 From: ebtest Date: Tue, 12 Mar 2019 11:51:59 +0000 Subject: [PATCH 0831/5331] add patches for GA issues fixed upstream and cleanup OpenMolcas eb --- .../GlobalArrays-5.7-intel-2018b.eb | 19 ++- ...balArrays-v5.7-intel-2018b-MKL_issue.patch | 42 +++++ .../GlobalArrays-v5.7_ga_diag_std.patch | 144 ++++++++++++++++++ .../OpenMolcas-18.09-intel-2018b.eb | 14 +- ...OpenMolcas-pymolcas_only_in_ebprefix.patch | 22 +++ 5 files changed, 235 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7-intel-2018b-MKL_issue.patch create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7_ga_diag_std.patch create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-pymolcas_only_in_ebprefix.patch diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb index 8c2bc3aa316..b922407f762 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb @@ -1,6 +1,6 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'ConfigureMake' - name = 'GlobalArrays' version = '5.7' @@ -12,11 +12,22 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] sources = ['v%(version)s/ga-%(version)s.tar.gz'] -checksums = ['3ed1ab47adfda7bceb7beca12fc05a2e1631732f0e55bbaf9036dad4e3da4774'] + +# patch for bugs on v5.7 causing errors on NWChem +patches = [ + 'GlobalArrays-v5.7_ga_diag_std.patch', # fix bug ga_diag_std https://github.com/GlobalArrays/ga/pull/101 + 'GlobalArrays-v5.7-intel-2018b-MKL_issue.patch', # fix MKL issue https://github.com/GlobalArrays/ga/pull/122 +] + +checksums = [ + '3ed1ab47adfda7bceb7beca12fc05a2e1631732f0e55bbaf9036dad4e3da4774', + 'b8b8c5d357bce34a37cdf640e88a3ecb72d7de3255cc3ec086a9c3949c2c2d33', # GlobalArrays-v5.7_ga_diag_std.patch + '0c25322731b5964d00c6fc18673881a755faa190f446a592dc3d49caf806a973', # GlobalArrays-v5.7-intel-2018b-MKL_issue.patch +] configopts = ' --with-mpi --enable-i8' -configopts += ' --with-blas8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' -configopts += ' --with-scalapack8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_scalapack_ilp64"' +configopts += ' --with-blas8="-L$EBROOTIMKL/mkl/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack8="-L$EBROOTIMKL/mkl/lib/intel64 -lmkl_sequential -lmkl_scalapack_ilp64"' # select armci network as (Comex) MPI-1 two-sided configopts += ' --with-mpi-ts' diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7-intel-2018b-MKL_issue.patch b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7-intel-2018b-MKL_issue.patch new file mode 100644 index 00000000000..1fa0a7e9d5a --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7-intel-2018b-MKL_issue.patch @@ -0,0 +1,42 @@ +diff --git a/global/src/scalapack.F b/global/src/scalapack.F +index 74ef1a9..cd80884 100644 +--- a/global/src/scalapack.F ++++ b/global/src/scalapack.F +@@ -3030,6 +3030,7 @@ c + integer alen, blen + integer block_dims_A(2),block_dims_B(2),blocks(2) + integer gridA(2), gridB(2) ++ double precision mywork + logical use_direct + + external pdlamch,iceil,indxg2p +@@ -3201,20 +3202,16 @@ c + c + c + liwork4=liwork +-#if 0 + lcwork4=-1 +- call pdsyevd(jobz, uplo, +- 1 n, dbl_mb(adrA), one4, one4, descA, +- 1 eval, dbl_mb(adrB), one4, one4, +- 2 descB, dbl_mb(adrcwork), lcwork4, +- 2 dum, liwork4, info) +- lcwork=dum +-#else +- +- lcwork = MAX( 1+6*N+2*NP*NQ, +- = 3*N + MAX( NB*( NP+1 ), 3*NB ))+ 2*N +- lcwork=max(lcwork,16384) +-#endif ++ call pdsyevd(jobz, uplo, ++ 1 n, dbl_mb(adrA), one4, one4, descA, ++ 1 eval, dbl_mb(adrB), one4, one4, ++ 2 descB, mywork, lcwork4, ++ 2 int_mb(adriwork), liwork4, info) ++ lcwork = MAX( 1+6*N+2*NP*NQ, ++ = 3*N + MAX( NB*( NP+1 ), 3*NB ))+ 2*N ++ lcwork=max(lcwork,16384) ++ lcwork=max(int(mywork),lcwork) + + c + if(lcwork.ne.0) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7_ga_diag_std.patch b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7_ga_diag_std.patch new file mode 100644 index 00000000000..ee80d5a56e2 --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7_ga_diag_std.patch @@ -0,0 +1,144 @@ +diff --git a/global/src/ga_diag_seq.F b/global/src/ga_diag_seq.F +index ee601729..d5653975 100644 +--- a/global/src/ga_diag_seq.F ++++ b/global/src/ga_diag_seq.F +@@ -1,6 +1,11 @@ + #if HAVE_CONFIG_H + # include "config.fh" + #endif ++#if (BLAS_SIZE ==4) ++#define INTGR4 integer*4 ++#else ++#define INTGR4 integer*8 ++#endif + c + c This file has been converted to use LAPACK circa 2011 + c instead of EISPACK circa 1983 by Jeff Hammond circa 2014. +@@ -15,7 +20,7 @@ c + integer g_v ! Global matrix to return evecs + double precision evals(*) ! Local array to return evals + c +- integer n, ierr ++ integer n + #if ENABLE_EISPACK + integer l_fv1, l_fv2, l_v + MA_ACCESS_INDEX_TYPE k_fv1, k_fv2, k_v +@@ -27,6 +32,7 @@ c + integer l_a, l_s + MA_ACCESS_INDEX_TYPE k_a, k_s + integer dim1, dim2, type, me ++ INTGR4 n4,ierr + logical status + c + c +@@ -47,6 +53,7 @@ c + $ call ga_error('ga_diag_seq: nonsquare matrix ',0) + + n = dim1 ++ n4 = n + me = ga_nodeid() + if (me .eq. 0) then + c +@@ -87,7 +94,7 @@ c + call rsg(n, n, dbl_mb(k_a), dbl_mb(k_s), evals, 1, + $ dbl_mb(k_v), dbl_mb(k_fv1), dbl_mb(k_fv2), ierr) + #else +- call dsygv(1,'V','U',n,dbl_mb(k_a),n,dbl_mb(k_s),n, ++ call dsygv(1,'V','U',n4,dbl_mb(k_a),n,dbl_mb(k_s),n4, + $ evals,dbl_mb(k_wrk),n2, ierr) + if (ierr.ne.0) + $ call ga_error('ga_diag_seq: dsygv failed',ierr) +@@ -139,7 +146,7 @@ c + integer g_v ! Global matrix to return evecs + double precision evals(*) ! Local array to return evals + c +- integer n, ierr ++ integer n + #if ENABLE_EISPACK + integer l_fv1, l_fv2, l_v + MA_ACCESS_INDEX_TYPE k_fv1, k_fv2, k_v +@@ -151,6 +158,7 @@ c + integer l_a + MA_ACCESS_INDEX_TYPE k_a + integer dim1, dim2, type, me ++ INTGR4 n4,n2_i4,ierr + logical status + c + c +@@ -170,6 +178,7 @@ c + $ call ga_error('ga_diag_std_seq: nonsquare matrix ',0) + + n = dim1 ++ n4 = n + me = ga_nodeid() + if (me .eq. 0) then + c +@@ -187,6 +196,7 @@ c + #else + c LAPACK fails for n=1 without this + n2 = max(n*n,3*n-1) ++ n2_i4=n2 + status=status.and.ma_push_get(MT_DBL, n2, + $ 'diag_std_seq:wrk', l_wrk, k_wrk) + #endif +@@ -205,8 +215,8 @@ c + call rs(n, n, dbl_mb(k_a), evals, 1, + $ dbl_mb(k_v), dbl_mb(k_fv1), dbl_mb(k_fv2), ierr) + #else +- call dsyev('V', 'L', n, dbl_mb(k_a), n, +- $ evals, dbl_mb(k_wrk), n2, ierr) ++ call dsyev('V', 'L', n4, dbl_mb(k_a), n4, ++ $ evals, dbl_mb(k_wrk), n2_i4, ierr) + if (ierr.ne.0) + $ call ga_error('ga_diag_std_seq: dsyev failed',ierr) + c We used to copy to preserve code symmetry with EISPACK +diff --git a/m4/ga_f2c_string.m4 b/m4/ga_f2c_string.m4 +index 51914c37..addde81f 100644 +--- a/m4/ga_f2c_string.m4 ++++ b/m4/ga_f2c_string.m4 +@@ -13,9 +13,9 @@ AC_COMPILE_IFELSE( + first_name = "John" + last_name = "Doe" + call csub(first_name, last_name) +- end]], [ ++ end]], [mv conftest.$ac_objext cfortran_test.$ac_objext + ga_save_LIBS=$LIBS +- LIBS="conftest.$ac_objext $LIBS $[]_AC_LANG_PREFIX[]LIBS" ++ LIBS="cfortran_test.$ac_objext $LIBS $[]_AC_LANG_PREFIX[]LIBS" + AC_LANG_PUSH([C]) + AC_RUN_IFELSE([AC_LANG_SOURCE( + [[#include +@@ -62,7 +62,7 @@ int main(int argc, char **argv) + LIBS=$ga_save_LIBS], + [m4_default([$3], :)]) + AC_LANG_POP([Fortran 77]) +-rm -rf conftest* ++rm -rf conftest* cfortran_test.$ac_objext + ])dnl + + +diff --git a/m4/ga_f77_check_sizeof.m4 b/m4/ga_f77_check_sizeof.m4 +index 6a773d12..3ee3897f 100644 +--- a/m4/ga_f77_check_sizeof.m4 ++++ b/m4/ga_f77_check_sizeof.m4 +@@ -10,9 +10,9 @@ AC_COMPILE_IFELSE([AC_LANG_SOURCE( + external size + $1 x(2) + call size(x(1),x(2)) +- end]])], [ ++ end]])], [mv conftest.$ac_objext cfortran_test.$ac_objext + ga_save_LIBS=$LIBS +- LIBS="conftest.$ac_objext $LIBS $[]_AC_LANG_PREFIX[]LIBS" ++ LIBS="cfortran_test.$ac_objext $LIBS $[]_AC_LANG_PREFIX[]LIBS" + AC_LANG_PUSH([C]) + AC_RUN_IFELSE([AC_LANG_SOURCE( + [[#include +@@ -44,7 +44,7 @@ int main(int argc, char **argv) + } + ]])], [AS_TR_SH([$2])=`cat conftestval`]) + LIBS=$ga_save_LIBS +- rm -f conftest* ++ rm -f conftest* cfortran_test* + AC_LANG_POP([C])]) + AC_LANG_POP([Fortran 77]) + ]) # GA_F77_COMPUTE_SIZEOF diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b.eb index 422c4da5c4f..9c84ecc07e9 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b.eb @@ -1,3 +1,4 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'CMakeMake' name = 'OpenMolcas' @@ -11,12 +12,21 @@ toolchainopts = {'usempi': True} source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] sources = ["OpenMolcas-v%(version)s.tar.gz"] -checksums = ['b4f310fb65205c865ccc6373ce9c3833a586f8ff63a71a624cf793559c9b39cf'] + +# This patch avoids the automatic extra copy of 'pymolcas' script +# in the first writable directory of the install user's $PATH +# The 'make install' process is going to install it in +# %(installdir)s/sbin/ which is the only place it should stay +patches = ["OpenMolcas-pymolcas_only_in_ebprefix.patch"] + +checksums = ['b4f310fb65205c865ccc6373ce9c3833a586f8ff63a71a624cf793559c9b39cf', + '130a40028ad1c231d69f109151029032cac26f2c0c6e636266faa5a69027cd1b'] + dependencies = [ ('GlobalArrays', '5.7'), - ('Python', '3.6.6'), ('HDF5', '1.10.2'), + ('Python', '3.6.6'), ] builddependencies = [('CMake', '3.12.1')] diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-pymolcas_only_in_ebprefix.patch b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-pymolcas_only_in_ebprefix.patch new file mode 100644 index 00000000000..19af4702e92 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-pymolcas_only_in_ebprefix.patch @@ -0,0 +1,22 @@ +--- a/sbin/install_pymolcas.sh 2018-09-02 09:35:13.000000000 +0200 ++++ b/sbin/install_pymolcas.sh 2019-03-11 16:53:29.224546598 +0100 +@@ -116,8 +116,8 @@ + echo "Is this OK? [Y/n] (will assume \"Yes\" in 25 seconds)" + while true ; do + if [ "$INTERACTIVE" = "0" ] ; then +- echo "Running in non-interactive mode, assuming \"Yes\"" +- answer="Yes" ++ echo "Running in non-interactive mode, assuming \"No\"" ++ answer="No" + else + read_timeout answer + fi +@@ -143,7 +143,7 @@ + echo "" + echo "*** You have to put pymolcas in any directory in your PATH" + if [ "$INTERACTIVE" = "0" ] ; then +- exit 3 ++ exit 0 + fi + break ;; + * ) echo "Please answer yes or no" From b03cd59e6e8ac05e53a43e7c88c759695f55485d Mon Sep 17 00:00:00 2001 From: ebtest Date: Tue, 12 Mar 2019 12:17:02 +0000 Subject: [PATCH 0832/5331] add python version suffix for OpenMolcas --- ...18b.eb => OpenMolcas-18.09-intel-2018b-Python-3.6.6.eb} | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/o/OpenMolcas/{OpenMolcas-18.09-intel-2018b.eb => OpenMolcas-18.09-intel-2018b-Python-3.6.6.eb} (92%) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-Python-3.6.6.eb similarity index 92% rename from easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b.eb rename to easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-Python-3.6.6.eb index 9c84ecc07e9..80340d09cc0 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-Python-3.6.6.eb @@ -1,8 +1,9 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'CMakeMake' name = 'OpenMolcas' version = '18.09' +versionsuffix = '-Python-%(pyver)s' homepage = "https://gitlab.com/Molcas/OpenMolcas" description = "OpenMolcas is a quantum chemistry software package" @@ -15,8 +16,8 @@ sources = ["OpenMolcas-v%(version)s.tar.gz"] # This patch avoids the automatic extra copy of 'pymolcas' script # in the first writable directory of the install user's $PATH -# The 'make install' process is going to install it in -# %(installdir)s/sbin/ which is the only place it should stay +# The 'make install' process is going to install it in +# %(installdir)s/sbin/ which is the only place it should stay patches = ["OpenMolcas-pymolcas_only_in_ebprefix.patch"] checksums = ['b4f310fb65205c865ccc6373ce9c3833a586f8ff63a71a624cf793559c9b39cf', From bc9bbded98b690eaba02615ed1837098380e4849 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 12 Mar 2019 13:50:09 +0100 Subject: [PATCH 0833/5331] added cpan-minus to list of extensions for recent perl easyconfigs --- .../easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb | 10 ++++++++++ .../easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb | 10 ++++++++++ .../easyconfigs/p/Perl/Perl-5.24.0-GCCcore-5.4.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.24.1-GCCcore-6.3.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.26.0-GCCcore-6.4.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.26.0-foss-2017b.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.26.0-intel-2018.00.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.26.0-intel-2018.01.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.26.1-GCCcore-6.4.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.26.1-foss-2018a.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb | 5 +++++ 15 files changed, 85 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb index ff9b04399d8..228331cd975 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb @@ -895,6 +895,16 @@ exts_list = [ 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb index e6b26a53322..1f1cc76f425 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb @@ -897,6 +897,16 @@ exts_list = [ 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-5.4.0.eb index c694d32b400..e52abbff7b4 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-5.4.0.eb @@ -898,6 +898,11 @@ exts_list = [ 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb index 41e1a649441..61d15dd724a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb @@ -895,6 +895,11 @@ exts_list = [ 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-GCCcore-6.3.0.eb index bff63b7c5c0..7d06d86e98b 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-GCCcore-6.3.0.eb @@ -1126,6 +1126,11 @@ exts_list = [ 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb index c0ab9b354af..3197957bdeb 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb @@ -1124,6 +1124,11 @@ exts_list = [ 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb index e827a0f69ac..98247f770a8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -1125,6 +1125,11 @@ exts_list = [ 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-GCCcore-6.4.0.eb index 565f874e8fd..2f1310c58ba 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-GCCcore-6.4.0.eb @@ -1170,6 +1170,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER/'], 'checksums': ['8ba24b0b459b01d6c5e5b0408829c7d5dfe47ff79b3548c813759048099b175e'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-foss-2017b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-foss-2017b.eb index c849503062d..bd8db0f2770 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-foss-2017b.eb @@ -1149,6 +1149,11 @@ exts_list = [ 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], 'checksums': ['7896bf250835ce47dcc813cb8cf9dc576c5455de42e822dcd7d8d3fef2125565'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb index 11d17e8a825..03fb91e39ef 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2017b.eb @@ -1153,6 +1153,11 @@ exts_list = [ 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], 'checksums': ['7896bf250835ce47dcc813cb8cf9dc576c5455de42e822dcd7d8d3fef2125565'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2018.00.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2018.00.eb index 5f4d0c12e00..cddde6cc428 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2018.00.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2018.00.eb @@ -1153,6 +1153,11 @@ exts_list = [ 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], 'checksums': ['7896bf250835ce47dcc813cb8cf9dc576c5455de42e822dcd7d8d3fef2125565'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2018.01.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2018.01.eb index 37fb8da4220..0c0d989d322 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2018.01.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.0-intel-2018.01.eb @@ -1153,6 +1153,11 @@ exts_list = [ 'source_urls': ['http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/'], 'checksums': ['7896bf250835ce47dcc813cb8cf9dc576c5455de42e822dcd7d8d3fef2125565'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.1-GCCcore-6.4.0.eb index 841e6b35d68..22c84fbbd37 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.26.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.1-GCCcore-6.4.0.eb @@ -1462,6 +1462,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], 'checksums': ['af53b05ef1387b4cab4427e6789179283e4f0da8cf036e8db516ddb344512b65'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.26.1-foss-2018a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.26.1-foss-2018a.eb index 0baa9f82e6e..43b97267a57 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.26.1-foss-2018a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.26.1-foss-2018a.eb @@ -1445,6 +1445,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['67583075f6d62b78aaa956389f113df789ddd41911394092a5a2b8c6fa863070'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb index a49205b1c14..8919ccf4b33 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb @@ -1465,6 +1465,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], 'checksums': ['6965f25c2c132d0ba7a6f72b57b8bc6d25cf8c1b7032caa3a9bda8612e41d759'], }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), ] moduleclass = 'lang' From 4efd6829bffcf165983c8489cbf0d255ffa8c41b Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 12 Mar 2019 13:52:04 +0100 Subject: [PATCH 0834/5331] fix typo --- easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb | 5 ----- easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb | 5 ----- 2 files changed, 10 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb index 228331cd975..62be28daccb 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb @@ -900,11 +900,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], }), - ('App::cpanminus', '1.7044', { - 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], - 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb index 1f1cc76f425..fd9a50299fb 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb @@ -902,11 +902,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], }), - ('App::cpanminus', '1.7044', { - 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], - 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], - }), ] moduleclass = 'lang' From 99193e878c7a1b628552a2d7de6071141053d608 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 12 Mar 2019 11:11:07 -0500 Subject: [PATCH 0835/5331] update the sanity_check for dirs --- .../easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb | 2 +- .../easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb | 2 +- .../h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb | 2 +- .../easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb index a2f49ebc765..2d71d7cdc61 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-2.7.14.eb @@ -27,7 +27,7 @@ download_dep_fail = True sanity_check_paths = { 'files': ["bin/htseq-count", "bin/htseq-qa"], - 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/"], } sanity_check_commands = [('htseq-count --help')] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb index 88dcb92dbdf..c18aae96747 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-foss-2017b-Python-3.6.3.eb @@ -27,7 +27,7 @@ download_dep_fail = True sanity_check_paths = { 'files': ["bin/htseq-count", "bin/htseq-qa"], - 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/"], } sanity_check_commands = [('htseq-count --help')] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb index c414bf1fb55..a2deee36ee5 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-2.7.14.eb @@ -27,7 +27,7 @@ download_dep_fail = True sanity_check_paths = { 'files': ["bin/htseq-count", "bin/htseq-qa"], - 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/"], } sanity_check_commands = [('htseq-count --help')] diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb index 78c6fbbe2f6..ba86ce1fb54 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.9.1-intel-2017b-Python-3.6.3.eb @@ -27,7 +27,7 @@ download_dep_fail = True sanity_check_paths = { 'files': ["bin/htseq-count", "bin/htseq-qa"], - 'dirs': ["lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg"], + 'dirs': ["lib/python%(pyshortver)s/site-packages/"], } sanity_check_commands = [('htseq-count --help')] From 56afd6b72649664533af0162c00736a725334d93 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 12 Mar 2019 11:33:15 -0500 Subject: [PATCH 0836/5331] remove the Pillow-5.3.0 for 2017b for introducing more conflicts --- .../Pillow-5.3.0-intel-2017b-Python-2.7.14.eb | 36 ------------------- .../Pillow-5.3.0-intel-2017b-Python-3.6.3.eb | 36 ------------------- 2 files changed, 72 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-2.7.14.eb delete mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-2.7.14.eb deleted file mode 100644 index 908e0e21aba..00000000000 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-2.7.14.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pillow' -version = '5.3.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://pillow.readthedocs.org/' -description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. - PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" - -toolchain = {'name': 'intel', 'version': '2017b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] - -dependencies = [ - ('Python', '2.7.14'), - ('libjpeg-turbo', '1.5.2'), - ('libpng', '1.6.32'), - ('zlib', '1.2.11'), - ('LibTIFF', '4.0.9'), - ('freetype', '2.8') -] - -download_dep_fail = True -use_pip = True - -options = {'modulename': 'PIL'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-3.6.3.eb deleted file mode 100644 index f9884e02e96..00000000000 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-intel-2017b-Python-3.6.3.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pillow' -version = '5.3.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://pillow.readthedocs.org/' -description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. - PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" - -toolchain = {'name': 'intel', 'version': '2017b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] - -dependencies = [ - ('Python', '3.6.3'), - ('libjpeg-turbo', '1.5.2'), - ('libpng', '1.6.32'), - ('zlib', '1.2.11'), - ('LibTIFF', '4.0.9'), - ('freetype', '2.8') -] - -download_dep_fail = True -use_pip = True - -options = {'modulename': 'PIL'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'vis' From 3f29dce22a66310ef08cc33e35f703464c4d69b7 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 12 Mar 2019 11:35:29 -0500 Subject: [PATCH 0837/5331] change original Pillow/5.3.0 to 5.0.0 for foss toolchain --- ...ython-2.7.14.eb => Pillow-5.0.0-foss-2017b-Python-2.7.14.eb} | 2 +- ...-Python-3.6.3.eb => Pillow-5.0.0-foss-2017b-Python-3.6.3.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/Pillow/{Pillow-5.3.0-foss-2017b-Python-2.7.14.eb => Pillow-5.0.0-foss-2017b-Python-2.7.14.eb} (97%) rename easybuild/easyconfigs/p/Pillow/{Pillow-5.3.0-foss-2017b-Python-3.6.3.eb => Pillow-5.0.0-foss-2017b-Python-3.6.3.eb} (97%) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb similarity index 97% rename from easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-2.7.14.eb rename to easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb index f2059ab279c..e7384e7f684 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'Pillow' -version = '5.3.0' +version = '5.0.0' versionsuffix = '-Python-%(pyver)s' homepage = 'http://pillow.readthedocs.org/' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb similarity index 97% rename from easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-3.6.3.eb rename to easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb index 6cf42f716b5..7e474e0a794 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.3.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'Pillow' -version = '5.3.0' +version = '5.0.0' versionsuffix = '-Python-%(pyver)s' homepage = 'http://pillow.readthedocs.org/' From 342d534d98784cbed208cc3a4fed221568f8e6de Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 12 Mar 2019 11:38:00 -0500 Subject: [PATCH 0838/5331] now use Pillow/5.0.0 for the NiBabel/2.3.0 --- .../n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb | 2 +- .../n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb | 2 +- .../n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb | 2 +- .../n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb index 72f0ee3f811..9434fafcc82 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-2.7.14.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('Pillow', '5.3.0', versionsuffix), + ('Pillow', '5.0.0', versionsuffix), ] use_pip = True diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb index 27fea58ea1b..8b4b5660029 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-foss-2017b-Python-3.6.3.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('Pillow', '5.3.0', versionsuffix), + ('Pillow', '5.0.0', versionsuffix), ] use_pip = True diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb index c9c6e760251..55de0ad583a 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-2.7.14.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('Pillow', '5.3.0', versionsuffix), + ('Pillow', '5.0.0', versionsuffix), ] use_pip = True diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb index 88556e71196..6280675c29e 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.3.0-intel-2017b-Python-3.6.3.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('Pillow', '5.3.0', versionsuffix), + ('Pillow', '5.0.0', versionsuffix), ] use_pip = True From 7ef04701a67e423fe9d06cb94452d8a14ce85bd5 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 12 Mar 2019 11:52:19 -0500 Subject: [PATCH 0839/5331] update the checksum number for Pillow 5.0.0/foss --- .../p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb | 2 +- .../p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb index e7384e7f684..3aeb1eb1247 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] +checksums = ['12f29d6c23424f704c66b5b68c02fe0b571504459605cfe36ab8158359b0e1bb'] dependencies = [ ('Python', '2.7.14'), diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb index 7e474e0a794..344c5ec4acd 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-5.0.0-foss-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['2ea3517cd5779843de8a759c2349a3cd8d3893e03ab47053b66d5ec6f8bc4f93'] +checksums = ['12f29d6c23424f704c66b5b68c02fe0b571504459605cfe36ab8158359b0e1bb'] dependencies = [ ('Python', '3.6.3'), From 289ef3fa0532b12cccaa470dc7eb2ca4eaac05cb Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 12 Mar 2019 13:01:42 -0500 Subject: [PATCH 0840/5331] adding easyconfigs: Go-1.12.eb --- easybuild/easyconfigs/g/Go/Go-1.12.eb | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.12.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.12.eb b/easybuild/easyconfigs/g/Go/Go-1.12.eb new file mode 100644 index 00000000000..c43fcce0469 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.12.eb @@ -0,0 +1,23 @@ +easyblock = 'Tarball' + +name = 'Go' +version = '1.12' + +homepage = 'http://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://storage.googleapis.com/golang/'] +sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] +checksums = ['750a07fef8579ae4839458701f4df690e0b20b8bcce33b437e4df89c451b6f13'] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +modextravars = {'GOROOT': '%(installdir)s'} + +moduleclass = 'compiler' From 22d84938120f31b21aa4dd2c7833b3189f2c772e Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 12 Mar 2019 13:38:29 -0500 Subject: [PATCH 0841/5331] adding easyconfigs: GDB-8.1.1-foss-2017b-Python-2.7.14.eb, GDB-8.1.1-foss-2017b-Python-3.6.3.eb, GDB-8.1.1-intel-2017b-Python-2.7.14.eb, GDB-8.1.1-intel-2017b-Python-3.6.3.eb --- .../GDB/GDB-8.1.1-foss-2017b-Python-2.7.14.eb | 38 +++++++++++++++++++ .../GDB/GDB-8.1.1-foss-2017b-Python-3.6.3.eb | 38 +++++++++++++++++++ .../GDB-8.1.1-intel-2017b-Python-2.7.14.eb | 38 +++++++++++++++++++ .../GDB/GDB-8.1.1-intel-2017b-Python-3.6.3.eb | 38 +++++++++++++++++++ 4 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..fb846ba3637 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '8.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['97dcc3169bd430270fc29adb65145846a58c1b55cdbb73382a4a89307bdad03c'] + +builddependencies = [ + ('texinfo', '6.5'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('expat', '2.2.5'), + ('Python', '2.7.14'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..82771a19645 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '8.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['97dcc3169bd430270fc29adb65145846a58c1b55cdbb73382a4a89307bdad03c'] + +builddependencies = [ + ('texinfo', '6.5'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('expat', '2.2.5'), + ('Python', '3.6.3'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..986e6acc968 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '8.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['97dcc3169bd430270fc29adb65145846a58c1b55cdbb73382a4a89307bdad03c'] + +builddependencies = [ + ('texinfo', '6.5'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('expat', '2.2.5'), + ('Python', '2.7.14'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..4787b9f78db --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '8.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['97dcc3169bd430270fc29adb65145846a58c1b55cdbb73382a4a89307bdad03c'] + +builddependencies = [ + ('texinfo', '6.5'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('expat', '2.2.5'), + ('Python', '3.6.3'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' From efc796c53537affcd2556d0b18962524de94f30d Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 12 Mar 2019 22:09:57 +0100 Subject: [PATCH 0842/5331] only update perl > 5.24 --- .../easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb | 5 ----- .../easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb | 5 ----- .../easyconfigs/p/Perl/Perl-5.24.0-GCCcore-5.4.0.eb | 5 ----- easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb | 9 --------- .../easyconfigs/p/Perl/Perl-5.24.1-GCCcore-6.3.0.eb | 5 ----- easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb | 5 ----- easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb | 5 ----- 7 files changed, 39 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb index 62be28daccb..ff9b04399d8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCC-5.4.0-2.26.eb @@ -895,11 +895,6 @@ exts_list = [ 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], }), - ('App::cpanminus', '1.7044', { - 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], - 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb index fd9a50299fb..e6b26a53322 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb @@ -897,11 +897,6 @@ exts_list = [ 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], }), - ('App::cpanminus', '1.7044', { - 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], - 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-5.4.0.eb index e52abbff7b4..c694d32b400 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-5.4.0.eb @@ -898,11 +898,6 @@ exts_list = [ 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], }), - ('App::cpanminus', '1.7044', { - 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], - 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb index 61d15dd724a..ca9c8a4dba8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb @@ -891,15 +891,6 @@ exts_list = [ 'source_tmpl': 'SVG-2.77.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], }), - ('Statistics::Basic', '1.6611', { - 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], - }), - ('App::cpanminus', '1.7044', { - 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], - 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-GCCcore-6.3.0.eb index 7d06d86e98b..bff63b7c5c0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-GCCcore-6.3.0.eb @@ -1126,11 +1126,6 @@ exts_list = [ 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], }), - ('App::cpanminus', '1.7044', { - 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], - 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb index 3197957bdeb..c0ab9b354af 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-foss-2017a.eb @@ -1124,11 +1124,6 @@ exts_list = [ 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], }), - ('App::cpanminus', '1.7044', { - 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], - 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb index 98247f770a8..e827a0f69ac 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.1-intel-2017a.eb @@ -1125,11 +1125,6 @@ exts_list = [ 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], }), - ('App::cpanminus', '1.7044', { - 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], - 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], - }), ] moduleclass = 'lang' From 2595cbd591aeff586cd8c78b859d4d238aaa51cc Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 12 Mar 2019 22:13:30 +0100 Subject: [PATCH 0843/5331] re-add extension I removed by mistake --- easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb index ca9c8a4dba8..41e1a649441 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb @@ -891,6 +891,10 @@ exts_list = [ 'source_tmpl': 'SVG-2.77.tar.gz', 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/'], }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-1.6611.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/J/JE/JETTERO/'], + }), ] moduleclass = 'lang' From 056eb02450cf090689a929e4dd67695323e216da Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 12 Mar 2019 22:24:41 +0100 Subject: [PATCH 0844/5331] fix the description length to pass the style checks --- easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb b/easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb index 48883f9ba0c..2b1dc8ecbf8 100644 --- a/easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb +++ b/easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb @@ -4,7 +4,8 @@ name = 'fastp' version = '0.19.7' homepage = 'https://github.com/OpenGene/fastp' -description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.""" +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" toolchain = {'name': 'foss', 'version': '2018b'} From 105c7c474f32f8016af5c2d117269cd2980cae79 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 12 Mar 2019 17:30:16 -0500 Subject: [PATCH 0845/5331] change the GDB version from 8.1.1 to 8.0.1 so that we can compile on Intel toolchain --- ...Python-2.7.14.eb => GDB-8.0.1-foss-2017b-Python-2.7.14.eb} | 4 ++-- ...b-Python-3.6.3.eb => GDB-8.0.1-foss-2017b-Python-3.6.3.eb} | 4 ++-- ...ython-2.7.14.eb => GDB-8.0.1-intel-2017b-Python-2.7.14.eb} | 4 ++-- ...-Python-3.6.3.eb => GDB-8.0.1-intel-2017b-Python-3.6.3.eb} | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/g/GDB/{GDB-8.1.1-foss-2017b-Python-2.7.14.eb => GDB-8.0.1-foss-2017b-Python-2.7.14.eb} (88%) rename easybuild/easyconfigs/g/GDB/{GDB-8.1.1-foss-2017b-Python-3.6.3.eb => GDB-8.0.1-foss-2017b-Python-3.6.3.eb} (88%) rename easybuild/easyconfigs/g/GDB/{GDB-8.1.1-intel-2017b-Python-2.7.14.eb => GDB-8.0.1-intel-2017b-Python-2.7.14.eb} (88%) rename easybuild/easyconfigs/g/GDB/{GDB-8.1.1-intel-2017b-Python-3.6.3.eb => GDB-8.0.1-intel-2017b-Python-3.6.3.eb} (88%) diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-2.7.14.eb similarity index 88% rename from easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-2.7.14.eb rename to easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-2.7.14.eb index fb846ba3637..236c668abb4 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-2.7.14.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'GDB' -version = '8.1.1' +version = '8.0.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.gnu.org/software/gdb/gdb.html' @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['97dcc3169bd430270fc29adb65145846a58c1b55cdbb73382a4a89307bdad03c'] +checksums = ['3dbd5f93e36ba2815ad0efab030dcd0c7b211d7b353a40a53f4c02d7d56295e3'] builddependencies = [ ('texinfo', '6.5'), diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-3.6.3.eb similarity index 88% rename from easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-3.6.3.eb rename to easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-3.6.3.eb index 82771a19645..f1b0516a616 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-3.6.3.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'GDB' -version = '8.1.1' +version = '8.0.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.gnu.org/software/gdb/gdb.html' @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['97dcc3169bd430270fc29adb65145846a58c1b55cdbb73382a4a89307bdad03c'] +checksums = ['3dbd5f93e36ba2815ad0efab030dcd0c7b211d7b353a40a53f4c02d7d56295e3'] builddependencies = [ ('texinfo', '6.5'), diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb similarity index 88% rename from easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-2.7.14.eb rename to easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb index 986e6acc968..352651afdfa 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'GDB' -version = '8.1.1' +version = '8.0.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.gnu.org/software/gdb/gdb.html' @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['97dcc3169bd430270fc29adb65145846a58c1b55cdbb73382a4a89307bdad03c'] +checksums = ['3dbd5f93e36ba2815ad0efab030dcd0c7b211d7b353a40a53f4c02d7d56295e3'] builddependencies = [ ('texinfo', '6.5'), diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb similarity index 88% rename from easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-3.6.3.eb rename to easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb index 4787b9f78db..67d0d3b585f 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-8.1.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'GDB' -version = '8.1.1' +version = '8.0.1' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.gnu.org/software/gdb/gdb.html' @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['97dcc3169bd430270fc29adb65145846a58c1b55cdbb73382a4a89307bdad03c'] +checksums = ['3dbd5f93e36ba2815ad0efab030dcd0c7b211d7b353a40a53f4c02d7d56295e3'] builddependencies = [ ('texinfo', '6.5'), From 1095b2cf985a6558afb344ca4b68d7a159f90e0f Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Wed, 13 Mar 2019 01:25:47 +0100 Subject: [PATCH 0846/5331] adding easyconfigs: Perl-5.28.1-GCCcore-8.2.0.eb --- .../p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb | 1475 +++++++++++++++++ 1 file changed, 1475 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..c697a59e7bc --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb @@ -0,0 +1,1475 @@ +name = 'Perl' +version = '5.28.1' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ebf85fe65df2ee165b22596540b7d5d42f84d4b72d84834f74e2e0b8956c347'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('zlib', '1.2.11'), # for Net::SSLeay + ('expat', '2.2.6'), # for XML::Parser +] + +# OpenSSL is required for Net::SSLeay +osdependencies = ['openssl', ('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# !! order of extensions is important !! +# extensions updated on March 13th 2019 +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['1e0050fcd6789a2179ec0db282bf1e90fb92be35d1171588bd9c47d52d959cf5'], + }), + ('ExtUtils::InstallPaths', '0.012', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], + }), + ('Test::Harness', '3.42', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['0fd90d4efea82d6e262e6933759e85d27cbcfa4091b14bf4042ae20bab528e53'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['bcdcef5c7b2790a187ebca810b0a08221a63256062cfab3c3b98685d91d1cbb0'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ae2b68b1b5616704598ce07f5118efe42dc4605834453b7b2be14e26f9cc9a08'], + }), + ('File::ShareDir', '1.116', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['59d90bfdf98c4656ff4173e62954ea8cf0de66565e35d108ecd7050596cb8328'], + }), + ('File::ShareDir::Install', '0.13', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['45befdf0d95cbefe7c25a1daf293d85f780d6d2576146546e6828aad26e580f9'], + }), + ('DateTime::Locale', '1.23', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['3a5a81e742da96d89b408e40f8bf4b21150663d8a5eb9dad7865db582193c015'], + }), + ('DateTime::TimeZone', '2.23', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['6ae40286031853a4319c5b34516f1c09e429d5caa5f782165cc27175c89fe54f'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': ['2768a391d50ab94b95cefe540b9232d7046c13ee86d01859e04c044903222eb5'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], + }), + ('Module::Build', '0.4224', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['a6ca15d78244a7b50fdbf27f85c85f4035aa799ce7dd018a0d98b358ef7bc782'], + }), + ('Module::Runtime', '0.016', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + 'checksums': ['68302ec646833547d410be28e09676db75006f4aa58a11f3bdb44ffe99f0f024'], + }), + ('Try::Tiny', '0.30', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['da5bd0d5c903519bbf10bb9ba0cb7bcac0563882bcfe4503aee3fb143eddef6b'], + }), + ('Params::Validate', '1.29', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['49a68dfb430bea028042479111d19068e08095e5a467e320b7ab7bde3d729733'], + }), + ('List::MoreUtils', '0.428', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['713e0945d5f16e62d81d5f3da2b6a7b14a4ce439f6d3a7de74df1fd166476cc2'], + }), + ('Exporter::Tiny', '1.002001', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': ['a82c334c02ce4b0f9ea77c67bf77738f76a9b8aa4bae5c7209d1c76453d3c48d'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['38220d04f02e3a803193c2575a1644cce0b95ad4b95c19eb932b94e2647ef678'], + }), + ('DateTime', '1.50', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['ed6b0c71ddd81310a82459508df9197074e6b13aea46fd279045c3ddc3c4b198'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['9a48433f86e08ce18e03526e2982de52162eb909d19735460f07eefcaf463ea6'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + 'checksums': ['4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e'], + }), + ('Git', '0.42', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + 'checksums': ['9469a9f398f3a2bf2b0500566ee41d3ff6fae460412a137185767a1cc4783a6d'], + }), + ('Tree::DAG_Node', '1.31', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['1c8ba69772568b3758054247097512c550efe31517c329fb65eef7afccc9d304'], + }), + ('Template', '2.28', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': ['71af368009f13582ef907e33d3812776b597f42b3da0bc0fd3bc7418e4785dd7'], + }), + ('DBI', '1.642', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': ['3f2025023a56286cebd15cb495e36ccd9b456c3cc229bf2ce1f69e9ebfc27f5d'], + }), + ('DBD::SQLite', '1.62', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['bd82ef322a9e5469a7a62d845c32fad1188b76ccb49a88520cec768343cce85c'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': ['11a815fc45fdf0efabb1822ab77faad8b9eea162572c5f0940c8ed7d56e6b8b8'], + }), + ('Archive::Extract', '0.80', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['25cbc2d5626c14d39a0b5e4fe8383941e085c9a7e0aa873d86e81b6e709025f4'], + }), + ('DBIx::Simple', '1.37', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + 'checksums': ['46d311aa2ce08907401c56119658426dbb044c5a40de73d9a7b79bf50390cae3'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + 'checksums': ['f7dbebf65261ed0e5abd0f57052b64d665a1a830bab4c8bbc220f235bd39caf5'], + }), + ('File::Spec', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('Test::Simple', '1.302162', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': 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'0.094001', { + 'source_tmpl': 'Pod-Eventual-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['be9fb8910b108e5d1a66f002b659ad22576e88d779b703dff9d15122c3f80834'], + }), + ('Pod::Elemental', '0.103004', { + 'source_tmpl': 'Pod-Elemental-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['43625cde7241fb174ad9c7eb45387fba410dc141d7de2323855eeab3590072c9'], + }), + ('Pod::Weaver', '4.015', { + 'source_tmpl': 'Pod-Weaver-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5af25b29a55783e495a9df5ef6293240e2c9ab02764613d79f1ed50b12dec5ae'], + }), + ('Dist::Zilla', '6.012', { + 'source_tmpl': 'Dist-Zilla-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['67583075f6d62b78aaa956389f113df789ddd41911394092a5a2b8c6fa863070'], + }), + ('XML::RegExp', '0.04', { + 'source_tmpl': 'XML-RegExp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'], + 'checksums': ['df1990096036085c8e2d45904fe180f82bfed40f1a7e05243f334ea10090fc54'], + }), + ('XML::DOM', '1.46', { + 'source_tmpl': 'XML-DOM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'], + 'checksums': ['8ba24b0b459b01d6c5e5b0408829c7d5dfe47ff79b3548c813759048099b175e'], + }), + ('Data::Dump', '1.23', { + 'source_tmpl': 'Data-Dump-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['af53b05ef1387b4cab4427e6789179283e4f0da8cf036e8db516ddb344512b65'], + }), + ('File::Next', '1.16', { + 'source_tmpl': 'File-Next-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['6965f25c2c132d0ba7a6f72b57b8bc6d25cf8c1b7032caa3a9bda8612e41d759'], + }), + ('App::cpanminus', '1.7044', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], + 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], + }), +] + +moduleclass = 'lang' From b8c6bf49d867c351e62db058590546e70a5069b7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 13 Mar 2019 08:55:27 +0200 Subject: [PATCH 0847/5331] adding easyconfigs: BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb --- ...UGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb | 59 +++++++++++++++++++ .../BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb | 40 +++++++++++++ .../b/BamTools/BamTools-2.5.1-intel-2018b.eb | 18 ++++++ ...Python-1.67.0-intel-2018b-Python-2.7.15.eb | 25 ++++++++ .../e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb | 52 ++++++++++++++++ .../l/libharu/libharu-2.3.0-intel-2018b.eb | 39 ++++++++++++ .../l/lpsolve/lpsolve-5.5.2.5-intel-2018b.eb | 32 ++++++++++ .../t/tabix/tabix-0.2.6-GCCcore-7.3.0.eb | 41 +++++++++++++ 8 files changed, 306 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/b/BUSCO/BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-intel-2018b.eb create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb create mode 100644 easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2018b.eb create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2018b.eb create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..c11f1d0f299 --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [ + 'http://bioinf.uni-greifswald.de/augustus/binaries/', + 'http://bioinf.uni-greifswald.de/augustus/binaries/old/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_fix-hardcoding.patch', + '%(name)s-%(version)s_additional_fix_hardcoding.patch', +] +checksums = [ + '989a95fe3a83d62af4d323a9727d11b2c566adcf4d789d5d86d7b842d83e7671', # augustus-3.3.2.tar.gz + '96e8d72b67e820dca0d6fdbda5b9735dc8259e27fe06167462f2bdbfef5ed7d7', # AUGUSTUS-3.3.2_fix-hardcoding.patch + # AUGUSTUS-3.3.2_additional_fix_hardcoding.patch + '2100c3c85a47228f1f2110b636f462305ba37a5f0c4b6f660d67f1696b25f79f', +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.15'), + ('Boost.Python', '1.67.0', versionsuffix), + ('GSL', '2.5'), + ('SAMtools', '1.9'), + ('HTSlib', '1.9'), + ('BCFtools', '1.9'), + ('tabix', '0.2.6'), + ('lpsolve', '5.5.2.5'), + ('SuiteSparse', '5.4.0', '-METIS-5.1.0'), + ('BamTools', '2.5.1'), + ('SQLite', '3.24.0'), +] + +skipsteps = ['configure'] + +prebuildopts = "unset LDFLAGS && unset LIBS && " +buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true CXX="$CXX" LINK.cc="$CXX" ' +installopts = 'INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/espoca', 'bin/etraining', + 'bin/fastBlockSearch', 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} + +modextrapaths = {'PATH': 'scripts'} +modextravars = {'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..f83be916ff2 --- /dev/null +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'BUSCO' +version = '3.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('Python', '2.7.15'), + ('BLAST+', '2.7.1'), + ('HMMER', '3.2.1'), + ('AUGUSTUS', '3.3.2', versionsuffix), + ('EMBOSS', '6.6.0'), +] + +download_dep_fail = True +use_pip = True + +postinstallcmds = [ + 'mkdir %(installdir)s/bin %(installdir)s/doc', + 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/BUSCO_v3_userguide.pdf %(installdir)s/doc', + 'cp %(builddir)s/%(namelower)s-%(version)s/LICENSE %(installdir)s/doc', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/sample_data %(installdir)s', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/config %(installdir)s', +] + +sanity_check_paths = { + 'files': ['bin/run_BUSCO.py'], + 'dirs': ['sample_data', 'lib/python%(pyshortver)s/site-packages/busco'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-intel-2018b.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-intel-2018b.eb new file mode 100644 index 00000000000..07ed573a15d --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.1-intel-2018b.eb @@ -0,0 +1,18 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'BamTools' +version = '2.5.1' + +homepage = 'https://github.com/pezmaster31/%(namelower)s' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pezmaster31/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4abd76cbe1ca89d51abc26bf43a92359e5677f34a8258b901a01f38c897873fc'] + +builddependencies = [('CMake', '3.12.1')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..01bdba8789c --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,25 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.67.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.sourceforge.net/boost/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8aa4e330c870ef50a896634c931adf468b21f8a69b77007e45c444151229f665'] + +dependencies = [ + ('Python', '2.7.15'), + ('Boost', version), +] + +only_python_bindings = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb new file mode 100644 index 00000000000..6c9d498a0a4 --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb @@ -0,0 +1,52 @@ +# authors: Kenneth Hoste (Ghent University), George Tsouloupas , Fotis Georgatos +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'EMBOSS' +version = '6.6.0' + +homepage = 'http://emboss.sourceforge.net/' +description = """EMBOSS is 'The European Molecular Biology Open Software Suite'. + EMBOSS is a free Open Source software analysis package specially developed for + the needs of the molecular biology (e.g. EMBnet) user community.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [ + 'ftp://emboss.open-bio.org/pub/EMBOSS/', + 'ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0', +] +sources = [SOURCE_TAR_GZ] +patches = ['EMBOSS_disable-embossupdate.patch'] +checksums = [ + '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', # EMBOSS-6.6.0.tar.gz + '3e5e0fbbcb78d62dbfb4586cc9c69d7e602c661f12414d193b2be46024377fd6', # EMBOSS_disable-embossupdate.patch +] + +dependencies = [ + ('X11', '20180604'), + ('libgd', '2.2.5'), + ('libharu', '2.3.0'), + ('Java', '1.8', '', True), +] + +configopts = " --with-hpdf=$EBROOTLIBHARU " + +# jemboss.jar does not build in a parallel build +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', + 'epcre', 'eplplot', 'ezlib', 'nucleus']] + + ['share/EMBOSS/jemboss/lib/jemboss.jar'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2018b.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2018b.eb new file mode 100644 index 00000000000..6a2cdb981d1 --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2018b.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Modified for foss-2016b by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'http://libharu.org/' +description = """libHaru is a free, cross platform, open source library for generating PDF files.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/libharu/libharu/archive/'] +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [('libpng', '1.6.34')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': ['if', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2018b.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2018b.eb new file mode 100644 index 00000000000..6c0dc559298 --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2018b.eb @@ -0,0 +1,32 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.5' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] + +lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % lpsolve_ver + +comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +comp_cmd += "sh ccc" +cmds_map = [('.*', comp_cmd)] + +lpsolve_libname = 'liblpsolve%s' % lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % lpsolve_libname, 'bin/ux64/%s.%s' % (lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % lpsolve_libname, 'lib/%s.%s' % (lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-7.3.0.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..7f02f9ef9e8 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-7.3.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Jens Timmerman, Ghent University + +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] +checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73'] + +builddependencies = [('binutils', '2.30')] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' From 3ca0235c7d263530c1d98290ed2295c42a0d2161 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 13 Mar 2019 10:15:47 +0200 Subject: [PATCH 0848/5331] Add missing checksums. --- .../easyconfigs/b/BUSCO/BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb | 1 + easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2018b.eb | 1 + easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2018b.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb index f83be916ff2..c1e0ead9f71 100644 --- a/easybuild/easyconfigs/b/BUSCO/BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-3.0.2-intel-2018b-Python-2.7.15.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['df022cffecb39b0bcbf32d5c5ae91217e6e44ca50c932ee6efdf9b2b1d4b9f5c'] dependencies = [ ('Python', '2.7.15'), diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2018b.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2018b.eb index 6a2cdb981d1..7f6f38d80d4 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2018b.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-intel-2018b.eb @@ -24,6 +24,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} source_urls = ['https://github.com/libharu/libharu/archive/'] sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] builddependencies = [('CMake', '3.12.1')] diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2018b.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2018b.eb index 6c0dc559298..f2851974227 100644 --- a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2018b.eb +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.5-intel-2018b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} source_urls = [SOURCEFORGE_SOURCE] sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['201a7c62b8b3360c884ee2a73ed7667e5716fc1e809755053b398c2f5b0cf28a'] lpsolve_ver = '%(version_major)s%(version_minor)s' start_dir = 'lpsolve%s' % lpsolve_ver From a55187847fde52873900b0c4b4bc76a9b4f984f7 Mon Sep 17 00:00:00 2001 From: "Nathan S. Watson-Haigh" Date: Wed, 13 Mar 2019 19:33:50 +1030 Subject: [PATCH 0849/5331] Add buildops so it works for non g++ toolchains --- easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb b/easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb index 2b1dc8ecbf8..6709641a6ee 100644 --- a/easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb +++ b/easybuild/easyconfigs/f/fastp/fastp-0.19.7-foss-2018b.eb @@ -15,6 +15,8 @@ checksums = ['de2737b2378a8dfc6aa141cb3bfed8c1fbcfbd6056e48515f856cfafcc5c3266'] skipsteps = ['configure'] +buildopts = ' CXX=${CXX}' + preinstallopts = 'mkdir -p %(installdir)s/bin && ' installopts = 'PREFIX=%(installdir)s' From 0e8d890ade13977ea184df4ea0a326b2cf075700 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 13 Mar 2019 12:19:44 +0200 Subject: [PATCH 0850/5331] Change back to xml parser 2.44_01 --- easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb index c697a59e7bc..d98bb1007cb 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb @@ -784,10 +784,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], }), - ('XML::Parser', '2.44', { + ('XML::Parser', '2.44_01', { 'source_tmpl': 'XML-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], - 'checksums': ['1ae9d07ee9c35326b3d9aad56eae71a6730a73a116b9fe9e8a4758b7cc033216'], + 'checksums': ['5310ea5c8c707f387589bba8934ab9112463a452f828adf2755792d968b9ac7e'], }), ('XML::XPath', '1.44', { 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', From 8313f7504c23edce2dde12a2c0effe8525f72cc0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 13 Mar 2019 12:30:10 +0200 Subject: [PATCH 0851/5331] Downgrade SuiteSparse to 5.1.2 to be consistent with 2018b toolchains. --- ...UGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb | 2 +- ...iteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb | 20 +++++++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb index c11f1d0f299..3e03a96422e 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb @@ -35,7 +35,7 @@ dependencies = [ ('BCFtools', '1.9'), ('tabix', '0.2.6'), ('lpsolve', '5.5.2.5'), - ('SuiteSparse', '5.4.0', '-METIS-5.1.0'), + ('SuiteSparse', '5.1.2', '-METIS-5.1.0'), ('BamTools', '2.5.1'), ('SQLite', '3.24.0'), ] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb new file mode 100644 index 00000000000..bc935b77248 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb @@ -0,0 +1,20 @@ +name = 'SuiteSparse' +version = '5.1.2' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4ec8d344bd8e95b898132ddffd7ee93bfbb2c1224925d11bab844b08f9b4c3b7'] + +dependencies = [('METIS', metis_ver)] + +parallel = 1 + +moduleclass = 'numlib' From fec2744dbd6d88a46bd83a555bd0123dc488be00 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Wed, 13 Mar 2019 13:11:48 +0100 Subject: [PATCH 0852/5331] Fix source url for template toolkit --- easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb index d98bb1007cb..9beb573da3c 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb @@ -186,7 +186,7 @@ exts_list = [ }), ('Template', '2.28', { 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], 'checksums': ['71af368009f13582ef907e33d3812776b597f42b3da0bc0fd3bc7418e4785dd7'], }), ('DBI', '1.642', { From 3d6a764dbbbdc1610640dd63da488343a93c6133 Mon Sep 17 00:00:00 2001 From: ebtest Date: Wed, 13 Mar 2019 12:22:00 +0000 Subject: [PATCH 0853/5331] add info on patch files --- .../g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb | 6 +++--- .../GlobalArrays-v5.7-intel-2018b-MKL_issue.patch | 2 ++ .../GlobalArrays/GlobalArrays-v5.7_ga_diag_std.patch | 2 ++ .../OpenMolcas-18.09-intel-2018b-Python-3.6.6.eb | 11 +++++------ .../OpenMolcas-pymolcas_only_in_ebprefix.patch | 4 ++++ 5 files changed, 16 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb index b922407f762..a2242363a05 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.7-intel-2018b.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild easyblock = 'ConfigureMake' name = 'GlobalArrays' @@ -21,8 +21,8 @@ patches = [ checksums = [ '3ed1ab47adfda7bceb7beca12fc05a2e1631732f0e55bbaf9036dad4e3da4774', - 'b8b8c5d357bce34a37cdf640e88a3ecb72d7de3255cc3ec086a9c3949c2c2d33', # GlobalArrays-v5.7_ga_diag_std.patch - '0c25322731b5964d00c6fc18673881a755faa190f446a592dc3d49caf806a973', # GlobalArrays-v5.7-intel-2018b-MKL_issue.patch + '8049543e6442e13acb54cb4afd9a6ad78102864b2ef138ad9f4b1a45bd0666bb', # GlobalArrays-v5.7_ga_diag_std.patch + 'e5b9fff47d471b3552b167b82153f8f1fd6406c52e39a11b693cb9c4bf12645e', # GlobalArrays-v5.7-intel-2018b-MKL_issue.patch ] configopts = ' --with-mpi --enable-i8' diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7-intel-2018b-MKL_issue.patch b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7-intel-2018b-MKL_issue.patch index 1fa0a7e9d5a..dafbf9ce45c 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7-intel-2018b-MKL_issue.patch +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7-intel-2018b-MKL_issue.patch @@ -1,3 +1,5 @@ +# fix for MKL error "PDSTEDC parameter number 10 had an illegal value" +# (github.com/GlobalArrays/ga/pull/122) diff --git a/global/src/scalapack.F b/global/src/scalapack.F index 74ef1a9..cd80884 100644 --- a/global/src/scalapack.F diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7_ga_diag_std.patch b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7_ga_diag_std.patch index ee80d5a56e2..8f2f94c9213 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7_ga_diag_std.patch +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-v5.7_ga_diag_std.patch @@ -1,3 +1,5 @@ +# fixes for ga_diag_std_seq 32-bit integer interface and for pgcc +# object handling (github.com/GlobalArrays/ga/pull/101) diff --git a/global/src/ga_diag_seq.F b/global/src/ga_diag_seq.F index ee601729..d5653975 100644 --- a/global/src/ga_diag_seq.F diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-Python-3.6.6.eb index 80340d09cc0..1caa3b3b070 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-18.09-intel-2018b-Python-3.6.6.eb @@ -14,15 +14,14 @@ toolchainopts = {'usempi': True} source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] sources = ["OpenMolcas-v%(version)s.tar.gz"] -# This patch avoids the automatic extra copy of 'pymolcas' script -# in the first writable directory of the install user's $PATH -# The 'make install' process is going to install it in -# %(installdir)s/sbin/ which is the only place it should stay +# This patch avoids a forced extra copy of 'pymolcas' script +# in a local folder of the user doing the build +# The 'make install' process will already install it in +# %(installdir)s/sbin/ patches = ["OpenMolcas-pymolcas_only_in_ebprefix.patch"] checksums = ['b4f310fb65205c865ccc6373ce9c3833a586f8ff63a71a624cf793559c9b39cf', - '130a40028ad1c231d69f109151029032cac26f2c0c6e636266faa5a69027cd1b'] - + '56165ab4a752ef7cdbe3340c8c922fca04510e8ee2e4024ea654e6bcd83198f8'] dependencies = [ ('GlobalArrays', '5.7'), diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-pymolcas_only_in_ebprefix.patch b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-pymolcas_only_in_ebprefix.patch index 19af4702e92..5d22621805c 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-pymolcas_only_in_ebprefix.patch +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-pymolcas_only_in_ebprefix.patch @@ -1,3 +1,7 @@ +# Avoid a forced copy of the 'pymolcas' script in a local path +# of the user doing the build +# 'make install' will install it using the proper prefix +# by A. Lozano (ULiege) --- a/sbin/install_pymolcas.sh 2018-09-02 09:35:13.000000000 +0200 +++ b/sbin/install_pymolcas.sh 2019-03-11 16:53:29.224546598 +0100 @@ -116,8 +116,8 @@ From 6c51240c2194e1d1bb3d5d42777cc6cb65de849d Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Wed, 13 Mar 2019 13:22:45 +0100 Subject: [PATCH 0854/5331] Fix source url for libwww-perl --- easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb index 9beb573da3c..38fa62b45e3 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb @@ -721,7 +721,7 @@ exts_list = [ }), ('LWP::Simple', '6.37', { 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], 'checksums': ['c6ed7c632aa05a7a03c8b75a3113b6f6f801be55b3384e770607e8973a234211'], }), ('Time::Piece::MySQL', '0.06', { From 27c214823f093cea3aced548156eca3baa8268ce Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Mar 2019 10:52:41 -0500 Subject: [PATCH 0855/5331] Compile from source --- .../easyconfigs/g/git-lfs/git-lfs-2.7.1.eb | 38 ++++++++----------- 1 file changed, 16 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb index e84feb4c13c..aea05b6656e 100644 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb @@ -1,35 +1,29 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = "Tarball" +easyblock = 'MakeCp' name = 'git-lfs' version = '2.7.1' -homepage = 'https://git-lfs.github.com/' -description = """Git Large File Storage (LFS) replaces large files such as audio samples, videos, - datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server - like GitHub.com or GitHub Enterprise.""" +homepage = 'https://git-lfs.github.com' +description = """Git Large File Storage (LFS) replaces large files such as audio + samples, videos, datasets, and graphics with text pointers inside Git, while + storing the file contents on a remote server like GitHub.com""" toolchain = {'name': 'dummy', 'version': ''} -source_urls = ['https://github.com/git-lfs/git-lfs/releases/download/v%(version)s/'] -sources = ['%(name)s-linux-amd64-v%(version)s.tar.gz'] -checksums = ['7be85238cbbb957ab25de52b60279d40ba40d3faa72eeb2cb9fa77d6d92381e5'] +source_urls = ['https://github.com/git-lfs/git-lfs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['af60c2370d135ab13724d302a0b1c226ec9fb0ee6d29ecc335e9add4c86497b4'] -sanity_check_paths = { - 'files': ["git-lfs"], - 'dirs': [""] -} +builddependencies = [('Go', '1.12', '', True)] -# add the installation dir to PATH -modextrapaths = { - 'PATH': '', +files_to_copy = [(['bin/%(name)s'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/git-lfs'], + 'dirs': [], } -# remove exec permission for the provided installation script -postinstallcmds = ["chmod og-x %(installdir)s/install.sh"] +sanity_check_commands = [('git-lfs', '--version')] + moduleclass = 'tools' From ca6841f8cc6f7736e213d8980e74d47f257bab34 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Mar 2019 10:59:45 -0500 Subject: [PATCH 0856/5331] Remove empty line --- easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb index aea05b6656e..f5db3277f23 100644 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb @@ -24,6 +24,5 @@ sanity_check_paths = { } sanity_check_commands = [('git-lfs', '--version')] - moduleclass = 'tools' From 59b04dead9eefc05928f5ecedf1065918a07f21b Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Mar 2019 11:19:23 -0500 Subject: [PATCH 0857/5331] Remove unnecessary dummy toolchain definition --- easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb index f5db3277f23..dd2cc50c158 100644 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/git-lfs/git-lfs/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['af60c2370d135ab13724d302a0b1c226ec9fb0ee6d29ecc335e9add4c86497b4'] -builddependencies = [('Go', '1.12', '', True)] +builddependencies = [('Go', '1.12')] files_to_copy = [(['bin/%(name)s'], 'bin')] From 8a3cffe96ab0a31e423db98450676bff6e68be5f Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 13 Mar 2019 19:41:24 +0200 Subject: [PATCH 0858/5331] adding easyconfigs: intltool-0.51.0-GCCcore-8.2.0.eb, X11-20190313-GCCcore-8.2.0.eb --- .../intltool/intltool-0.51.0-GCCcore-8.2.0.eb | 33 ++ .../x/X11/X11-20190313-GCCcore-8.2.0.eb | 355 ++++++++++++++++++ 2 files changed, 388 insertions(+) create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..511f01f67ff --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-8.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'http://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('Perl', '5.28.1'), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..b4d6ec5d9d5 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb @@ -0,0 +1,355 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20190313' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'http://xcb.freedesktop.org/dist/', + 'http://xkbcommon.org/download/', + 'http://cgit.freedesktop.org/xorg/util/macros/snapshot', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] +checksums = [ + '5d6e62803c9f20830b28ad8a9800c97a9987635089229e3e380ef3848c84d2a6', # util-macros-1.19.2.tar.gz + '50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9', # libpthread-stubs-0.4.tar.gz + 'de68a1a9dd1a1219ad73531bff9f662bc62fcd777387549c43cd282399f4a6ea', # bigreqsproto-1.1.2.tar.gz + '22195b7e50036440b1c6b3b2d63eb03dfa6e71c8a1263ed1f07b0f31ae7dad50', # compositeproto-0.4.2.tar.gz + 'f65ccbf1de9750a527ea6e85694085b179f2d06495cbdb742b3edb2149fef303', # damageproto-1.2.1.tar.gz + '3262bbf5902211a3ce88f5c6ab4528145ff84f69c52fd386ae0312bc45fb8a40', # dmxproto-2.3.1.tar.gz + '7e65b031eaa6ebe23c75583d4abd993ded7add8009b4200a4db7aa10728b0f61', # dri2proto-2.8.tar.gz + 'e1a0dad3009ecde52c0bf44187df5f95cc9a7cc0e76dfc2f2bbf3e909fe03fa9', # dri3proto-1.0.tar.gz + '67865a0e3cdc7dec1fd676f0927f7011ad4036c18eb320a2b41dbd56282f33b8', # fixesproto-5.0.tar.gz + '72c44e63044b2b66f6fa112921621ecc20c71193982de4f198d9a29cda385c5e', # fontsproto-2.1.3.tar.gz + '9d8130fec2b98bd032db7730fa092dd9dec39f3de34f4bb03ceb43b9903dbc96', # glproto-1.4.17.tar.gz + '10eaadd531f38f7c92ab59ef0708ca195caf3164a75c4ed99f0c04f2913f6ef3', # inputproto-2.3.2.tar.gz + '828cb275b91268b1a3ea950d5c0c5eb076c678fdf005d517411f89cc8c3bb416', # kbproto-1.0.7.tar.gz + '114252e97afb4dfae8b31e6b0d5e24e4babda26b364e2be57abc2f3c30248b87', # presentproto-1.1.tar.gz + '8f8a716d6daa6ba05df97d513960d35a39e040600bf04b313633f11679006fab', # randrproto-1.5.0.tar.gz + '485f792570dd7afe49144227f325bf2827bc7d87aae6a8ab6c1de2b06b1c68c5', # recordproto-1.14.2.tar.gz + 'a0a4be3cad9381ae28279ba5582e679491fc2bec9aab8a65993108bf8dbce5fe', # renderproto-0.11.1.tar.gz + '469029d14fdeeaa7eed1be585998ff4cb92cf664f872d1d69c04140815b78734', # resourceproto-1.2.0.tar.gz + 'd8dee19c52977f65af08fad6aa237bacee11bc5a33e1b9b064e8ac1fd99d6e79', # scrnsaverproto-1.2.2.tar.gz + 'df8dfeb158767f843054248d020e291a2c40f7f5e0ac6d8706966686fee7c5c0', # videoproto-2.3.3.tar.gz + '48013cfbe4bd5580925a854a43e2bccbb4c7a5a31128070644617b6dc7f8ef85', # xcmiscproto-1.2.2.tar.gz + '1b1bcdf91221e78c6c33738667a57bd9aaa63d5953174ad8ed9929296741c9f5', # xextproto-7.3.0.tar.gz + 'd190e6462b2bbbac6ee9a007fb8eccb9ad9f5f70544154f388266f031d4bbb23', # xf86bigfontproto-1.2.0.tar.gz + '73bc6fc830cce5a0ec9c750d4702601fc0fca12d6353ede8b4c0092c9c4ca2af', # xf86dgaproto-2.1.tar.gz + '18ff8de129b89fa24a412a1ec1799f8687f96c186c655b44b1a714a3a5d15d6c', # xf86driproto-2.1.1.tar.gz + 'c3512b11cefa7558576551f8582c6e7071c8a24d78176059d94b84b48b262979', # xf86vidmodeproto-2.3.1.tar.gz + 'd99e121edf7b310008d7371ac5dbe3aa2810996d476b754dc78477cc26e5e7c1', # xineramaproto-1.2.1.tar.gz + '6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7', # xproto-7.0.31.tar.gz + '1f123d8304b082ad63a9e89376400a3b1d4c29e67e3ea07b3f659cccca690eea', # libXau-1.0.9.tar.gz + '6f7c7e491a23035a26284d247779174dedc67e34e93cc3548b648ffdb6fc57c0', # libXdmcp-1.1.2.tar.gz + '0698e8f596e4c0dbad71d3dc754d95eb0edbb42df5464e0f782621216fa33ba7', # xcb-proto-1.13.tar.gz + '0bb3cfd46dbd90066bf4d7de3cad73ec1024c7325a4a0cbf5f4a0d4fa91155fb', # libxcb-1.13.tar.gz + 'b7a577c1b6c75030145e53b4793db9c88f9359ac49e7d771d4385d21b3e5945d', # xtrans-1.3.5.tar.gz + '60ddcff932b7fd352752d51a5c4f04f3d0403230a584df9a2e0d5ed87c486c8b', # libxkbcommon-0.8.4.tar.xz + 'f62ab88c2a87b55e1dc338726a55bb6ed8048084fe6a3294a7ae324ca45159d1', # libX11-1.6.7.tar.gz + 'eb0b88050491fef4716da4b06a4d92b4fc9e76f880d6310b2157df604342cfe5', # libXext-1.3.3.tar.gz + 'e3da723257f4f4c0c629aec402e0a36fbec66a9418f70d24a159cb0470ec83d2', # libFS-1.0.8.tar.gz + '7812a824a66dd654c830d21982749b3b563d9c2dfe0b88b203cefc14a891edc0', # libICE-1.0.9.tar.gz + '1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320', # libSM-1.2.3.tar.gz + '4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a', # libXScrnSaver-1.2.3.tar.gz + 'b59bee38a9935565fa49dc1bfe84cb30173e2e07e1dcdf801430d4b54eb0caa3', # libXt-1.1.5.tar.gz + 'e5fd4bacef068f9509b8226017205040e38d3fba8d2de55037200e7176c13dba', # libXmu-1.1.2.tar.gz + '2523acc780eac01db5163267b36f5b94374bfb0de26fc0b5a7bee76649fd8501', # libXpm-3.5.12.tar.gz + '7e74ac3e5f67def549722ff0333d6e6276b8becd9d89615cda011e71238ab694', # libXaw-1.0.13.tar.gz + '9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570', # libXfixes-5.0.3.tar.gz + '581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c', # libXcomposite-0.4.5.tar.gz + '770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf', # libXrender-0.9.10.tar.gz + 'ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8', # libXcursor-1.2.0.tar.gz + '630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019', # libXdamage-1.1.5.tar.gz + '895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41', # libfontenc-1.1.4.tar.gz + '59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e', # libXfont-1.5.4.tar.gz + 'a4b761a37528353a2b83dba364d7c1fd6aef2d554a1a019815f24f7f8866890e', # libXfont2-2.0.3.tar.gz + '26cdddcc70b187833cbe9dc54df1864ba4c03a7175b2ca9276de9f05dce74507', # libXft-2.3.2.tar.gz + '463cc5370191404bc0f8a450fdbf6d9159efbbf274e5e0f427a60191fed9cf4b', # libXi-1.7.9.tar.gz + '64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18', # libXinerama-1.1.4.tar.gz + '2baa7fb3eca78fe7e11a09b373ba898b717f7eeba4a4bfd68187e04b4789b0d3', # libXrandr-1.5.1.tar.gz + '5b62feee09f276d74054787df030fceb41034de84174abec6d81c591145e043a', # libXres-1.2.0.tar.gz + 'a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2', # libXtst-1.2.3.tar.gz + 'c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1', # libXv-1.0.11.tar.gz + 'd8306f71c798d10409bb181b747c2644e1d60c05773c742c12304ab5aa5c8436', # libXvMC-1.0.10.tar.gz + 'e6361620a15ceba666901ca8423e8be0c6ed0271a7088742009160349173766b', # libXxf86dga-1.1.4.tar.gz + '5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99', # libXxf86vm-1.1.4.tar.gz + '4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925', # libdmx-1.1.4.tar.gz + '8d86e64893917be3dfb1c5e837888d1275399c818783474002203d751312b03c', # libpciaccess-0.14.tar.gz + '95df50570f38e720fb79976f603761ae6eff761613eb56f258c3cb6bab4fd5e3', # libxkbfile-1.0.9.tar.gz + '7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c', # libxshmfence-1.3.tar.gz + '0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7', # xcb-util-0.4.0.tar.gz + 'cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42', # xcb-util-image-0.4.0.tar.gz + '0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96', # xcb-util-keysyms-0.4.0.tar.gz + '55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5', # xcb-util-renderutil-0.3.9.tar.gz + '038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334', # xcb-util-wm-0.4.1.tar.gz + 'a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8', # xcb-util-cursor-0.1.3.tar.gz + '8d7e2aaa4e9d66843540e6ef3ebadf79d665d954bfa37d8829be428da6e08bbe', # xkeyboard-config-2.26.tar.gz + 'e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc', # printproto-1.0.5.tar.gz + 'f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c', # libXp-1.0.3.tar.gz + '27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265', # xbitmaps-1.1.2.tar.gz +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('fontconfig', '2.13.1'), + ('freetype', '2.9.1'), + ('zlib', '1.2.11'), +] +builddependencies = [ + ('binutils', '2.31.1'), + ('Autotools', '20180311'), + ('Bison', '3.0.5'), + ('gettext', '0.19.8.1'), + ('pkg-config', '0.29.2'), + ('intltool', '0.51.0'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} +components = [ + ('xorg-macros', '1.19.2', { # 2018-03-04 + 'sources': ['util-macros-%(version)s.tar.gz'], + 'checksums': ['5d6e62803c9f20830b28ad8a9800c97a9987635089229e3e380ef3848c84d2a6'], + 'start_dir': 'util-macros-%(version)s', + }), + ('libpthread-stubs', '0.4', { # 2017-03-14 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('bigreqsproto', '1.1.2', { # 2012-03-23 + 'checksums': ['de68a1a9dd1a1219ad73531bff9f662bc62fcd777387549c43cd282399f4a6ea'], + }), + ('compositeproto', '0.4.2', { # 2010-10-30 + 'checksums': ['22195b7e50036440b1c6b3b2d63eb03dfa6e71c8a1263ed1f07b0f31ae7dad50'], + }), + ('damageproto', '1.2.1', { # 2010-10-30 + 'checksums': ['f65ccbf1de9750a527ea6e85694085b179f2d06495cbdb742b3edb2149fef303'], + }), + ('dmxproto', '2.3.1', { # 2011-01-06 + 'checksums': ['3262bbf5902211a3ce88f5c6ab4528145ff84f69c52fd386ae0312bc45fb8a40'], + }), + ('dri2proto', '2.8', { # 2012-07-11 + 'checksums': ['7e65b031eaa6ebe23c75583d4abd993ded7add8009b4200a4db7aa10728b0f61'], + }), + ('dri3proto', '1.0', { # 2013-11-01 + 'checksums': ['e1a0dad3009ecde52c0bf44187df5f95cc9a7cc0e76dfc2f2bbf3e909fe03fa9'], + }), + ('fixesproto', '5.0', { # 2011-03-08 + 'checksums': ['67865a0e3cdc7dec1fd676f0927f7011ad4036c18eb320a2b41dbd56282f33b8'], + }), + ('fontsproto', '2.1.3', { # 2014-04-14 + 'checksums': ['72c44e63044b2b66f6fa112921621ecc20c71193982de4f198d9a29cda385c5e'], + }), + ('glproto', '1.4.17', { # 2013-12-10 + 'checksums': ['9d8130fec2b98bd032db7730fa092dd9dec39f3de34f4bb03ceb43b9903dbc96'], + }), + ('inputproto', '2.3.2', { # 2016-04-04 + 'checksums': ['10eaadd531f38f7c92ab59ef0708ca195caf3164a75c4ed99f0c04f2913f6ef3'], + }), + ('kbproto', '1.0.7', { # 2015-05-01 + 'checksums': ['828cb275b91268b1a3ea950d5c0c5eb076c678fdf005d517411f89cc8c3bb416'], + }), + ('presentproto', '1.1', { # 2017-01-26 + 'checksums': ['114252e97afb4dfae8b31e6b0d5e24e4babda26b364e2be57abc2f3c30248b87'], + }), + ('randrproto', '1.5.0', { # 2015-05-17 + 'checksums': ['8f8a716d6daa6ba05df97d513960d35a39e040600bf04b313633f11679006fab'], + }), + ('recordproto', '1.14.2', { # 2012-03-23 + 'checksums': ['485f792570dd7afe49144227f325bf2827bc7d87aae6a8ab6c1de2b06b1c68c5'], + }), + ('renderproto', '0.11.1', { # 2010-08-10 + 'checksums': ['a0a4be3cad9381ae28279ba5582e679491fc2bec9aab8a65993108bf8dbce5fe'], + }), + ('resourceproto', '1.2.0', { # 2011-05-28 + 'checksums': ['469029d14fdeeaa7eed1be585998ff4cb92cf664f872d1d69c04140815b78734'], + }), + ('scrnsaverproto', '1.2.2', { # 2012-03-23 + 'checksums': ['d8dee19c52977f65af08fad6aa237bacee11bc5a33e1b9b064e8ac1fd99d6e79'], + }), + ('videoproto', '2.3.3', { # 2016-03-11 + 'checksums': ['df8dfeb158767f843054248d020e291a2c40f7f5e0ac6d8706966686fee7c5c0'], + }), + ('xcmiscproto', '1.2.2', { # 2012-03-23 + 'checksums': ['48013cfbe4bd5580925a854a43e2bccbb4c7a5a31128070644617b6dc7f8ef85'], + }), + ('xextproto', '7.3.0', { # 2013-12-27 + 'checksums': ['1b1bcdf91221e78c6c33738667a57bd9aaa63d5953174ad8ed9929296741c9f5'], + }), + ('xf86bigfontproto', '1.2.0', { # 2009-08-27 + 'checksums': ['d190e6462b2bbbac6ee9a007fb8eccb9ad9f5f70544154f388266f031d4bbb23'], + }), + ('xf86dgaproto', '2.1', { # 2009-10-01 + 'checksums': ['73bc6fc830cce5a0ec9c750d4702601fc0fca12d6353ede8b4c0092c9c4ca2af'], + }), + ('xf86driproto', '2.1.1', { # 2011-01-06 + 'checksums': ['18ff8de129b89fa24a412a1ec1799f8687f96c186c655b44b1a714a3a5d15d6c'], + }), + ('xf86vidmodeproto', '2.3.1', { # 2011-01-06 + 'checksums': ['c3512b11cefa7558576551f8582c6e7071c8a24d78176059d94b84b48b262979'], + }), + ('xineramaproto', '1.2.1', { # 2011-01-06 + 'checksums': ['d99e121edf7b310008d7371ac5dbe3aa2810996d476b754dc78477cc26e5e7c1'], + }), + ('xproto', '7.0.31', { # 2016-09-23 + 'checksums': ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'], + }), + ('libXau', '1.0.9', { # 2019-02-10 + }), + ('libXdmcp', '1.1.2', { # 2015-03-21 + 'checksums': ['6f7c7e491a23035a26284d247779174dedc67e34e93cc3548b648ffdb6fc57c0'], + }), + ('xcb-proto', '1.13', { # 2018-03-05 + 'checksums': ['0698e8f596e4c0dbad71d3dc754d95eb0edbb42df5464e0f782621216fa33ba7'], + }), + ('libxcb', '1.13', { # 2018-03-05 + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['0bb3cfd46dbd90066bf4d7de3cad73ec1024c7325a4a0cbf5f4a0d4fa91155fb'], + 'start_dir': '%(name)s-%(version)s', + }), + ('xtrans', '1.3.5', { # 2014-09-22 + 'checksums': ['b7a577c1b6c75030145e53b4793db9c88f9359ac49e7d771d4385d21b3e5945d'], + }), + ('libxkbcommon', '0.8.4', { # 2019-02-22 + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'start_dir': 'libxkbcommon-%(version)s', + }), + ('libX11', '1.6.7', { # 2018-10-09 + 'checksums': ['3abce972ba62620611fab5b404dafb852da3da54e7c287831c30863011d28fb3'], + }), + ('libXext', '1.3.3', { # 2014-07-24 + 'checksums': ['eb0b88050491fef4716da4b06a4d92b4fc9e76f880d6310b2157df604342cfe5'], + }), + ('libFS', '1.0.8', { # 2019-03-10 + 'checksums': ['91bf1c5ce4115b7dbf4e314fdbee54052708e8f7b6a2ec6e82c309bcbe40ef3d'], + }), + ('libICE', '1.0.9', { # 2014-06-07 + 'checksums': ['7812a824a66dd654c830d21982749b3b563d9c2dfe0b88b203cefc14a891edc0'], + }), + ('libSM', '1.2.3', { # 2018-10-10 + }), + ('libXScrnSaver', '1.2.3', { # 2018-07-05 + }), + ('libXt', '1.1.5', { # 2015-05-01 + 'checksums': ['b59bee38a9935565fa49dc1bfe84cb30173e2e07e1dcdf801430d4b54eb0caa3'], + }), + ('libXmu', '1.1.2', { # 2013-09-08 + 'checksums': ['e5fd4bacef068f9509b8226017205040e38d3fba8d2de55037200e7176c13dba'], + }), + ('libXpm', '3.5.12', { # 2016-12-15 + 'checksums': ['2523acc780eac01db5163267b36f5b94374bfb0de26fc0b5a7bee76649fd8501'], + }), + ('libXaw', '1.0.13', { # 2015-05-01 + 'checksums': ['7e74ac3e5f67def549722ff0333d6e6276b8becd9d89615cda011e71238ab694'], + }), + ('libXfixes', '5.0.3', { # 2016-10-04 + 'checksums': ['9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570'], + }), + ('libXcomposite', '0.4.5', { # 2019-03-11 + }), + ('libXrender', '0.9.10', { # 2016-10-04 + 'checksums': ['770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf'], + }), + ('libXcursor', '1.2.0', { # 2019-03-11 + }), + ('libXdamage', '1.1.5', { # 2019-03-11 + }), + ('libfontenc', '1.1.4', { # 2019-02-20 + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.3', { # 2017-11-28 + 'checksums': ['a4b761a37528353a2b83dba364d7c1fd6aef2d554a1a019815f24f7f8866890e'], + }), + ('libXft', '2.3.2', { # 2014-06-06 + 'checksums': ['26cdddcc70b187833cbe9dc54df1864ba4c03a7175b2ca9276de9f05dce74507'], + }), + ('libXi', '1.7.9', { # 2017-01-23 + 'checksums': ['463cc5370191404bc0f8a450fdbf6d9159efbbf274e5e0f427a60191fed9cf4b'], + }), + ('libXinerama', '1.1.4', { # 2018-07-05 + 'checksums': ['0ba243222ae5aba4c6a3d7a394c32c8b69220a6872dbb00b7abae8753aca9a44'], + }), + ('libXrandr', '1.5.1', { # 2016-10-04 + 'checksums': ['2baa7fb3eca78fe7e11a09b373ba898b717f7eeba4a4bfd68187e04b4789b0d3'], + }), + ('libXres', '1.2.0', { # 2017-10-11 + 'checksums': ['5b62feee09f276d74054787df030fceb41034de84174abec6d81c591145e043a'], + }), + ('libXtst', '1.2.3', { # 2016-10-04 + 'checksums': ['a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2'], + }), + ('libXv', '1.0.11', { # 2016-10-04 + 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], + }), + ('libXvMC', '1.0.10', { # 2016-10-04 + 'checksums': ['d8306f71c798d10409bb181b747c2644e1d60c05773c742c12304ab5aa5c8436'], + }), + ('libXxf86dga', '1.1.4', { # 2013-05-31 + 'checksums': ['e6361620a15ceba666901ca8423e8be0c6ed0271a7088742009160349173766b'], + }), + ('libXxf86vm', '1.1.4', { # 2015-02-24 + 'checksums': ['5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99'], + }), + ('libdmx', '1.1.4', { # 2018-05-14 + 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], + }), + ('libpciaccess', '0.14', { # 2017-10-23 + 'checksums': ['8d86e64893917be3dfb1c5e837888d1275399c818783474002203d751312b03c'], + }), + ('libxkbfile', '1.0.9', { # 2015-05-01 + 'checksums': ['95df50570f38e720fb79976f603761ae6eff761613eb56f258c3cb6bab4fd5e3'], + }), + ('libxshmfence', '1.3', { # 2018-02-26 + 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], + }), + ('xcb-util', '0.4.0', { # 2014-10-15 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.0', { # 2014-10-15 + 'checksums': ['cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42'], + }), + ('xcb-util-keysyms', '0.4.0', { # 2014-10-01 + 'checksums': ['0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96'], + }), + ('xcb-util-renderutil', '0.3.9', { # 2014-06-13 + 'checksums': ['55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5'], + }), + ('xcb-util-wm', '0.4.1', { # 2014-02-19 + 'checksums': ['038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334'], + }), + ('xcb-util-cursor', '0.1.3', { # 2016-05-12 + 'checksums': ['a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8'], + }), + ('xkeyboard-config', '2.26', { # 2019-02-02 + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.3', { # 2015-02-21 + 'checksums': ['f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c'], + }), + ('xbitmaps', '1.1.2', { # 2018-03-10 + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' From a943fac252e272886820c6221a7f12351ea94ae1 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 13 Mar 2019 20:24:21 +0200 Subject: [PATCH 0859/5331] Use xorgproto, proper checksum placement --- .../x/X11/X11-20190313-GCCcore-8.2.0.eb | 176 ++---------------- 1 file changed, 15 insertions(+), 161 deletions(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb index b4d6ec5d9d5..005c39171fc 100644 --- a/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb @@ -17,84 +17,6 @@ source_urls = [ XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] -checksums = [ - '5d6e62803c9f20830b28ad8a9800c97a9987635089229e3e380ef3848c84d2a6', # util-macros-1.19.2.tar.gz - '50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9', # libpthread-stubs-0.4.tar.gz - 'de68a1a9dd1a1219ad73531bff9f662bc62fcd777387549c43cd282399f4a6ea', # bigreqsproto-1.1.2.tar.gz - '22195b7e50036440b1c6b3b2d63eb03dfa6e71c8a1263ed1f07b0f31ae7dad50', # compositeproto-0.4.2.tar.gz - 'f65ccbf1de9750a527ea6e85694085b179f2d06495cbdb742b3edb2149fef303', # damageproto-1.2.1.tar.gz - '3262bbf5902211a3ce88f5c6ab4528145ff84f69c52fd386ae0312bc45fb8a40', # dmxproto-2.3.1.tar.gz - '7e65b031eaa6ebe23c75583d4abd993ded7add8009b4200a4db7aa10728b0f61', # dri2proto-2.8.tar.gz - 'e1a0dad3009ecde52c0bf44187df5f95cc9a7cc0e76dfc2f2bbf3e909fe03fa9', # dri3proto-1.0.tar.gz - '67865a0e3cdc7dec1fd676f0927f7011ad4036c18eb320a2b41dbd56282f33b8', # fixesproto-5.0.tar.gz - '72c44e63044b2b66f6fa112921621ecc20c71193982de4f198d9a29cda385c5e', # fontsproto-2.1.3.tar.gz - '9d8130fec2b98bd032db7730fa092dd9dec39f3de34f4bb03ceb43b9903dbc96', # glproto-1.4.17.tar.gz - '10eaadd531f38f7c92ab59ef0708ca195caf3164a75c4ed99f0c04f2913f6ef3', # inputproto-2.3.2.tar.gz - '828cb275b91268b1a3ea950d5c0c5eb076c678fdf005d517411f89cc8c3bb416', # kbproto-1.0.7.tar.gz - '114252e97afb4dfae8b31e6b0d5e24e4babda26b364e2be57abc2f3c30248b87', # presentproto-1.1.tar.gz - '8f8a716d6daa6ba05df97d513960d35a39e040600bf04b313633f11679006fab', # randrproto-1.5.0.tar.gz - '485f792570dd7afe49144227f325bf2827bc7d87aae6a8ab6c1de2b06b1c68c5', # recordproto-1.14.2.tar.gz - 'a0a4be3cad9381ae28279ba5582e679491fc2bec9aab8a65993108bf8dbce5fe', # renderproto-0.11.1.tar.gz - '469029d14fdeeaa7eed1be585998ff4cb92cf664f872d1d69c04140815b78734', # resourceproto-1.2.0.tar.gz - 'd8dee19c52977f65af08fad6aa237bacee11bc5a33e1b9b064e8ac1fd99d6e79', # scrnsaverproto-1.2.2.tar.gz - 'df8dfeb158767f843054248d020e291a2c40f7f5e0ac6d8706966686fee7c5c0', # videoproto-2.3.3.tar.gz - '48013cfbe4bd5580925a854a43e2bccbb4c7a5a31128070644617b6dc7f8ef85', # xcmiscproto-1.2.2.tar.gz - '1b1bcdf91221e78c6c33738667a57bd9aaa63d5953174ad8ed9929296741c9f5', # xextproto-7.3.0.tar.gz - 'd190e6462b2bbbac6ee9a007fb8eccb9ad9f5f70544154f388266f031d4bbb23', # xf86bigfontproto-1.2.0.tar.gz - '73bc6fc830cce5a0ec9c750d4702601fc0fca12d6353ede8b4c0092c9c4ca2af', # xf86dgaproto-2.1.tar.gz - '18ff8de129b89fa24a412a1ec1799f8687f96c186c655b44b1a714a3a5d15d6c', # xf86driproto-2.1.1.tar.gz - 'c3512b11cefa7558576551f8582c6e7071c8a24d78176059d94b84b48b262979', # xf86vidmodeproto-2.3.1.tar.gz - 'd99e121edf7b310008d7371ac5dbe3aa2810996d476b754dc78477cc26e5e7c1', # xineramaproto-1.2.1.tar.gz - '6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7', # xproto-7.0.31.tar.gz - '1f123d8304b082ad63a9e89376400a3b1d4c29e67e3ea07b3f659cccca690eea', # libXau-1.0.9.tar.gz - '6f7c7e491a23035a26284d247779174dedc67e34e93cc3548b648ffdb6fc57c0', # libXdmcp-1.1.2.tar.gz - '0698e8f596e4c0dbad71d3dc754d95eb0edbb42df5464e0f782621216fa33ba7', # xcb-proto-1.13.tar.gz - '0bb3cfd46dbd90066bf4d7de3cad73ec1024c7325a4a0cbf5f4a0d4fa91155fb', # libxcb-1.13.tar.gz - 'b7a577c1b6c75030145e53b4793db9c88f9359ac49e7d771d4385d21b3e5945d', # xtrans-1.3.5.tar.gz - '60ddcff932b7fd352752d51a5c4f04f3d0403230a584df9a2e0d5ed87c486c8b', # libxkbcommon-0.8.4.tar.xz - 'f62ab88c2a87b55e1dc338726a55bb6ed8048084fe6a3294a7ae324ca45159d1', # libX11-1.6.7.tar.gz - 'eb0b88050491fef4716da4b06a4d92b4fc9e76f880d6310b2157df604342cfe5', # libXext-1.3.3.tar.gz - 'e3da723257f4f4c0c629aec402e0a36fbec66a9418f70d24a159cb0470ec83d2', # libFS-1.0.8.tar.gz - '7812a824a66dd654c830d21982749b3b563d9c2dfe0b88b203cefc14a891edc0', # libICE-1.0.9.tar.gz - '1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320', # libSM-1.2.3.tar.gz - '4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a', # libXScrnSaver-1.2.3.tar.gz - 'b59bee38a9935565fa49dc1bfe84cb30173e2e07e1dcdf801430d4b54eb0caa3', # libXt-1.1.5.tar.gz - 'e5fd4bacef068f9509b8226017205040e38d3fba8d2de55037200e7176c13dba', # libXmu-1.1.2.tar.gz - '2523acc780eac01db5163267b36f5b94374bfb0de26fc0b5a7bee76649fd8501', # libXpm-3.5.12.tar.gz - '7e74ac3e5f67def549722ff0333d6e6276b8becd9d89615cda011e71238ab694', # libXaw-1.0.13.tar.gz - '9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570', # libXfixes-5.0.3.tar.gz - '581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c', # libXcomposite-0.4.5.tar.gz - '770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf', # libXrender-0.9.10.tar.gz - 'ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8', # libXcursor-1.2.0.tar.gz - '630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019', # libXdamage-1.1.5.tar.gz - '895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41', # libfontenc-1.1.4.tar.gz - '59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e', # libXfont-1.5.4.tar.gz - 'a4b761a37528353a2b83dba364d7c1fd6aef2d554a1a019815f24f7f8866890e', # libXfont2-2.0.3.tar.gz - '26cdddcc70b187833cbe9dc54df1864ba4c03a7175b2ca9276de9f05dce74507', # libXft-2.3.2.tar.gz - '463cc5370191404bc0f8a450fdbf6d9159efbbf274e5e0f427a60191fed9cf4b', # libXi-1.7.9.tar.gz - '64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18', # libXinerama-1.1.4.tar.gz - '2baa7fb3eca78fe7e11a09b373ba898b717f7eeba4a4bfd68187e04b4789b0d3', # libXrandr-1.5.1.tar.gz - '5b62feee09f276d74054787df030fceb41034de84174abec6d81c591145e043a', # libXres-1.2.0.tar.gz - 'a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2', # libXtst-1.2.3.tar.gz - 'c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1', # libXv-1.0.11.tar.gz - 'd8306f71c798d10409bb181b747c2644e1d60c05773c742c12304ab5aa5c8436', # libXvMC-1.0.10.tar.gz - 'e6361620a15ceba666901ca8423e8be0c6ed0271a7088742009160349173766b', # libXxf86dga-1.1.4.tar.gz - '5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99', # libXxf86vm-1.1.4.tar.gz - '4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925', # libdmx-1.1.4.tar.gz - '8d86e64893917be3dfb1c5e837888d1275399c818783474002203d751312b03c', # libpciaccess-0.14.tar.gz - '95df50570f38e720fb79976f603761ae6eff761613eb56f258c3cb6bab4fd5e3', # libxkbfile-1.0.9.tar.gz - '7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c', # libxshmfence-1.3.tar.gz - '0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7', # xcb-util-0.4.0.tar.gz - 'cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42', # xcb-util-image-0.4.0.tar.gz - '0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96', # xcb-util-keysyms-0.4.0.tar.gz - '55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5', # xcb-util-renderutil-0.3.9.tar.gz - '038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334', # xcb-util-wm-0.4.1.tar.gz - 'a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8', # xcb-util-cursor-0.1.3.tar.gz - '8d7e2aaa4e9d66843540e6ef3ebadf79d665d954bfa37d8829be428da6e08bbe', # xkeyboard-config-2.26.tar.gz - 'e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc', # printproto-1.0.5.tar.gz - 'f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c', # libXp-1.0.3.tar.gz - '27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265', # xbitmaps-1.1.2.tar.gz -] dependencies = [ ('bzip2', '1.0.6'), @@ -126,85 +48,11 @@ components = [ ('libpthread-stubs', '0.4', { # 2017-03-14 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], }), - ('bigreqsproto', '1.1.2', { # 2012-03-23 - 'checksums': ['de68a1a9dd1a1219ad73531bff9f662bc62fcd777387549c43cd282399f4a6ea'], - }), - ('compositeproto', '0.4.2', { # 2010-10-30 - 'checksums': ['22195b7e50036440b1c6b3b2d63eb03dfa6e71c8a1263ed1f07b0f31ae7dad50'], - }), - ('damageproto', '1.2.1', { # 2010-10-30 - 'checksums': ['f65ccbf1de9750a527ea6e85694085b179f2d06495cbdb742b3edb2149fef303'], - }), - ('dmxproto', '2.3.1', { # 2011-01-06 - 'checksums': ['3262bbf5902211a3ce88f5c6ab4528145ff84f69c52fd386ae0312bc45fb8a40'], - }), - ('dri2proto', '2.8', { # 2012-07-11 - 'checksums': ['7e65b031eaa6ebe23c75583d4abd993ded7add8009b4200a4db7aa10728b0f61'], - }), - ('dri3proto', '1.0', { # 2013-11-01 - 'checksums': ['e1a0dad3009ecde52c0bf44187df5f95cc9a7cc0e76dfc2f2bbf3e909fe03fa9'], - }), - ('fixesproto', '5.0', { # 2011-03-08 - 'checksums': ['67865a0e3cdc7dec1fd676f0927f7011ad4036c18eb320a2b41dbd56282f33b8'], - }), - ('fontsproto', '2.1.3', { # 2014-04-14 - 'checksums': ['72c44e63044b2b66f6fa112921621ecc20c71193982de4f198d9a29cda385c5e'], - }), - ('glproto', '1.4.17', { # 2013-12-10 - 'checksums': ['9d8130fec2b98bd032db7730fa092dd9dec39f3de34f4bb03ceb43b9903dbc96'], - }), - ('inputproto', '2.3.2', { # 2016-04-04 - 'checksums': ['10eaadd531f38f7c92ab59ef0708ca195caf3164a75c4ed99f0c04f2913f6ef3'], - }), - ('kbproto', '1.0.7', { # 2015-05-01 - 'checksums': ['828cb275b91268b1a3ea950d5c0c5eb076c678fdf005d517411f89cc8c3bb416'], - }), - ('presentproto', '1.1', { # 2017-01-26 - 'checksums': ['114252e97afb4dfae8b31e6b0d5e24e4babda26b364e2be57abc2f3c30248b87'], - }), - ('randrproto', '1.5.0', { # 2015-05-17 - 'checksums': ['8f8a716d6daa6ba05df97d513960d35a39e040600bf04b313633f11679006fab'], - }), - ('recordproto', '1.14.2', { # 2012-03-23 - 'checksums': ['485f792570dd7afe49144227f325bf2827bc7d87aae6a8ab6c1de2b06b1c68c5'], - }), - ('renderproto', '0.11.1', { # 2010-08-10 - 'checksums': ['a0a4be3cad9381ae28279ba5582e679491fc2bec9aab8a65993108bf8dbce5fe'], - }), - ('resourceproto', '1.2.0', { # 2011-05-28 - 'checksums': ['469029d14fdeeaa7eed1be585998ff4cb92cf664f872d1d69c04140815b78734'], - }), - ('scrnsaverproto', '1.2.2', { # 2012-03-23 - 'checksums': ['d8dee19c52977f65af08fad6aa237bacee11bc5a33e1b9b064e8ac1fd99d6e79'], - }), - ('videoproto', '2.3.3', { # 2016-03-11 - 'checksums': ['df8dfeb158767f843054248d020e291a2c40f7f5e0ac6d8706966686fee7c5c0'], - }), - ('xcmiscproto', '1.2.2', { # 2012-03-23 - 'checksums': ['48013cfbe4bd5580925a854a43e2bccbb4c7a5a31128070644617b6dc7f8ef85'], - }), - ('xextproto', '7.3.0', { # 2013-12-27 - 'checksums': ['1b1bcdf91221e78c6c33738667a57bd9aaa63d5953174ad8ed9929296741c9f5'], - }), - ('xf86bigfontproto', '1.2.0', { # 2009-08-27 - 'checksums': ['d190e6462b2bbbac6ee9a007fb8eccb9ad9f5f70544154f388266f031d4bbb23'], - }), - ('xf86dgaproto', '2.1', { # 2009-10-01 - 'checksums': ['73bc6fc830cce5a0ec9c750d4702601fc0fca12d6353ede8b4c0092c9c4ca2af'], - }), - ('xf86driproto', '2.1.1', { # 2011-01-06 - 'checksums': ['18ff8de129b89fa24a412a1ec1799f8687f96c186c655b44b1a714a3a5d15d6c'], - }), - ('xf86vidmodeproto', '2.3.1', { # 2011-01-06 - 'checksums': ['c3512b11cefa7558576551f8582c6e7071c8a24d78176059d94b84b48b262979'], - }), - ('xineramaproto', '1.2.1', { # 2011-01-06 - 'checksums': ['d99e121edf7b310008d7371ac5dbe3aa2810996d476b754dc78477cc26e5e7c1'], - }), - ('xproto', '7.0.31', { # 2016-09-23 - 'checksums': ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'], + ('xorgproto', '2018.4', { # 2018-02-28 + 'checksums': ['8e48d851efea0e951bcb6cf0d537f84ba3803de95e488bd039fe59fc75ec8f7d'], }), ('libXau', '1.0.9', { # 2019-02-10 + 'checksums': ['1f123d8304b082ad63a9e89376400a3b1d4c29e67e3ea07b3f659cccca690eea'], }), ('libXdmcp', '1.1.2', { # 2015-03-21 'checksums': ['6f7c7e491a23035a26284d247779174dedc67e34e93cc3548b648ffdb6fc57c0'], @@ -222,23 +70,26 @@ components = [ }), ('libxkbcommon', '0.8.4', { # 2019-02-22 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'checksums': ['60ddcff932b7fd352752d51a5c4f04f3d0403230a584df9a2e0d5ed87c486c8b'], 'start_dir': 'libxkbcommon-%(version)s', }), ('libX11', '1.6.7', { # 2018-10-09 - 'checksums': ['3abce972ba62620611fab5b404dafb852da3da54e7c287831c30863011d28fb3'], + 'checksums': ['f62ab88c2a87b55e1dc338726a55bb6ed8048084fe6a3294a7ae324ca45159d1'], }), ('libXext', '1.3.3', { # 2014-07-24 'checksums': ['eb0b88050491fef4716da4b06a4d92b4fc9e76f880d6310b2157df604342cfe5'], }), ('libFS', '1.0.8', { # 2019-03-10 - 'checksums': ['91bf1c5ce4115b7dbf4e314fdbee54052708e8f7b6a2ec6e82c309bcbe40ef3d'], + 'checksums': ['e3da723257f4f4c0c629aec402e0a36fbec66a9418f70d24a159cb0470ec83d2'], }), ('libICE', '1.0.9', { # 2014-06-07 'checksums': ['7812a824a66dd654c830d21982749b3b563d9c2dfe0b88b203cefc14a891edc0'], }), ('libSM', '1.2.3', { # 2018-10-10 + 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], }), ('libXScrnSaver', '1.2.3', { # 2018-07-05 + 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], }), ('libXt', '1.1.5', { # 2015-05-01 'checksums': ['b59bee38a9935565fa49dc1bfe84cb30173e2e07e1dcdf801430d4b54eb0caa3'], @@ -256,15 +107,19 @@ components = [ 'checksums': ['9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570'], }), ('libXcomposite', '0.4.5', { # 2019-03-11 + 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], }), ('libXrender', '0.9.10', { # 2016-10-04 'checksums': ['770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf'], }), ('libXcursor', '1.2.0', { # 2019-03-11 + 'checksums': ['ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8'], }), ('libXdamage', '1.1.5', { # 2019-03-11 + 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], }), ('libfontenc', '1.1.4', { # 2019-02-20 + 'checksums': ['895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41'], }), ('libXfont', '1.5.4', { # 2017-11-28 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], @@ -279,7 +134,7 @@ components = [ 'checksums': ['463cc5370191404bc0f8a450fdbf6d9159efbbf274e5e0f427a60191fed9cf4b'], }), ('libXinerama', '1.1.4', { # 2018-07-05 - 'checksums': ['0ba243222ae5aba4c6a3d7a394c32c8b69220a6872dbb00b7abae8753aca9a44'], + 'checksums': ['64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18'], }), ('libXrandr', '1.5.1', { # 2016-10-04 'checksums': ['2baa7fb3eca78fe7e11a09b373ba898b717f7eeba4a4bfd68187e04b4789b0d3'], @@ -333,14 +188,13 @@ components = [ 'checksums': ['a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8'], }), ('xkeyboard-config', '2.26', { # 2019-02-02 - }), - ('printproto', '1.0.5', { # 2011-01-06 - 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + 'checksums': ['8d7e2aaa4e9d66843540e6ef3ebadf79d665d954bfa37d8829be428da6e08bbe'], }), ('libXp', '1.0.3', { # 2015-02-21 'checksums': ['f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c'], }), ('xbitmaps', '1.1.2', { # 2018-03-10 + 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], }), ] From 22f6a75fb90bcd8d13402934dde64a4cd22500e9 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 13 Mar 2019 20:40:08 +0200 Subject: [PATCH 0860/5331] Include printproto again as it didn't build without --- easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb index 005c39171fc..088b8369cbb 100644 --- a/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb @@ -190,6 +190,9 @@ components = [ ('xkeyboard-config', '2.26', { # 2019-02-02 'checksums': ['8d7e2aaa4e9d66843540e6ef3ebadf79d665d954bfa37d8829be428da6e08bbe'], }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), ('libXp', '1.0.3', { # 2015-02-21 'checksums': ['f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c'], }), From 1505300a3231b7d85b180e62c33decac055f786b Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 13 Mar 2019 13:20:23 -0700 Subject: [PATCH 0861/5331] Postgres 10.3 foss 2018b - Clean No Perl or Python --- .../PostgreSQL/PostgreSQL-10.3-foss-2018b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-10.3-foss-2018b.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-10.3-foss-2018b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-10.3-foss-2018b.eb new file mode 100644 index 00000000000..76f14bc368b --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-10.3-foss-2018b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '10.3' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational + database system. It is fully ACID compliant, has full support for foreign + keys, joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, + CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of + binary large objects, including pictures, sounds, or video. It has native + programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, + among others, and exceptional documentation.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['87584285af8c5fd6e599b4d9789f455f8cd55759ed81a9e575ebaebc7a03e796'] + +dependencies = [ + ('libreadline', '7.0'), + ('zlib', '1.2.11'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.4'), +] + +configopts = ' --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' From 38a26eaae9eda07830e70f424bb5683ff641dd63 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Mar 2019 15:48:00 -0500 Subject: [PATCH 0862/5331] Add missing pkgconfig --- ...kgconfig-1.2.2-foss-2017b-Python-2.7.14.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..05a89d482df --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3685ba02a9b72654a764b728b559f327e1dbd7dc6ebc310a1bd429666ee202aa'] + +dependencies = [ + ('Python', '2.7.14'), + ('pkg-config', '0.29.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'devel' From bd610840f0e5f987ed15792bae3c01854bab0629 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Mar 2019 15:50:52 -0500 Subject: [PATCH 0863/5331] Use pip for existing pkgconfig --- .../p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-3.6.3.eb | 3 +++ .../p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-2.7.14.eb | 3 +++ .../p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-3.6.3.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-3.6.3.eb index c8aacfeff42..0541ac57e11 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-foss-2017b-Python-3.6.3.eb @@ -19,6 +19,9 @@ dependencies = [ ('pkg-config', '0.29.2'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-2.7.14.eb index c5a488bfbe0..e0c07d8bde6 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-2.7.14.eb @@ -19,6 +19,9 @@ dependencies = [ ('pkg-config', '0.29.2'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-3.6.3.eb index 7ea38e5e571..86f7de3311a 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.2.2-intel-2017b-Python-3.6.3.eb @@ -19,6 +19,9 @@ dependencies = [ ('pkg-config', '0.29.2'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], From 2ad4e8fee5424c2ed71e0201487dae1780e28a6a Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 13 Mar 2019 15:51:55 -0500 Subject: [PATCH 0864/5331] Corrected order --- .../h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb | 8 ++++---- .../h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb | 8 ++++---- .../h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb | 8 ++++---- .../h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb | 8 ++++---- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb index 25b1d68cb54..da90cccec5c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-2.7.14.eb @@ -16,16 +16,16 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] -# To really use mpi enabled hdf5 we now seem to need a configure step -# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html -preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - dependencies = [ ('Python', '2.7.14'), ('HDF5', '1.10.1'), ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), ] +# To really use mpi enabled hdf5 we now seem to need a configure step +# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + use_pip = True download_dep_fail = True diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb index cadc0900f29..7aaecb0ed9a 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-foss-2017b-Python-3.6.3.eb @@ -16,16 +16,16 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] -# To really use mpi enabled hdf5 we now seem to need a configure step -# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html -preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - dependencies = [ ('Python', '3.6.3'), ('HDF5', '1.10.1'), ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), ] +# To really use mpi enabled hdf5 we now seem to need a configure step +# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + use_pip = True download_dep_fail = True diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb index 6a30d279da7..6afc1986df9 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-2.7.14.eb @@ -16,16 +16,16 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] -# To really use mpi enabled hdf5 we now seem to need a configure step -# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html -preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - dependencies = [ ('Python', '2.7.14'), ('HDF5', '1.10.1'), ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), ] +# To really use mpi enabled hdf5 we now seem to need a configure step +# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + use_pip = True download_dep_fail = True diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb index e407a9389b7..7331785ea92 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.7.1-intel-2017b-Python-3.6.3.eb @@ -16,16 +16,16 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['180a688311e826ff6ae6d3bda9b5c292b90b28787525ddfcb10a29d5ddcae2cc'] -# To really use mpi enabled hdf5 we now seem to need a configure step -# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html -preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - dependencies = [ ('Python', '3.6.3'), ('HDF5', '1.10.1'), ('pkgconfig', '1.2.2', '-Python-%(pyver)s'), ] +# To really use mpi enabled hdf5 we now seem to need a configure step +# Works with pip. Tested with examples in http://docs.h5py.org/en/stable/mpi.html +preinstallopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + use_pip = True download_dep_fail = True From 70b87eb5e68de126e700d3b9a8922a3f179e0093 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 13 Mar 2019 23:44:57 +0200 Subject: [PATCH 0865/5331] adding easyconfigs: DBus-1.13.8-GCCcore-8.2.0.eb --- .../d/DBus/DBus-1.13.8-GCCcore-8.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.13.8-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.8-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..2e4a146618e --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.8-GCCcore-8.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.13.8' + +homepage = 'http://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['82a89f64e1b55e459725186467770995f33cac5eb8a050b5d8cbeb338078c4f6'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('expat', '2.2.6'), +] + +configopts = '--without-systemdsystemunitdir' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' From 47c1a2e180c7371c37e1a09333593f6f0843135e Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 13 Mar 2019 17:43:55 -0500 Subject: [PATCH 0866/5331] adding easyconfigs: GATE-8.0-foss-2017b-Python-2.7.14.eb --- .../GATE/GATE-8.0-foss-2017b-Python-2.7.14.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATE/GATE-8.0-foss-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/g/GATE/GATE-8.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GATE/GATE-8.0-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..336062edfd8 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-8.0-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,27 @@ +name = 'GATE' +version = '8.0' +versionsuffix = '-Python-2.7.14' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://www.opengatecollaboration.org/sites/default/files/'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] +patches = ['GATE-7.0_Makefile-prefix.patch'] +checksums = [ + '09f62d6fc7db9997379ffbdacfa4f8f7853a602ec06e20c50494ffeb05d2e416', # gate_v8.0.tar.gz + 'e72c230df1cdd05c07ac405b22bf26931abdcd3e5f7b942e9c88251ac24cc6af', # GATE-7.0_Makefile-prefix.patch +] + +builddependencies = [('CMake', '3.9.5')] +dependencies = [ + ('Geant4', '10.03.p03'), + ('CLHEP', '2.3.4.3'), + ('ROOT', '6.10.08', versionsuffix), +] + +moduleclass = 'cae' From a7b91907d1c2bc31f303d9a15f4224ab54fd8eac Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 14 Mar 2019 00:59:18 +0200 Subject: [PATCH 0867/5331] adding easyconfigs: NSS-3.42.1-GCCcore-8.2.0.eb, NSPR-4.21-GCCcore-8.2.0.eb --- .../n/NSPR/NSPR-4.21-GCCcore-8.2.0.eb | 28 ++++++++++++ .../n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb | 43 +++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.21-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.21-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.21-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..5b5b3b399a2 --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.21-GCCcore-8.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.21' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://archive.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['15ea32c7b100217b6e3193bc03e77f485d9bf7504051443ba9ce86d1c17c6b5a'] + +builddependencies = [('binutils', '2.31.1')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..165b3e41cc6 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.42.1' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_1_RTM/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['NSS-3.39_pkgconfig.patch'] +checksums = [ + '087db37d38fd49dfd584dd2a8b5baa7fc88de7c9bd97c0c2d5be4abcafc61fc6', # nss-3.42.1.tar.gz + '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch +] + +builddependencies = [('binutils', '2.31.1')] +dependencies = [ + ('NSPR', '4.21'), + ('zlib', '1.2.11'), +] + +# building in parallel fails +parallel = 1 + +# fix for not being able to find header files +buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['lib/libnss.a'], + 'dirs': ['bin', 'include/dbm', 'include/nss'], +} + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' From 264248df113ba4220f98af4fee3a14cbd240f737 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 14 Mar 2019 01:19:35 +0200 Subject: [PATCH 0868/5331] adding easyconfigs: git-2.21.0-GCCcore-8.2.0.eb --- .../g/git/git-2.21.0-GCCcore-8.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.21.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/git/git-2.21.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/git/git-2.21.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..089e77d8460 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.21.0-GCCcore-8.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.21.0' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7a601275abcc6ff51cc79a6d402e83c90ae37d743b0b8d073aa009dd4b22d432'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Autotools', '20180311'), +] +dependencies = [ + ('cURL', '7.63.0'), + ('expat', '2.2.6'), + ('gettext', '0.19.8.1'), + ('Perl', '5.28.1'), +] + +# asciidoc and xmlto are required for git man/doc build +osdependencies = ['asciidoc', 'xmlto'] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +# required to also install documentation +buildopts = "doc" +installopts = "install-doc" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['share/man'], +} + +moduleclass = 'tools' From 16b5223887e9b23d5d2ba43c4974cf6ca8437729 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 14 Mar 2019 01:26:47 +0200 Subject: [PATCH 0869/5331] adding easyconfigs: GLPK-4.65-GCCcore-8.2.0.eb --- .../g/GLPK/GLPK-4.65-GCCcore-8.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..03deab2b890 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-4.65-GCCcore-8.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '4.65' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4281e29b628864dfe48d393a7bedd781e5b475387c20d8b0158f329994721a10'] + +builddependencies = [('binutils', '2.31.1')] +dependencies = [('GMP', '6.1.2')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' From 0786affff957508f405429aad4b5ac8b915bf2e6 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 14 Mar 2019 01:34:07 +0200 Subject: [PATCH 0870/5331] adding easyconfigs: FriBidi-1.0.5-GCCcore-8.2.0.eb --- .../f/FriBidi/FriBidi-1.0.5-GCCcore-8.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..952a02c3f63 --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.2.0.eb @@ -0,0 +1,35 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.5' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +# https://github.com/fribidi/fribidi/releases/download/v1.0.2/fribidi-1.0.2.tar.bz2 +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6a64f2a687f5c4f203a46fa659f43dd43d1f8b845df8d723107e8a7e6158e4ce'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +configopts = '--disable-docs' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' From 1ebbabef903ea857371e7ccad0794e0b29796ff6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 10:19:24 +0100 Subject: [PATCH 0871/5331] stick to intervaltree 2.1.0 as required extension for VCF-kit + fix stripping out of hardcoded versions for dependencies --- .../v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb index 093d5479d1f..2143c42d364 100644 --- a/easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/v/VCF-kit/VCF-kit-0.1.6-intel-2018b-Python-2.7.15.eb @@ -41,9 +41,9 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], }), - ('intervaltree', '3.0.2', { + ('intervaltree', '2.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/i/intervaltree'], - 'checksums': ['cb4f61c81dcb4fea6c09903f3599015a83c9bdad1f0bbd232495e6681e19e273'], + 'checksums': ['aca5804b88f70cb49050c37b6de59090570f77a75aec1932966cf69f6a48810b'], }), ('args', '0.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/args'], @@ -78,8 +78,7 @@ exts_list = [ (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/V/VCF-kit'], 'checksums': ['e44319bc057ff4f90cc3a777bb6b1794e5dc3dcf56fe2753fee199f782fed6b6'], - # get rid of hardcoded versions for dependencies - 'prebuildopts': "sed -i 's/==[0-9.]*//g' requirements.txt && ", + 'preinstallopts': "sed -i 's/==[0-9.]*//g' requirements.txt && ", 'modulename': 'vcfkit', }), ] @@ -89,4 +88,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["vk --help"] + moduleclass = 'bio' From b30e1ee5af9db1562ffcf834d45567c29b410224 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 11:07:16 +0100 Subject: [PATCH 0872/5331] adding easyconfigs: PGI-19.1-GCC-8.2.0-2.31.1.eb --- .../p/PGI/PGI-19.1-GCC-8.2.0-2.31.1.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PGI/PGI-19.1-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/p/PGI/PGI-19.1-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/p/PGI/PGI-19.1-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..72262bb10c0 --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-19.1-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '19.1' + +homepage = 'http://www.pgroup.com/' +description = "C, C++ and Fortran compilers from The Portland Group - PGI" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86-64.tar.gz'] +checksums = ['3e05a6db2bf80b5d15f6ff83188f20cb89dc23e233417921e5c0822e7e57d34f'] + +gccver = '8.2.0' +binutilsver = '2.31.1' +versionsuffix = '-GCC-%s-%s' % (gccver, binutilsver) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '', ('GCCcore', gccver)), + ('numactl', '2.0.12', '', ('GCCcore', gccver)), +] + +# license file +license_file = HOME + '/licenses/pgi/license.dat' + +moduleclass = 'compiler' From 7d4aaf1febc8c09cb279b1a043216771c084b33c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 11:30:07 +0100 Subject: [PATCH 0873/5331] adding easyconfigs: slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb --- ...gwindow-0.0.13-intel-2018b-Python-3.6.6.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..b107852e5ce --- /dev/null +++ b/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'slidingwindow' +version = '0.0.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/adamrehn/slidingwindow' +description = """slidingwindow is a simple little Python library for computing a set of windows into a larger dataset, + designed for use with image-processing algorithms that utilise a sliding window to break the processing up + into a series of smaller chunks.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [('Python', '3.6.6')] + +#use_pip = True + +exts_list = [ + ('psutil', '5.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], + }), + (name, version, { + 'source_urls': ['https://github.com/adamrehn/slidingwindow/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['8be4df997c1659226201db89610488bb4f85e08811b7cc1775a83e9499b09c82'], + }), +] + +moduleclass = 'data' From 6b4c99c14052cf611e738417c8791ad03f04090b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 11:57:07 +0100 Subject: [PATCH 0874/5331] enable use_pip in easyconfig for slidingwindow --- .../slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb index b107852e5ce..06a7ce25c3a 100644 --- a/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-3.6.6.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} dependencies = [('Python', '3.6.6')] -#use_pip = True +use_pip = True exts_list = [ ('psutil', '5.6.1', { From ee72efe22019a60eb9082d4330826c40a35bdac1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 12:00:26 +0100 Subject: [PATCH 0875/5331] fix typo in comment in pplacer easyconfig --- easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb index 28d3bf694be..add3919aeec 100644 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb @@ -10,7 +10,7 @@ description = """Pplacer places query sequences on a fixed reference phylogeneti toolchain = {'name': 'dummy', 'version': ''} -# compiler pplacer from source requires an ancient OCaml version, +# compiling pplacer from source requires an ancient OCaml version, # which is a huge PITA with recent compilers # cfr. http://matsen.github.io/pplacer/compiling.html # so we use the recommended pre-built binaries instead... From 25b22f655453a48078c1ed82268cf90ac8492ce9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 13:17:20 +0100 Subject: [PATCH 0876/5331] whitelist missing checksums for OCaml, since extensions are auto-downloaded on installation by OPAM (for now) --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c0129534add..ff5c9261f55 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -340,7 +340,7 @@ def check_sha256_checksums(self, changed_ecs): # list of software for which checksums can not be required, # e.g. because 'source' files need to be constructed manually - whitelist = ['Kent_tools-*', 'MATLAB-*'] + whitelist = ['Kent_tools-*', 'MATLAB-*', 'OCaml-*'] # the check_sha256_checksums function (again) creates an EasyBlock instance # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter From c6ba6956157507541195ed77453058f17301c548 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 13:39:22 +0100 Subject: [PATCH 0877/5331] add missing Perl dep in CD-Hit 4.6.8 easyconfigs --- easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-foss-2018b.eb | 2 ++ easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2017a.eb | 2 ++ easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2018a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-foss-2018b.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-foss-2018b.eb index 63b2706742c..55cd0c78024 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-foss-2018b.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-foss-2018b.eb @@ -16,6 +16,8 @@ source_urls = ['https://github.com/weizhongli/cdhit/archive/'] sources = ['V%(version)s.tar.gz'] checksums = ['37d685e4aa849314401805fe4d4db707e1d06070368475e313d6f3cb8fb65949'] +dependencies = [('Perl', '5.28.0')] + # make sure compilation flags are passed down (e.g. to enable OpenMP) buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2017a.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2017a.eb index 4985a93e269..57f60dd797f 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2017a.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2017a.eb @@ -16,6 +16,8 @@ source_urls = ['https://github.com/weizhongli/cdhit/archive/'] sources = ['V%(version)s.tar.gz'] checksums = ['37d685e4aa849314401805fe4d4db707e1d06070368475e313d6f3cb8fb65949'] +dependencies = [('Perl', '5.24.1')] + # make sure compilation flags are passed down (e.g. to enable OpenMP) buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2018a.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2018a.eb index 0037242748d..e8a98a39346 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2018a.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.6.8-intel-2018a.eb @@ -16,6 +16,8 @@ source_urls = ['https://github.com/weizhongli/cdhit/archive/'] sources = ['V%(version)s.tar.gz'] checksums = ['37d685e4aa849314401805fe4d4db707e1d06070368475e313d6f3cb8fb65949'] +dependencies = [('Perl', '5.26.1')] + # make sure compilation flags are passed down (e.g. to enable OpenMP) buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' From d4b7cd12a2c1c5c726589b9c914faad73a0cd197 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Thu, 14 Mar 2019 15:09:39 +0200 Subject: [PATCH 0878/5331] adding easyconfigs: astropy-2.0.12-foss-2018b-Python-2.7.15.eb, astropy-2.0.12-intel-2018b-Python-2.7.15.eb --- ...astropy-2.0.12-foss-2018b-Python-2.7.15.eb | 66 +++++++++++++++++++ ...stropy-2.0.12-intel-2018b-Python-2.7.15.eb | 66 +++++++++++++++++++ 2 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-2.0.12-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/a/astropy/astropy-2.0.12-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-2.0.12-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/astropy/astropy-2.0.12-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..dd72f1b5271 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-2.0.12-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '2.0.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), + ('future', '0.16.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('py', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/py/'], + 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], + }), + ('atomicwrites', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/A/atomicwrites/'], + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], + }), + ('more-itertools', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/more-itertools/'], + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + ('pluggy', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/P/pluggy/'], + 'checksums': ['95eb8364a4708392bae89035f45341871286a333f749c3141c20573d2b3876e1'], + }), + ('attrs', '19.1.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/A/attrs/'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], + }), + ('pytest', '3.6.4', { + 'source_urls': ['https://pypi.python.org/packages/source/P/pytest/'], + 'checksums': ['341ec10361b64a24accaec3c7ba5f7d5ee1ca4cebea30f76fad3dd12db9f0541'], + }), + ('astropy-helpers', '2.0.9', { + 'source_urls': ['https://pypi.python.org/packages/source/A/astropy-helpers/'], + 'checksums': ['3bb4c3b85f5778a3f727e72b5d2243f567d57b28761ebaab71ee8c7ee9c9d0e8'], + }), + (name, version, { + 'patches': ['astropy-ah_no_auto_use.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/A/astropy/'], + 'checksums': [ + '81bae35320d7c72ae8569eeabc596e3a5ed416249b3fb2de9b40f30673085d0b', # astropy-2.0.12.tar.gz + 'fb339ff90fff8ed760b5ea9b8b65be3babb355f956a5588fd7e2e2656b4a7ca8', # astropy_ah_no_auto_use.patch + ], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], +} + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/a/astropy/astropy-2.0.12-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/astropy/astropy-2.0.12-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..11b78a048e5 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-2.0.12-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '2.0.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), + ('future', '0.16.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('py', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/py/'], + 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], + }), + ('atomicwrites', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/A/atomicwrites/'], + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], + }), + ('more-itertools', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/more-itertools/'], + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + ('pluggy', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/P/pluggy/'], + 'checksums': ['95eb8364a4708392bae89035f45341871286a333f749c3141c20573d2b3876e1'], + }), + ('attrs', '19.1.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/A/attrs/'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], + }), + ('pytest', '3.6.4', { + 'source_urls': ['https://pypi.python.org/packages/source/P/pytest/'], + 'checksums': ['341ec10361b64a24accaec3c7ba5f7d5ee1ca4cebea30f76fad3dd12db9f0541'], + }), + ('astropy-helpers', '2.0.9', { + 'source_urls': ['https://pypi.python.org/packages/source/A/astropy-helpers/'], + 'checksums': ['3bb4c3b85f5778a3f727e72b5d2243f567d57b28761ebaab71ee8c7ee9c9d0e8'], + }), + (name, version, { + 'patches': ['astropy-ah_no_auto_use.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/A/astropy/'], + 'checksums': [ + '81bae35320d7c72ae8569eeabc596e3a5ed416249b3fb2de9b40f30673085d0b', # astropy-2.0.12.tar.gz + 'fb339ff90fff8ed760b5ea9b8b65be3babb355f956a5588fd7e2e2656b4a7ca8', # astropy_ah_no_auto_use.patch + ], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], +} + +moduleclass = 'astro' From 4ed0e95709f092205db727447ea2dee3136c2066 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 14:34:33 +0100 Subject: [PATCH 0879/5331] enhance sanity check for DAS_Tool --- .../DAS_Tool/DAS_Tool-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb index 166fefe7cc4..818759d8e1f 100644 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2018b-R-3.5.1-Python-2.7.15.eb @@ -40,7 +40,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['DAS_Tool'], + 'files': ['DAS_Tool', 'arc.all.faa', 'arc.scg.lookup'], 'dirs': ['DASTool/R'], } From 098f124b65cef0e3b9393b01d10d8c5ed6077d01 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Thu, 14 Mar 2019 15:01:13 +0100 Subject: [PATCH 0880/5331] +patch for proper handling of astropy-helpers --- .../a/astropy/astropy-ah_no_auto_use.patch | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-ah_no_auto_use.patch diff --git a/easybuild/easyconfigs/a/astropy/astropy-ah_no_auto_use.patch b/easybuild/easyconfigs/a/astropy/astropy-ah_no_auto_use.patch new file mode 100644 index 00000000000..51b8d133c0b --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-ah_no_auto_use.patch @@ -0,0 +1,17 @@ +# this patch avoids downloading astropy-helpers by astropy installer, +# failing in EasyBuild. Instead, we download astropy-helpers as a part +# of the bundle. +# +# - 14.3.2019, J. Dvoracek (Institute of Physics | Czech Academy of Sciences, www.fzu.cz +# +--- ./setup.cfg.orig 2019-03-13 18:46:28.060712000 +0100 ++++ ./setup.cfg 2019-03-13 18:46:36.431744000 +0100 +@@ -26,7 +26,7 @@ + bitmap = static/wininst_background.bmp + + [ah_bootstrap] +-auto_use = True ++auto_use = False + + [flake8] + exclude = extern,*parsetab.py,*lextab.py From 8dce0f7310d6a42a605a1b1cc0f6823c4c2eebd6 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Thu, 14 Mar 2019 17:09:23 +0200 Subject: [PATCH 0881/5331] exts_list updated, sync with #7647 --- ...thon-5.8.0-fosscuda-2018b-Python-2.7.15.eb | 244 ++++++++++++++++++ ...IPython-5.8.0-intel-2018b-Python-2.7.15.eb | 4 + 2 files changed, 248 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..17052e37bc5 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,244 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '5.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), + ('ZeroMQ', '4.2.5'), + ('matplotlib', '2.2.3', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('Pygments', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], + }), + ('ipython_genutils', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], + }), + ('certifi', '2018.11.29', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + }), + ('pexpect', '4.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], + }), + ('scandir', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], + }), + ('pathlib2', '2.3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], + }), + ('pickleshare', '0.7.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('wcwidth', '0.1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + }), + ('prompt_toolkit', '1.0.15', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], + 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], + }), + ('ptyprocess', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('traitlets', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], + }), + ('parso', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], + 'checksums': ['68406ebd7eafe17f8e40e15a84b56848eccbf27d7c1feb89e93d8fca395706db'], + }), + ('jedi', '0.13.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], + 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], + }), + ('testpath', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], + 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('configparser', '3.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], + 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], + }), + ('defusedxml', '0.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], + 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], + }), + ('nbconvert', '5.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], + }), + ('nbformat', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], + }), + ('MarkupSafe', '1.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('ipywidgets', '7.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + 'checksums': ['a3e224f430163f767047ab9a042fc55adbcab0c24bbe6cf9f306c4f89fdf0ba3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('Send2Trash', '1.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], + 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], + }), + ('webencodings', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], + 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], + }), + ('bleach', '3.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], + 'checksums': ['3fdf7f77adcf649c9911387df51254b813185e32b2c6619f690b593a617e19fa'], + }), + ('pyrsistent', '0.14.11', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyrsistent/'], + 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), + ('attrs', '19.1.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], + }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], + }), + ('jsonschema', '3.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], + }), + ('pandocfilters', '1.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], + }), + ('pyzmq', '18.0.0', { + 'modulename': 'zmq', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], + 'checksums': ['b30c339eb58355f51f4f54dd61d785f1ff58c86bca1c3a5916977631d121867b'], + }), + ('entrypoints', '0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('jupyter_core', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], + }), + ('mistune', '0.8.4', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('terminado', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], + }), + ('futures', '3.2.0', { + 'modulename': 'concurrent.futures', + 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], + 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], + }), + ('tornado', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], + }), + ('jupyter_client', '5.2.4', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + 'checksums': ['b5f9cb06105c1d2d30719db5ffb3ea67da60919fb68deaefa583deccd8813551'], + }), + ('backcall', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], + 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], + }), + ('ipykernel', '4.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + 'checksums': ['699103c8e64886e3ec7053f2a6aa83bb90426063526f63a818732ff385202bad'], + }), + ('prometheus_client', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], + 'checksums': ['1b38b958750f66f208bcd9ab92a633c0c994d8859c831f7abc1f46724fcee490'], + }), + ('notebook', '5.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + 'checksums': ['d908673a4010787625c8952e91a22adf737db031f2aa0793ad92f6558918a74a'], + }), + ('widgetsnbextension', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + 'checksums': ['fa618be8435447a017fd1bf2c7ae922d0428056cfc7449f7a8641edf76b48265'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "iptest", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb index ad97fad0c41..2d0c1c43dba 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb @@ -150,6 +150,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], + }), ('jsonschema', '3.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], From c2fa0b36724d5b4cb59dd60424ec074a911809dc Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Thu, 14 Mar 2019 17:24:41 +0100 Subject: [PATCH 0882/5331] updated versions, sanity_checks, removed modextrapaths --- ...thon-5.8.0-fosscuda-2018b-Python-2.7.15.eb | 81 ++++++++++++------- 1 file changed, 50 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb index f72df2c79b5..17052e37bc5 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb @@ -23,9 +23,9 @@ dependencies = [ use_pip = True exts_list = [ - ('Pygments', '2.2.0', { + ('Pygments', '2.3.1', { 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], - 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], + 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], }), ('ipython_genutils', '0.2.0', { 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], @@ -36,6 +36,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), + ('certifi', '2018.11.29', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + }), ('pexpect', '4.6.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], @@ -44,9 +48,9 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], }), - ('pathlib2', '2.3.2', { + ('pathlib2', '2.3.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], - 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], + 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), ('pickleshare', '0.7.5', { 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], @@ -73,9 +77,9 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], }), - ('parso', '0.3.1', { + ('parso', '0.3.4', { 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], - 'checksums': ['35704a43a3c113cce4de228ddb39aab374b8004f4f2407d070b6a2ca784ce8a2'], + 'checksums': ['68406ebd7eafe17f8e40e15a84b56848eccbf27d7c1feb89e93d8fca395706db'], }), ('jedi', '0.13.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], @@ -97,17 +101,21 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], }), - ('nbconvert', '5.4.0', { + ('nbconvert', '5.4.1', { 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - 'checksums': ['a8a2749f972592aa9250db975304af6b7337f32337e523a2c995cc9e12c07807'], + 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], }), ('nbformat', '4.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), - ('MarkupSafe', '1.0', { + ('MarkupSafe', '1.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], - 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('ipywidgets', '7.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + 'checksums': ['a3e224f430163f767047ab9a042fc55adbcab0c24bbe6cf9f306c4f89fdf0ba3'], }), ('Jinja2', '2.10', { 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], @@ -125,43 +133,48 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], }), - ('bleach', '3.0.2', { + ('bleach', '3.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], - 'checksums': ['48d39675b80a75f6d1c3bdbffec791cf0bbbab665cf01e20da701c77de278718'], + 'checksums': ['3fdf7f77adcf649c9911387df51254b813185e32b2c6619f690b593a617e19fa'], + }), + ('pyrsistent', '0.14.11', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyrsistent/'], + 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], }), ('functools32', '3.2.3-2', { 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), + ('attrs', '19.1.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], + }), ('vcversioner', '2.16.0.0', { 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], }), - ('jsonschema', '2.6.0', { + ('jsonschema', '3.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], + 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], }), ('pandocfilters', '1.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], }), - ('pyzmq', '17.1.2', { + ('pyzmq', '18.0.0', { 'modulename': 'zmq', 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], - 'checksums': ['a72b82ac1910f2cf61a49139f4974f994984475f771b0faa730839607eeedddf'], + 'checksums': ['b30c339eb58355f51f4f54dd61d785f1ff58c86bca1c3a5916977631d121867b'], }), - ('entrypoints', '0.2.3', { + ('entrypoints', '0.3', { 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], - 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), ('jupyter_core', '4.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), - ('jupyter_client', '5.2.3', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], - 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], - }), ('mistune', '0.8.4', { 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], @@ -191,26 +204,32 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), + ('jupyter_client', '5.2.4', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + 'checksums': ['b5f9cb06105c1d2d30719db5ffb3ea67da60919fb68deaefa583deccd8813551'], + }), ('backcall', '0.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], }), - ('prometheus_client', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], - 'checksums': ['046cb4fffe75e55ff0e6dfd18e2ea16e54d86cc330f369bebcc683475c8b68a9'], - }), ('ipykernel', '4.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], 'checksums': ['699103c8e64886e3ec7053f2a6aa83bb90426063526f63a818732ff385202bad'], }), - ('notebook', '5.7.0', { + ('prometheus_client', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], + 'checksums': ['1b38b958750f66f208bcd9ab92a633c0c994d8859c831f7abc1f46724fcee490'], + }), + ('notebook', '5.7.4', { 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], - 'checksums': ['b85e4de3d54cf4f14fe1d0515a980ccb49ddd4cdd21250cc0d4fb6374d50b1a7'], + 'checksums': ['d908673a4010787625c8952e91a22adf737db031f2aa0793ad92f6558918a74a'], + }), + ('widgetsnbextension', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + 'checksums': ['fa618be8435447a017fd1bf2c7ae922d0428056cfc7449f7a8641edf76b48265'], }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], @@ -218,7 +237,7 @@ sanity_check_paths = { sanity_check_commands = [ "ipython -h", - "ipython notebook --help", + "jupyter notebook --help", "iptest", ] From 23f92f2da701f83339fa9ac18646b382ab687e3e Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Thu, 14 Mar 2019 17:28:15 +0100 Subject: [PATCH 0883/5331] adding easyconfigs: CUDA-10.1.105.eb --- easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb new file mode 100644 index 00000000000..b04b0274996 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb @@ -0,0 +1,18 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +name = 'CUDA' +version = '10.1.105' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] +sources = ['%(namelower)s_%(version)s_418.39_linux.run'] + +moduleclass = 'system' From 86d69eba410517e718c5fa14f4bdbc0b4f5c4bf0 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 14 Mar 2019 11:41:20 -0500 Subject: [PATCH 0884/5331] Removed redundant and obsolete parts --- .../matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb | 11 ++++------- .../matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb | 5 ----- .../matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb | 5 ----- .../matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb | 5 ----- 4 files changed, 4 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb index ac87ee91e7c..b49e9160930 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb @@ -45,13 +45,10 @@ exts_list = [ }), ] -# specify that PythonBundle easyblock should run a full sanity check, rather than just trying to load the module -full_sanity_check = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} +#sanity_check_paths = { +# 'files': [], +# 'dirs': [], +#} sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb index b8628e29dab..21c2041da1c 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-3.6.3.eb @@ -37,11 +37,6 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb index 0ef0b93950c..397c47c2b67 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-2.7.14.eb @@ -41,11 +41,6 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb index b732dd8e6e4..015c530a04f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-intelcuda-2017b-Python-3.6.3.eb @@ -33,11 +33,6 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] moduleclass = 'vis' From 5a286477ae4c2b025e70457fb0eb5401f9c172ae Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Thu, 14 Mar 2019 18:02:17 +0100 Subject: [PATCH 0885/5331] Checksum added --- easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb index b04b0274996..5653d0295c0 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb @@ -14,5 +14,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] sources = ['%(namelower)s_%(version)s_418.39_linux.run'] +checksums = ['33ac60685a3e29538db5094259ea85c15906cbd0f74368733f4111eab6187c8f'] moduleclass = 'system' From cb27ac5d57713c42bee8f9c67611373725084c93 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 14 Mar 2019 19:09:04 +0200 Subject: [PATCH 0886/5331] Update GStreamer to not enable dw and fix some missing dependencies. --- .../g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb index 154e2541f1f..0a975f2473e 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.15.1-fosscuda-2018b.eb @@ -17,14 +17,20 @@ checksums = ['780ae2347f9780fea264a602a7c04a87a43998188e7bd9c59afb4d7c864f3117'] builddependencies = [ ('Bison', '3.0.5'), + ('flex', '2.6.4'), ('GObject-Introspection', '1.54.1', '-Python-2.7.15'), + ('gettext', '0.19.8.1'), + ('pkg-config', '0.29.2'), ] dependencies = [ ('GLib', '2.54.3'), ('zlib', '1.2.11'), + ('libunwind', '1.2.1'), ] +configopts = '--with-dw=no ' + sanity_check_paths = { 'files': [], 'dirs': ['include', 'share', 'libexec'], From 6c0fb91a2b4c26a7de0765efb40dd9c4c72f920c Mon Sep 17 00:00:00 2001 From: jose_d Date: Thu, 14 Mar 2019 18:59:15 +0100 Subject: [PATCH 0887/5331] Python-5.8.0-fosscuda-2018b-Python-2.7.15.eb will go via #7805 https://github.com/akesandgren/easybuild-easyconfigs/pull/7 --- ...thon-5.8.0-fosscuda-2018b-Python-2.7.15.eb | 244 ------------------ 1 file changed, 244 deletions(-) delete mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb deleted file mode 100644 index 17052e37bc5..00000000000 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-fosscuda-2018b-Python-2.7.15.eb +++ /dev/null @@ -1,244 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'IPython' -version = '5.8.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://ipython.org/index.html' -description = """IPython provides a rich architecture for interactive computing with: - Powerful interactive shells (terminal and Qt-based). - A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. - Support for interactive data visualization and use of GUI toolkits. - Flexible, embeddable interpreters to load into your own projects. - Easy to use, high performance tools for parallel computing.""" - -toolchain = {'name': 'fosscuda', 'version': '2018b'} - -dependencies = [ - ('Python', '2.7.15'), - ('ZeroMQ', '4.2.5'), - ('matplotlib', '2.2.3', versionsuffix), -] - -use_pip = True - -exts_list = [ - ('Pygments', '2.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], - 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], - }), - ('ipython_genutils', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('ipython', version, { - 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], - 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], - }), - ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], - }), - ('pexpect', '4.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], - 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], - }), - ('scandir', '1.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], - 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], - }), - ('pathlib2', '2.3.3', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], - 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], - }), - ('pickleshare', '0.7.5', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], - 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], - }), - ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], - 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], - }), - ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], - 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], - }), - ('ptyprocess', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], - }), - ('simplegeneric', '0.8.1', { - 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], - 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], - }), - ('traitlets', '4.3.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], - 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], - }), - ('parso', '0.3.4', { - 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], - 'checksums': ['68406ebd7eafe17f8e40e15a84b56848eccbf27d7c1feb89e93d8fca395706db'], - }), - ('jedi', '0.13.1', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], - 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], - }), - ('testpath', '0.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], - 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], - }), - ('nose', '1.3.7', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], - 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], - }), - ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], - 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], - }), - ('defusedxml', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], - 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], - }), - ('nbconvert', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], - }), - ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], - }), - ('MarkupSafe', '1.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], - 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], - }), - ('ipywidgets', '7.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], - 'checksums': ['a3e224f430163f767047ab9a042fc55adbcab0c24bbe6cf9f306c4f89fdf0ba3'], - }), - ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], - 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], - }), - ('Send2Trash', '1.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], - 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], - }), - ('webencodings', '0.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], - 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], - }), - ('html5lib', '1.0.1', { - 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], - 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], - }), - ('bleach', '3.1.0', { - 'source_urls': 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['https://pypi.python.org/packages/source/j/jsonschema/'], - 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], - }), - ('pandocfilters', '1.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], - 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], - }), - ('pyzmq', '18.0.0', { - 'modulename': 'zmq', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], - 'checksums': ['b30c339eb58355f51f4f54dd61d785f1ff58c86bca1c3a5916977631d121867b'], - }), - ('entrypoints', '0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], - 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], - }), - ('jupyter_core', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], - 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], - }), - ('mistune', '0.8.4', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], - 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], - }), - ('terminado', '0.8.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], - 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], - }), - ('futures', '3.2.0', { - 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], - 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], - }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], - }), - ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], - }), - ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], - 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], - }), - ('tornado', '5.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], - 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], - }), - ('jupyter_client', '5.2.4', { - 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], - 'checksums': ['b5f9cb06105c1d2d30719db5ffb3ea67da60919fb68deaefa583deccd8813551'], - }), - ('backcall', '0.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], - 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], - }), - ('ipykernel', '4.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], - 'checksums': ['699103c8e64886e3ec7053f2a6aa83bb90426063526f63a818732ff385202bad'], - }), - ('prometheus_client', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], - 'checksums': ['1b38b958750f66f208bcd9ab92a633c0c994d8859c831f7abc1f46724fcee490'], - }), - ('notebook', '5.7.4', { - 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], - 'checksums': ['d908673a4010787625c8952e91a22adf737db031f2aa0793ad92f6558918a74a'], - }), - ('widgetsnbextension', '3.4.2', { - 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], - 'checksums': ['fa618be8435447a017fd1bf2c7ae922d0428056cfc7449f7a8641edf76b48265'], - }), -] - -sanity_check_paths = { - 'files': ['bin/ipython'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], -} - -sanity_check_commands = [ - "ipython -h", - "jupyter notebook --help", - "iptest", -] - -moduleclass = 'tools' From dc1f8de609d723a4e1bda9aef890c76bea032488 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 19:18:32 +0100 Subject: [PATCH 0888/5331] adding easyconfigs: bmtagger-3.101-foss-2018b.eb, SRPRISM-3.0.0-foss-2018b.eb and patches: bmtagger-3.101_fix-hardcoding.patch, SRPRISM-3.0.0_fix-GCC-7.patch --- .../b/bmtagger/bmtagger-3.101-foss-2018b.eb | 37 +++++++++++++ .../bmtagger-3.101_fix-hardcoding.patch | 11 ++++ .../s/SRPRISM/SRPRISM-3.0.0-foss-2018b.eb | 33 ++++++++++++ .../s/SRPRISM/SRPRISM-3.0.0_fix-GCC-7.patch | 54 +++++++++++++++++++ 4 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/b/bmtagger/bmtagger-3.101-foss-2018b.eb create mode 100644 easybuild/easyconfigs/b/bmtagger/bmtagger-3.101_fix-hardcoding.patch create mode 100644 easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0-foss-2018b.eb create mode 100644 easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0_fix-GCC-7.patch diff --git a/easybuild/easyconfigs/b/bmtagger/bmtagger-3.101-foss-2018b.eb b/easybuild/easyconfigs/b/bmtagger/bmtagger-3.101-foss-2018b.eb new file mode 100644 index 00000000000..e8b3d484f58 --- /dev/null +++ b/easybuild/easyconfigs/b/bmtagger/bmtagger-3.101-foss-2018b.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'bmtagger' +version = '3.101' + +homepage = 'ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/' +description = "Best Match Tagger for removing human reads from metagenomics datasets" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'cstd': 'c++98'} + +source_urls = ['ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/'] +sources = [{'download_filename': 'bmtools.tar.gz', 'filename': 'bmtools-%(version)s.tar.gz'}] +patches = ['bmtagger-%(version)s_fix-hardcoding.patch'] +checksums = [ + '81ac6d47aa478c2e0ef760f15b9c71e1c52430c96a2c8d064667ebbef148e873', # bmtools-3.101.tar.gz + '8779edd4dab6c0a3bc1bbcc5f265d61ccfd685972a0570bc3a84f5a131972195', # bmtagger-3.101_fix-hardcoding.patch +] + +dependencies = [ + ('BLAST+', '2.7.1'), + ('SRPRISM', '3.0.0'), +] + +files_to_copy = [(['bmtagger/bmfilter', 'bmtagger/bmtagger.sh', 'bmtagger/bmtool', 'bmtagger/extract_fullseq'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bmfilter', 'bin/bmtagger.sh', 'bin/bmtool', 'bin/extract_fullseq'], + 'dirs': [], +} + +sanity_check_commands = [ + "bmtool -h", + "bmfilter -h", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bmtagger/bmtagger-3.101_fix-hardcoding.patch b/easybuild/easyconfigs/b/bmtagger/bmtagger-3.101_fix-hardcoding.patch new file mode 100644 index 00000000000..247e57a03f5 --- /dev/null +++ b/easybuild/easyconfigs/b/bmtagger/bmtagger-3.101_fix-hardcoding.patch @@ -0,0 +1,11 @@ +fix hardcoding of compiler command & flags, by passing down $CXX, $CXX and $CXXFLAGS +--- Makefile.orig 2014-02-21 01:20:50.000000000 +0100 ++++ Makefile 2019-03-14 16:20:18.415277482 +0100 +@@ -4,6 +4,6 @@ + + + all depend test clean: +- set -e ; for file in $(SUBDIRS) ; do make -C $$file $(MAKEFLAGS:%=-%) $@ ; done ++ set -e ; for file in $(SUBDIRS) ; do make -C $$file $@ CC="${CC}" CXX="${CXX}" FLAGS="${CFLAGS}"; done + + diff --git a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0-foss-2018b.eb b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0-foss-2018b.eb new file mode 100644 index 00000000000..51c27db6997 --- /dev/null +++ b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0-foss-2018b.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'SRPRISM' +version = '3.0.0' + +homepage = 'https://github.com/ncbi/SRPRISM' +description = "Single Read Paired Read Indel Substitution Minimizer" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/ncbi/SRPRISM/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['SRPRISM-%(version)s_fix-GCC-7.patch'] +checksums = [ + 'ff40ad5b3d41fa5980550425b5f7ad570f1ee830c158bfd6cb468372091e11f0', # v3.0.0.tar.gz + 'b65a594851f25e22fce28ad16732f110eec118a6f7125ecd7ea163f95b1f5121', # SRPRISM-3.0.0_fix-GCC-7.patch +] + +dependencies = [('NGS', '2.9.3', '-Java-1.8')] + +prebuildopts = "cd srprism/lib && " +buildopts = " && cd ../app && make" + +files_to_copy = [(['srprism/app/srprism'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/srprism'], + 'dirs': [], +} + +sanity_check_commands = ["srprism help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0_fix-GCC-7.patch b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0_fix-GCC-7.patch new file mode 100644 index 00000000000..038cbdf5686 --- /dev/null +++ b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0_fix-GCC-7.patch @@ -0,0 +1,54 @@ +fix compilation with GCC 7.x +author: Kenneth Hoste (HPC-UGent) +see also https://github.com/ncbi/SRPRISM/issues/1 +--- srprism/lib/srprism/query_acct.hpp.orig 2019-03-14 17:53:26.960989751 +0100 ++++ srprism/lib/srprism/query_acct.hpp 2019-03-14 18:47:10.461173398 +0100 +@@ -112,10 +112,10 @@ + + template< bool paired > + bool BestLevelFull( TQNum qn ) const +- { return query_info_[qn].BestLevelFull< paired >( res_lim_ ); } ++ { return query_info_[qn].template BestLevelFull< paired >( res_lim_ ); } + + template< bool paired > int MaxErr( TQNum qn ) const +- { return query_info_[qn].MaxErr< paired >(); } ++ { return query_info_[qn].template MaxErr< paired >(); } + + int GroupMaxErr( TQNum dup_idx ) const + { return t_scoring::template MaxErr< true >( dup_data_[dup_idx] ); } +--- srprism/lib/srprism/query_store.hpp.orig 2019-03-14 17:58:03.219288045 +0100 ++++ srprism/lib/srprism/query_store.hpp 2019-03-14 18:48:45.310588004 +0100 +@@ -662,7 +662,7 @@ + else AdjustMinRankInfo< t_scoring >( qn ); + } + +- int max_err( qa->MaxErr< true >( qn ) ); ++ int max_err( qa->template MaxErr< true >( qn ) ); + + if( max_err < min_err || + (max_err == min_err && +@@ -687,7 +687,7 @@ + qn, align_len, n_err, n_gap, n_del, n_gopen ) ); + + if( res ) { +- int max_err( qa->MaxErr< false >( qn ) ); ++ int max_err( qa->template MaxErr< false >( qn ) ); + + if( max_err < min_err || + (max_err == min_err && +@@ -715,13 +715,13 @@ + TSeqSize MaxQueryLen( void ) const { return max_query_len_; } + + template< typename t_scoring, bool paired > int MaxErr( TQNum qn ) const +- { return GetScoringData< t_scoring >()->MaxErr< paired >( qn ); } ++ { return GetScoringData< t_scoring >()->template MaxErr< paired >( qn ); } + + template< typename t_scoring, bool paired > int + GroupMaxErr( TQNum qn ) const + { + if( IsUnique( qn ) || DupDataStart( qn )[N_MIN_RANK] == 0 ) { +- return GetScoringData< t_scoring >()->MaxErr< paired >( qn ); ++ return GetScoringData< t_scoring >()->template MaxErr< paired >( qn ); + } + else { + return GetScoringData< t_scoring >()->GroupMaxErr( From 68a1911525a556db77448a1a1f6f0bb61051b9f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 19:31:12 +0100 Subject: [PATCH 0889/5331] {bio}[foss/2018b] CONCOCT v1.0.0 (+ deps) w/ Python 2.7.15 --- .../CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb | 42 +++++++++++++++++++ .../parallel/parallel-20190222-foss-2018b.eb | 24 +++++++++++ ...t-learn-0.20.2-foss-2018b-Python-2.7.15.eb | 34 +++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20190222-foss-2018b.eb create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..b8d52d0019d --- /dev/null +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'CONCOCT' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://concoct.readthedocs.io' +description = """Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning + of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data + from paired end reads.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/BinPro/CONCOCT/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4428a1d7bce5c7546106bea0a0ff6c2168e3680f6422adce5ef523bce46dc180'] + +dependencies = [ + ('Python', '2.7.15'), + ('GSL', '2.5'), + # gslcblas + ('Biopython', '1.72', versionsuffix), + ('scikit-learn', '0.20.2', versionsuffix), + ('MEGAHIT', '1.1.4', versionsuffix), + ('BEDTools', '2.27.1'), + ('picard', '2.18.27', '-Java-1.8', True), + ('SAMtools', '1.9'), + ('Bowtie2', '2.3.4.2'), + ('parallel', '20190222'), + ('Pysam', '0.15.1', versionsuffix), + ('CheckM', '1.0.13', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/concoct'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20190222-foss-2018b.eb b/easybuild/easyconfigs/p/parallel/parallel-20190222-foss-2018b.eb new file mode 100644 index 00000000000..408602b14ed --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20190222-foss-2018b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20190222' + +homepage = 'http://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['86b1badc56ee2de1483107c2adf634604fd72789c91f65e40138d21425906b1c'] + +dependencies = [ + ('Perl', '5.28.0'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-2.7.15.eb new file mode 100755 index 00000000000..2c34a989744 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.2-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.20.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['bc5bc7c7ee2572a1edcb51698a6caf11fae554194aaab9a38105d9ec419f29e6'] + +dependencies = [ + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' From b0114847553e928cc8d9a45f3e7aaa230a621a9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 19:34:20 +0100 Subject: [PATCH 0890/5331] adding easyconfigs: prokka-1.13.4-foss-2018b.eb --- .../p/prokka/prokka-1.13.4-foss-2018b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.13.4-foss-2018b.eb diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.13.4-foss-2018b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.13.4-foss-2018b.eb new file mode 100644 index 00000000000..1c9d46ea449 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.13.4-foss-2018b.eb @@ -0,0 +1,36 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.13.4' + +homepage = 'http://www.vicbioinformatics.com/software.prokka.shtml' +description = """Prokka is a software tool for the rapid annotation of prokaryotic genomes.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['b5621af689ffb5348eab699a378d45d7566cd63a7da52845229b484af33ea8e2'] + +dependencies = [('BioPerl', '1.7.2', '-Perl-5.28.0')] + +bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' From 9f366193efdf9ccab8b431000640a1283a91ca55 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 19:37:15 +0100 Subject: [PATCH 0891/5331] {bio}[foss/2018b] Trim_Galore v0.6.0 w/ Python 2.7.15 & 3.6.6 --- ...m_Galore-0.6.0-foss-2018b-Python-2.7.15.eb | 37 ++++++++++++++++++ ...im_Galore-0.6.0-foss-2018b-Python-3.6.6.eb | 38 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100755 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb create mode 100755 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb new file mode 100755 index 00000000000..e30697fa9a2 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,37 @@ +easyblock = "Tarball" + +name = 'Trim_Galore' +version = '0.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """A wrapper tool around Cutadapt and FastQC to consistently apply + quality and adapter trimming to FastQ files, with some extra functionality for + MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f374dfa4c94e2ad50c63276dda0f341fd95b29cb1d5a0e2ad56e8b0168b758ec'] + +dependencies = [ + ('Python', '2.7.15'), + ('FastQC', '0.11.8', '-Java-1.8', True), + ('cutadapt', '1.18', versionsuffix), + ('Perl', '5.28.0'), +] + +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s", +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb new file mode 100755 index 00000000000..f03c582405b --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,38 @@ +easyblock = "Tarball" + +name = 'Trim_Galore' +version = '0.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """A wrapper tool around Cutadapt and FastQC to consistently apply + quality and adapter trimming to FastQ files, with some extra functionality for + MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f374dfa4c94e2ad50c63276dda0f341fd95b29cb1d5a0e2ad56e8b0168b758ec'] + +dependencies = [ + ('Python', '3.6.6'), # multi-core support requires Python 3.x + pigz + ('pigz', '2.4'), + ('FastQC', '0.11.8', '-Java-1.8', True), + ('cutadapt', '1.18', versionsuffix), + ('Perl', '5.28.0'), +] + +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s", +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' From 6c397418c9c0eaf7c8aaa04321e8d0237f472a16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 19:39:34 +0100 Subject: [PATCH 0892/5331] adding easyconfigs: taxator-tk-1.3.3-foss-2018b.eb --- .../taxator-tk/taxator-tk-1.3.3-foss-2018b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-foss-2018b.eb diff --git a/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-foss-2018b.eb b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-foss-2018b.eb new file mode 100644 index 00000000000..b440d707b6e --- /dev/null +++ b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-foss-2018b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'taxator-tk' +version = '1.3.3' + +homepage = 'https://github.com/fungs/taxator-tk' +description = "A set of programs for the taxonomic analysis of nucleotide sequence data" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/fungs/taxator-tk/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c1da90bee42337a994c66653208c820b7b0d203093981eaec4eef0a9f6fdd156'] + +builddependencies = [('CMake', '3.12.1')] +dependencies = [ + ('SeqAn', '2.4.0'), + ('Boost', '1.67.0'), +] + +separate_build_dir = True + +buildopts = "&& mkdir -p %(installdir)s/bin" +buildopts += " && cp -a {alignments-filter,binner,taxator,taxknife,unittest_ncbitaxonomy} %(installdir)s/bin/" + +skipsteps = ['install'] + +sanity_check_paths = { + 'files': ['bin/alignments-filter', 'bin/binner', 'bin/taxator', 'bin/taxknife', 'bin/unittest_ncbitaxonomy'], + 'dirs': [], +} + +#sanity_check_commands = ["srprism help"] + +moduleclass = 'bio' From da79e7debea33289c2dc4c98a55dad242e6eec5d Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 14 Mar 2019 19:45:26 +0100 Subject: [PATCH 0893/5331] Change version --- ...-20190313-GCCcore-8.2.0.eb => X11-20190311-GCCcore-8.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/x/X11/{X11-20190313-GCCcore-8.2.0.eb => X11-20190311-GCCcore-8.2.0.eb} (99%) diff --git a/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20190311-GCCcore-8.2.0.eb similarity index 99% rename from easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb rename to easybuild/easyconfigs/x/X11/X11-20190311-GCCcore-8.2.0.eb index 088b8369cbb..b9303be117b 100644 --- a/easybuild/easyconfigs/x/X11/X11-20190313-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20190311-GCCcore-8.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'X11' -version = '20190313' +version = '20190311' homepage = 'https://www.x.org' description = "The X Window System (X11) is a windowing system for bitmap displays" From 9a7226010fc88e71b4a2ba6f46f387249f28ef69 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 19:45:37 +0100 Subject: [PATCH 0894/5331] adding easyconfigs: metaWRAP-1.1.5-foss-2018b-Python-2.7.15.eb --- ...metaWRAP-1.1.5-foss-2018b-Python-2.7.15.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.1.5-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.1.5-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.1.5-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..3c5a2be60ce --- /dev/null +++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.1.5-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,53 @@ +easyblock = 'Tarball' + +name = 'metaWRAP' +commit = '689cb92' +version = '1.1.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/bxlab/metaWRAP' +description = """MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of + metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, + extracting draft genomes (binning), and functional annotation.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/bxlab/metaWRAP/archive/'] +sources = [{'download_filename': '%s.tar.gz' % commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['4aee033cd4af0b59525dffb792c074c6948c8bfc0552645f3639a975ac78e3b7'] + +# see https://github.com/bxlab/metaWRAP/blob/master/installation/dependancies.md +dependencies = [ + ('Python', '2.7.15'), + ('Perl', '5.28.0'), + ('R', '3.5.1', versionsuffix), # incl. ggplot2 + ('SPAdes', '3.13.0'), + ('BWA', '0.7.17'), + ('MEGAHIT', '1.1.4', versionsuffix), + ('QUAST', '5.0.2', versionsuffix), + ('SAMtools', '1.9'), + ('MetaBAT', '2.12.1', versionsuffix), + ('CONCOCT', '1.0.0', versionsuffix), + ('MaxBin', '2.2.6', '-Perl-%(perlver)s'), + ('Kraken', '1.1', '-Perl-%(perlver)s'), + ('KronaTools', '2.7'), + ('CheckM', '1.0.13', versionsuffix), + ('Salmon', '0.12.0'), + ('Seaborn', '0.9.0', versionsuffix), + ('BLAST+', '2.7.1'), + ('Bowtie2', '2.3.4.2'), + ('FastQC', '0.11.8', '-Java-1.8', True), + ('Trim_Galore', '0.6.0', versionsuffix), + ('bmtagger', '3.101'), + ('taxator-tk', '1.3.3'), + ('prokka', '1.13.4'), +] + +sanity_check_paths = { + 'files': ['bin/config-metawrap', 'bin/metaWRAP'], + 'dirs': [], +} + +sanity_check_commands = ["metaWRAP --help"] + +moduleclass = 'bio' From 7290b09424a4f854d74c25587f031cc33b54f05c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 14 Mar 2019 13:50:41 -0500 Subject: [PATCH 0895/5331] Remove commented section --- .../matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb index b49e9160930..7399ef71449 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.1.0-fosscuda-2017b-Python-2.7.14.eb @@ -45,11 +45,6 @@ exts_list = [ }), ] -#sanity_check_paths = { -# 'files': [], -# 'dirs': [], -#} - sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] moduleclass = 'vis' From 8261e1673bfcd97b6daa8a1f315194855480baeb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 19:56:57 +0100 Subject: [PATCH 0896/5331] add missing use_pip in QUAST easyconfig --- .../easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb index c37e4091704..595f99f75e4 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb @@ -20,6 +20,8 @@ dependencies = [ ('Boost', '1.67.0'), ] +use_pip = True + exts_list = [ ('simplejson', '3.16.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson'], From 5bfc4ee88203aeb545f19434d25cbb32871b4cab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 20:36:27 +0100 Subject: [PATCH 0897/5331] add missing bzip2 dep --- easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0-foss-2018b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0-foss-2018b.eb b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0-foss-2018b.eb index 51c27db6997..a0329725285 100644 --- a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0-foss-2018b.eb +++ b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.0.0-foss-2018b.eb @@ -16,7 +16,10 @@ checksums = [ 'b65a594851f25e22fce28ad16732f110eec118a6f7125ecd7ea163f95b1f5121', # SRPRISM-3.0.0_fix-GCC-7.patch ] -dependencies = [('NGS', '2.9.3', '-Java-1.8')] +dependencies = [ + ('NGS', '2.9.3', '-Java-1.8'), + ('bzip2', '1.0.6'), +] prebuildopts = "cd srprism/lib && " buildopts = " && cd ../app && make" From 2199dffb50753e820c173221bfe65853849981b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 20:38:58 +0100 Subject: [PATCH 0898/5331] add missing XZ dependency to most recent Pysam easyconfigs --- .../easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-2.7.15.eb | 1 + .../easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-3.6.6.eb | 1 + .../p/Pysam/Pysam-0.15.1-intel-2018b-Python-2.7.15.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-2.7.15.eb index 2cc85caec1f..ba3660fcfba 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-2.7.15.eb @@ -28,6 +28,7 @@ dependencies = [ ('Python', '2.7.15'), ('ncurses', '6.1'), ('cURL', '7.60.0'), + ('XZ', '5.2.4'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-3.6.6.eb index ce321c73faa..9ef8a62dda2 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-3.6.6.eb @@ -28,6 +28,7 @@ dependencies = [ ('Python', '3.6.6'), ('ncurses', '6.1'), ('cURL', '7.60.0'), + ('XZ', '5.2.4'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-2.7.15.eb index 4617cf01511..6c844cfb15e 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-2.7.15.eb @@ -28,6 +28,7 @@ dependencies = [ ('Python', '2.7.15'), ('ncurses', '6.1'), ('cURL', '7.60.0'), + ('XZ', '5.2.4'), ] sanity_check_paths = { From 4acd8f69c6d866d506d2b0a40bb6c6469f08b6a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 21:08:50 +0100 Subject: [PATCH 0899/5331] add missing 'download_dep_fail' and 'use_pip' in Pysam 0.15.1 easyconfigs --- .../p/Pysam/Pysam-0.15.1-foss-2018b-Python-2.7.15.eb | 3 +++ .../p/Pysam/Pysam-0.15.1-foss-2018b-Python-3.6.6.eb | 3 +++ .../p/Pysam/Pysam-0.15.1-intel-2018b-Python-2.7.15.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-2.7.15.eb index ba3660fcfba..d4ca642e270 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-2.7.15.eb @@ -31,6 +31,9 @@ dependencies = [ ('XZ', '5.2.4'), ] +download_dep_fail = True +use_pip = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-3.6.6.eb index 9ef8a62dda2..5401488276c 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-foss-2018b-Python-3.6.6.eb @@ -31,6 +31,9 @@ dependencies = [ ('XZ', '5.2.4'), ] +download_dep_fail = True +use_pip = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-2.7.15.eb index 6c844cfb15e..238f28e7cf2 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-2.7.15.eb @@ -31,6 +31,9 @@ dependencies = [ ('XZ', '5.2.4'), ] +download_dep_fail = True +use_pip = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 29c7558cb63087a1ad7a257fcb713775253cab04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 21:38:16 +0100 Subject: [PATCH 0900/5331] move parallel to GCCcore --- ...190222-foss-2018b.eb => parallel-20190222-GCCcore-7.3.0.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/p/parallel/{parallel-20190222-foss-2018b.eb => parallel-20190222-GCCcore-7.3.0.eb} (83%) diff --git a/easybuild/easyconfigs/p/parallel/parallel-20190222-foss-2018b.eb b/easybuild/easyconfigs/p/parallel/parallel-20190222-GCCcore-7.3.0.eb similarity index 83% rename from easybuild/easyconfigs/p/parallel/parallel-20190222-foss-2018b.eb rename to easybuild/easyconfigs/p/parallel/parallel-20190222-GCCcore-7.3.0.eb index 408602b14ed..b9eeb2dd27f 100644 --- a/easybuild/easyconfigs/p/parallel/parallel-20190222-foss-2018b.eb +++ b/easybuild/easyconfigs/p/parallel/parallel-20190222-GCCcore-7.3.0.eb @@ -6,12 +6,13 @@ version = '20190222' homepage = 'http://savannah.gnu.org/projects/parallel/' description = """parallel: Build and execute shell commands in parallel""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_BZ2] checksums = ['86b1badc56ee2de1483107c2adf634604fd72789c91f65e40138d21425906b1c'] +builddependencies = [('binutils', '2.30')] dependencies = [ ('Perl', '5.28.0'), ] From fe8db7ff8572d7e54cd888a7d99e00743f4ca17b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 21:54:31 +0100 Subject: [PATCH 0901/5331] fix sanity check command for taxator-tk --- .../easyconfigs/t/taxator-tk/taxator-tk-1.3.3-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-foss-2018b.eb b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-foss-2018b.eb index b440d707b6e..b3ee7156e82 100644 --- a/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-foss-2018b.eb +++ b/easybuild/easyconfigs/t/taxator-tk/taxator-tk-1.3.3-foss-2018b.eb @@ -30,6 +30,6 @@ sanity_check_paths = { 'dirs': [], } -#sanity_check_commands = ["srprism help"] +sanity_check_commands = ["taxator --help"] moduleclass = 'bio' From 8670236c20718efbc47dd1eb4945507b0df86210 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2019 22:02:06 +0100 Subject: [PATCH 0902/5331] {lang}[GCCcore/8.2.0] Python v3.7.2 (WIP) --- .../p/Python/Python-3.7.2-GCCcore-8.2.0.eb | 263 ++++++++++++++++++ 1 file changed, 263 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..24515f58772 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb @@ -0,0 +1,263 @@ +name = 'Python' +version = '3.7.2' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['f09d83c773b9cc72421abba2c317e4e6e05d919f9bcf34468e192b6a6c8e328d'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('bzip2', '1.0.6'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.1'), + ('SQLite', '3.27.2'), + ('XZ', '5.2.4'), + ('GMP', '6.1.2'), # required for pycrypto + ('libffi', '3.2.1'), # required for cryptography + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) + # ('OpenSSL', '1.1.0j'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# symlink 'pip' command to 'pip3' that is included with Python installation +# required so we can update pip to version included in extensions, using pip +installopts = " && ln -s %(installdir)s/bin/pip3 %(installdir)s/bin/pip" + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +# order is important! +# package versions updated Mar 6th 2019 +exts_list = [ + ('pip', '19.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + 'checksums': ['6e6f197a1abfb45118dbb878b5c859a0edbdd33fd250100bc015b67fded4b9f2'], + # don't use --ignore-installed, i.e. let pip remove older pip version included with Python + 'pip_ignore_installed': False, + }), + ('setuptools', '40.8.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['6e4eec90337e849ade7103723b9a99631c1f0d19990d6e8412dc42f5ae8b304d'], + # don't use --ignore-installed, i.e. let pip remove older setuptools version included with Python + 'pip_ignore_installed': False, + }), + ('wheel', '0.33.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wheel'], + 'checksums': ['66a8fd76f28977bb664b098372daef2b27f60dc4d1688cfab7b37a09448f0e9d'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '5.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + 'checksums': ['8c361cc353d988e4f5b998555c88098b9d5964c2e11acf7b0d21925a66bb5824'], + }), + ('Cython', '0.29.6', { + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'checksums': ['6c5d33f1b5c864382fbce810a8fd9e015447869ae42e98e6301e977b8165e7ae'], + }), + ('six', '1.12.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'checksums': ['d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73'], + }), + ('setuptools_scm', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], + }), + ('python-dateutil', '2.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + 'checksums': ['c89805f6f4d64db21ed966fda138f8a5ed7a4fdbc1a8ee329ce1b74e3c74da9e'], + 'modulename': 'dateutil', + }), + ('deap', '1.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'checksums': ['95c63e66d755ec206c80fdb2908851c0bef420ee8651ad7be4f0578e9e909bcf'], + }), + ('decorator', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + 'checksums': ['33cd704aea07b4c28b3eb2c97d288a06918275dac0ecebdaf1bc8a48d98adb9e'], + }), + ('liac-arff', '2.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + 'checksums': ['47afcd1fd248b2892f66075987422d0576fc2c2fd0811d0cbd32f2135b065df5'], + 'modulename': 'arff', + }), + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'checksums': ['f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'], + 'modulename': 'Crypto', + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], + }), + ('ipaddress', '1.0.22', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipaddress/'], + 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], + }), + ('asn1crypto', '0.24.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/asn1crypto/'], + 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], + }), + ('idna', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/i/idna/'], + 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], + }), + ('pycparser', '2.19', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycparser/'], + 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], + }), + ('cffi', '1.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cffi/'], + 'checksums': ['e113878a446c6228669144ae8a56e268c91b7f1fafae927adc4879d9849e0ea7'], + }), + ('cryptography', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + 'checksums': ['26c821cbeb683facb966045e2064303029d572a87ee69ca5a1bf54bf55f93ca6'], + }), + ('pyasn1', '0.4.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyasn1/'], + 'checksums': ['da2420fe13a9452d8ae97a0e478adde1dee153b11ba832a95b223a2ba01c10f7'], + }), + ('PyNaCl', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pynacl/'], + 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], + 'modulename': 'nacl', + }), + ('bcrypt', '3.1.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bcrypt/'], + 'checksums': ['44636759d222baa62806bbceb20e96f75a015a6381690d1bc2eda91c01ec02ea'], + }), + ('paramiko', '2.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + 'checksums': ['a8975a7df3560c9f1e2b43dc54ebd40fd00a7017392ca5445ce7df409f900fcb'], + }), + ('pyparsing', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + 'checksums': ['66c9268862641abcac4a96ba74506e594c884e3f57690a696d21ad8210ed667a'], + }), + ('netifaces', '0.10.9', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces/'], + 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], + }), + ('netaddr', '0.7.19', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr/'], + 'checksums': ['38aeec7cdd035081d3a4c306394b19d677623bf76fa0913f6695127c7753aefd'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], + 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], + }), + ('pytz', '2018.9', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz/'], + 'checksums': ['d5f05e487007e29e03409f9398d074e158d920d36eb82eaf66fb1136b0c5374c'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring/'], + 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], + }), + ('virtualenv', '16.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv/'], + 'checksums': ['984d7e607b0a5d1329425dd8845bd971b957424b5ba664729fab51ab8c11bc39'], + }), + ('docopt', '0.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docopt/'], + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.13.2', { + 'source_urls': ['https://pypi.python.org/packages/source/j/joblib/'], + 'checksums': ['315d6b19643ec4afd4c41c671f9f2d65ea9d787da093487a81ead7b0bac94524'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('certifi', '2018.11.29', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + }), + ('urllib3', '1.24.1', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], + }), + ('requests', '2.21.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], + }), + ('xlrd', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xlrd'], + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('py_expression_eval', '0.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py_expression_eval'], + 'checksums': ['0907cef96a7c370b2a58ea2179f88e48f421f5a41821b32f7defb81ca4e5247e'], + }), + ('tabulate', '0.8.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tabulate/'], + 'checksums': ['8af07a39377cee1103a5c8b3330a421c2d99b9141e9cc5ddd2e3263fea416943'], + }), + ('ujson', '1.35', { + 'source_urls': ['https://pypi.python.org/packages/source/u/ujson'], + 'checksums': ['f66073e5506e91d204ab0c614a148d5aa938bdbf104751be66f8ad7a222f5f86'], + }), + ('atomicwrites', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites'], + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], + }), + ('py', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py'], + 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], + }), + ('scandir', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir'], + 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], + }), + ('pathlib2', '2.3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2'], + 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], + }), + ('pluggy', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy'], + 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], + }), + ('more-itertools', '6.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools'], + 'checksums': ['590044e3942351a1bdb1de960b739ff4ce277960f2425ad4509446dbace8d9d1'], + }), + ('attrs', '19.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], + 'modulename': 'attr', + }), + ('pytest', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytest'], + 'checksums': ['067a1d4bf827ffdd56ad21bd46674703fce77c5957f6c1eef731f6146bfcef1c'], + }), +] + +moduleclass = 'lang' From e6ffabeb7dc5ab9051f005ff27f6434820ea9f02 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 14 Mar 2019 17:09:30 -0500 Subject: [PATCH 0903/5331] change GDB/8.0.1 from foss/intel to GCCcore --- ... GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb} | 0 ...> GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb} | 0 .../GDB-8.0.1-intel-2017b-Python-2.7.14.eb | 38 ------------------- .../GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb | 38 ------------------- 4 files changed, 76 deletions(-) rename easybuild/easyconfigs/g/GDB/{GDB-8.0.1-foss-2017b-Python-2.7.14.eb => GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb} (100%) rename easybuild/easyconfigs/g/GDB/{GDB-8.0.1-foss-2017b-Python-3.6.3.eb => GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb} (100%) delete mode 100644 easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb delete mode 100644 easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb similarity index 100% rename from easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-2.7.14.eb rename to easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb similarity index 100% rename from easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-3.6.3.eb rename to easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb deleted file mode 100644 index 352651afdfa..00000000000 --- a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDB' -version = '8.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.gnu.org/software/gdb/gdb.html' -description = "The GNU Project Debugger" - -toolchain = {'name': 'intel', 'version': '2017b'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['3dbd5f93e36ba2815ad0efab030dcd0c7b211d7b353a40a53f4c02d7d56295e3'] - -builddependencies = [ - ('texinfo', '6.5'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('libreadline', '7.0'), - ('ncurses', '6.0'), - ('expat', '2.2.5'), - ('Python', '2.7.14'), -] - -configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' -configopts += '--with-system-readline --enable-tui --enable-plugins' - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/gdb', 'bin/gdbserver'], - 'dirs': [], -} - -moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb deleted file mode 100644 index 67d0d3b585f..00000000000 --- a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDB' -version = '8.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.gnu.org/software/gdb/gdb.html' -description = "The GNU Project Debugger" - -toolchain = {'name': 'intel', 'version': '2017b'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['3dbd5f93e36ba2815ad0efab030dcd0c7b211d7b353a40a53f4c02d7d56295e3'] - -builddependencies = [ - ('texinfo', '6.5'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('libreadline', '7.0'), - ('ncurses', '6.0'), - ('expat', '2.2.5'), - ('Python', '3.6.3'), -] - -configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' -configopts += '--with-system-readline --enable-tui --enable-plugins' - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/gdb', 'bin/gdbserver'], - 'dirs': [], -} - -moduleclass = 'debugger' From 394142c3c9926baf58352626825fdf134b7e8c15 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 14 Mar 2019 17:13:51 -0500 Subject: [PATCH 0904/5331] downgrade the toolchain to GCCcore --- .../easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb | 2 +- .../easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb index 236c668abb4..2e2f8cc2a5c 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "The GNU Project Debugger" -toolchain = {'name': 'foss', 'version': '2017b'} +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb index f1b0516a616..95bda36505f 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "The GNU Project Debugger" -toolchain = {'name': 'foss', 'version': '2017b'} +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] From 1236f99ff53e017358488c03a221fb61b4f52ea2 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 14 Mar 2019 17:23:11 -0500 Subject: [PATCH 0905/5331] we still need to bring foss/intel version back because this GDB has python support, than it depends on python therefore it can not go down to the GCCcore toolchain. --- ... => GDB-8.0.1-foss-2017b-Python-2.7.14.eb} | 2 +- ...b => GDB-8.0.1-foss-2017b-Python-3.6.3.eb} | 2 +- .../GDB-8.0.1-intel-2017b-Python-2.7.14.eb | 38 +++++++++++++++++++ .../GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb | 38 +++++++++++++++++++ 4 files changed, 78 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/GDB/{GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb => GDB-8.0.1-foss-2017b-Python-2.7.14.eb} (94%) rename easybuild/easyconfigs/g/GDB/{GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb => GDB-8.0.1-foss-2017b-Python-3.6.3.eb} (94%) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-2.7.14.eb similarity index 94% rename from easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb rename to easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-2.7.14.eb index 2e2f8cc2a5c..236c668abb4 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-2.7.14.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "The GNU Project Debugger" -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'foss', 'version': '2017b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-3.6.3.eb similarity index 94% rename from easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb rename to easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-3.6.3.eb index 95bda36505f..f1b0516a616 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-GCCcore-6.4.0-Python-3.6.3.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-foss-2017b-Python-3.6.3.eb @@ -7,7 +7,7 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.gnu.org/software/gdb/gdb.html' description = "The GNU Project Debugger" -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'foss', 'version': '2017b'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..352651afdfa --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '8.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['3dbd5f93e36ba2815ad0efab030dcd0c7b211d7b353a40a53f4c02d7d56295e3'] + +builddependencies = [ + ('texinfo', '6.5'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('expat', '2.2.5'), + ('Python', '2.7.14'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..67d0d3b585f --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '8.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['3dbd5f93e36ba2815ad0efab030dcd0c7b211d7b353a40a53f4c02d7d56295e3'] + +builddependencies = [ + ('texinfo', '6.5'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('expat', '2.2.5'), + ('Python', '3.6.3'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' From c3cce8628649296c5c756ea09ce58ab60077b2f0 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 15 Mar 2019 01:33:49 +0200 Subject: [PATCH 0906/5331] adding easyconfigs: libdrm-2.4.97-GCCcore-8.2.0.eb --- .../l/libdrm/libdrm-2.4.97-GCCcore-8.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.97-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.97-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.97-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..237c9e36a51 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.97-GCCcore-8.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.97' + +homepage = 'http://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8c6f4d0934f5e005cc61bc05a917463b0c867403de176499256965f6797092f1'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] +dependencies = [('X11', '20190311')] + +sanity_check_paths = { + 'files': ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.%s' % SHLIB_EXT, + 'lib/libdrm_radeon.%s' % SHLIB_EXT, 'lib/libdrm.%s' % SHLIB_EXT, 'lib/libkms.%s' % SHLIB_EXT], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' From e93759ccc7dfe89ce792cdfb34fd49139fe11fa2 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 15 Mar 2019 01:54:33 +0200 Subject: [PATCH 0907/5331] adding easyconfigs: libxslt-1.1.33-GCCcore-8.2.0.eb --- .../l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..0df6959430a --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.33' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8e36605144409df979cab43d835002f63988f3dc94d5d3537c12796db90e38c8'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('zlib', '1.2.11'), + ('libxml2', '2.9.8'), +] + +moduleclass = 'lib' From aea096f00e04e819d8648005a4930509edcb691d Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 15 Mar 2019 02:09:37 +0200 Subject: [PATCH 0908/5331] adding easyconfigs: nettle-3.4.1-GCCcore-8.2.0.eb --- .../n/nettle/nettle-3.4.1-GCCcore-8.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.4.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.4.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.4.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..b546d09ce53 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.4.1-GCCcore-8.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.4.1' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f941cf1535cd5d1819be5ccae5babef01f6db611f9b5a777bae9c7604b8a92ad'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' From 6c9b4b535857e6693e9f2dd4b7c1c965eaf31a03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2019 10:06:13 +0100 Subject: [PATCH 0909/5331] add Jinja2, Sphinx, Click psutil, future extensiosn to Python 2.7.15 with GCCcore/8.2.0 toolchain --- .../p/Python/Python-2.7.15-GCCcore-8.2.0.eb | 77 +++++++++++++++++-- 1 file changed, 69 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb index 4fa4382da03..48a50a65bf9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb @@ -35,7 +35,7 @@ exts_default_options = { } # order is important! -# package versions updated Mar 6th 2019 +# package versions updated Mar 15th 2019 exts_list = [ ('setuptools', '40.8.0', { 'source_tmpl': '%(name)s-%(version)s.zip', @@ -77,7 +77,7 @@ exts_list = [ 'checksums': ['d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.8.0', { @@ -198,9 +198,9 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), - ('certifi', '2018.11.29', { + ('certifi', '2019.3.9', { 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + 'checksums': ['b26104d6835d1f5e49452a26eb2ff87fe7090b89dfcaee5ea2212697e1e1d7ae'], }), ('urllib3', '1.24.1', { 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], @@ -234,9 +234,9 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/py'], 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), - ('scandir', '1.9.0', { + ('scandir', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scandir'], - 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], }), ('pathlib2', '2.3.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2'], @@ -255,9 +255,70 @@ exts_list = [ 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], 'modulename': 'attr', }), - ('pytest', '4.3.0', { + ('pytest', '4.3.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytest'], - 'checksums': ['067a1d4bf827ffdd56ad21bd46674703fce77c5957f6c1eef731f6146bfcef1c'], + 'checksums': ['592eaa2c33fae68c7d75aacf042efc9f77b27c08a6224a4f59beab8d9a420523'], + }), + ('MarkupSafe', '1.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('packaging', '19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + 'checksums': ['0c98a5d0be38ed775798ece1b9727178c4469d9c3b4ada66e8e6b7849f8732af'], + }), + ('sphinxcontrib-websupport', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], + 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], + 'modulename': 'sphinxcontrib.websupport', + }), + ('Pygments', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], + 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], + }), + ('imagesize', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], + }), + ('docutils', '0.14', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docutils/'], + 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], + }), + ('Babel', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], + }), + ('alabaster', '0.7.12', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], + 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], + }), + ('Sphinx', '1.8.5', { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + 'checksums': ['c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08'], + }), + ('Click', '7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('psutil', '5.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], + }), + ('future', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future'], + 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ] From eafcbe3de84ab847d0b3708f4d41623306a376ad Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 15 Mar 2019 12:42:31 +0100 Subject: [PATCH 0910/5331] Add download_dep_fail = True --- .../m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb index 1444a9daf93..552875e2e07 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb @@ -16,6 +16,8 @@ checksums = ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'] dependencies = [('Python', '3.6.6')] +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'], From a3a3a6379b2a8d56256cd844cc7b8e5b7d55916a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Fri, 15 Mar 2019 13:37:44 +0100 Subject: [PATCH 0911/5331] Add usepip to mpi4py --- .../m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb index 552875e2e07..f34dbfc2192 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.0.1-intel-2018b-Python-3.6.6.eb @@ -17,6 +17,7 @@ checksums = ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'] dependencies = [('Python', '3.6.6')] download_dep_fail = True +use_pip = True sanity_check_paths = { 'files': [], From cc6fa08289d19aa5f064105eb2313fa0c50d4f83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2019 13:44:30 +0100 Subject: [PATCH 0912/5331] add PresenceAbsence, GUTS, GenSA extensions to R 3.5.1 easyconfigs --- .../easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 9 +++++++++ easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index 6ff8ddc0089..b0157208052 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -2096,6 +2096,15 @@ exts_list = [ ('lqa', '1.0-3', { 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.0', { + 'checksums': ['af326f918bd46f3f653be1907e01551025fd961077ca719c861ab0f29d14d516'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 81b17d2a3e7..4860a03bc25 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -2094,6 +2094,15 @@ exts_list = [ ('lqa', '1.0-3', { 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.0', { + 'checksums': ['af326f918bd46f3f653be1907e01551025fd961077ca719c861ab0f29d14d516'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), ] moduleclass = 'lang' From 99abc8a99d424453cc2e30ad467202f92764d9d7 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 15 Mar 2019 08:12:11 -0500 Subject: [PATCH 0913/5331] adding easyconfigs: Mono-5.4.1.6-foss-2017b.eb --- .../m/Mono/Mono-5.4.1.6-foss-2017b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mono/Mono-5.4.1.6-foss-2017b.eb diff --git a/easybuild/easyconfigs/m/Mono/Mono-5.4.1.6-foss-2017b.eb b/easybuild/easyconfigs/m/Mono/Mono-5.4.1.6-foss-2017b.eb new file mode 100644 index 00000000000..62d6ede4010 --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-5.4.1.6-foss-2017b.eb @@ -0,0 +1,22 @@ +name = 'Mono' +version = '5.4.1.6' + +homepage = 'http://www.mono-project.com/' +description = """An open source, cross-platform, implementation of C# and the CLR that is + binary compatible with Microsoft.NET.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['bdfda0fe9ad5ce20bb2cf9e9bf28fed40f324141297479824e1f65d97da565df'] + +builddependencies = [ + ('Autotools', '20170619'), + ('CMake', '3.9.5'), + ('gettext', '0.19.8.1'), +] + +configopts = "--with-large-heap=yes --without-x" + +moduleclass = 'lang' From a8c5a7568662c0a8e9924e4a79baecde8cb86b95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2019 14:40:47 +0100 Subject: [PATCH 0914/5331] {bio}[intel/2018b] Seaborn v0.9.0 w/ Python 2.7.15 & 3.6.6 --- ...Seaborn-0.9.0-intel-2018b-Python-2.7.15.eb | 34 +++++++++++++++++++ .../Seaborn-0.9.0-intel-2018b-Python-3.6.6.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..debe3ec3068 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] + +dependencies = [ + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..61fdbde00d4 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.9.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f'] + +dependencies = [ + ('Python', '3.6.6'), + ('matplotlib', '3.0.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 316226d62a9be3c468857d3a6e742c7be94852ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2019 15:26:48 +0100 Subject: [PATCH 0915/5331] fix style issue in TensorFlow 1.13.1 easyconfig --- .../TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb index 47ab80905ce..9c524481aa0 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb @@ -88,9 +88,13 @@ exts_list = [ 'unpack_sources': False, }), (name, version, { - 'patches': ['TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.13.1_lrt-flag.patch'], - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'patches': [ + 'TensorFlow-1.11.0_swig-env.patch', + 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', + 'TensorFlow-1.13.1_lrt-flag.patch', + ], 'checksums': [ '7cd19978e6bc7edc2c847bce19f95515a742b34ea5e28e4389dade35348f58ed', # v1.13.1.tar.gz 'aa53c7f6d42b4a9e91e0ba639d79f69a7db3c0a88c3b8e43d332479b6368391a', # TensorFlow-1.11.0_swig-env.patch From c15f577b31f3d0cab69af8afe1f112c6ff860f3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2019 15:31:44 +0100 Subject: [PATCH 0916/5331] add missing patch file for TensorFlow 1.13.1 --- .../TensorFlow-1.13.1_lrt-flag.patch | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_lrt-flag.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_lrt-flag.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_lrt-flag.patch new file mode 100644 index 00000000000..4facc2e51ee --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_lrt-flag.patch @@ -0,0 +1,58 @@ +# Required on CentOS6 +# https://github.com/tensorflow/tensorflow/issues/15129 +--- tensorflow-1.13.1/tensorflow/tensorflow.bzl.orig 2019-03-01 10:57:59.056530606 +0100 ++++ tensorflow-1.13.1/tensorflow/tensorflow.bzl 2019-03-01 11:03:28.555868154 +0100 +@@ -377,7 +377,7 @@ + srcs = [], + deps = [], + data = [], +- linkopts = [], ++ linkopts = ["-lrt"], + framework_so = tf_binary_additional_srcs(), + kernels = [], + **kwargs): +@@ -413,7 +413,7 @@ + srcs = [], + deps = [], + data = [], +- linkopts = [], ++ linkopts = ["-lrt"], + copts = tf_copts(), + kernels = [], + **kwargs): +@@ -470,7 +470,7 @@ + tf_cc_binary( + name = tool, + copts = tf_copts(), +- linkopts = if_not_windows(["-lm", "-Wl,-ldl"]), ++ linkopts = if_not_windows(["-lm", "-Wl,-ldl", "-lrt"]), + linkstatic = 1, # Faster to link this one-time-use binary dynamically + deps = [op_gen] + deps, + ) +@@ -638,7 +638,7 @@ + hidden_file = None, + generated_target_name = None, + op_whitelist = [], +- cc_linkopts = [], ++ cc_linkopts = ["-lrt"], + api_def_srcs = []): + if (hidden or hidden_file) and op_whitelist: + fail("Cannot pass specify both hidden and op_whitelist.") +@@ -650,7 +650,7 @@ + tf_cc_binary( + name = tool_name, + copts = tf_copts(), +- linkopts = if_not_windows(["-lm", "-Wl,-ldl"]) + cc_linkopts, ++ linkopts = if_not_windows(["-lm", "-Wl,-ldl", "-lrt"]) + cc_linkopts, + linkstatic = 1, # Faster to link this one-time-use binary dynamically + visibility = [clean_dep("//tensorflow:internal")], + deps = ([ +@@ -924,7 +924,7 @@ + tags = [], + size = "medium", + args = None, +- linkopts = [], ++ linkopts = ["-lrt"], + kernels = [], + nocopts = None): + for src in srcs: From ad73e03d48cc961d9e22e5bbd8a656c65ad97582 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2019 15:24:54 +0100 Subject: [PATCH 0917/5331] add Jinja2, Sphinx, Click psutil, future extensiosn to Python 3.6.6 with GCCcore/8.2.0 toolchain --- .../p/Python/Python-3.7.2-GCCcore-8.2.0.eb | 77 +++++++++++++++++-- 1 file changed, 69 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb index 24515f58772..c0ad9295e62 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb @@ -41,7 +41,7 @@ exts_default_options = { } # order is important! -# package versions updated Mar 6th 2019 +# package versions updated Mar 15th 2019 exts_list = [ ('pip', '19.0.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], @@ -85,7 +85,7 @@ exts_list = [ 'checksums': ['d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73'], }), ('setuptools_scm', '3.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools_scm/'], 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.8.0', { @@ -197,9 +197,9 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], }), - ('certifi', '2018.11.29', { + ('certifi', '2019.3.9', { 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + 'checksums': ['b26104d6835d1f5e49452a26eb2ff87fe7090b89dfcaee5ea2212697e1e1d7ae'], }), ('urllib3', '1.24.1', { 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], @@ -233,9 +233,9 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/py'], 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), - ('scandir', '1.9.0', { + ('scandir', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scandir'], - 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], }), ('pathlib2', '2.3.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2'], @@ -254,9 +254,70 @@ exts_list = [ 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], 'modulename': 'attr', }), - ('pytest', '4.3.0', { + ('pytest', '4.3.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytest'], - 'checksums': ['067a1d4bf827ffdd56ad21bd46674703fce77c5957f6c1eef731f6146bfcef1c'], + 'checksums': ['592eaa2c33fae68c7d75aacf042efc9f77b27c08a6224a4f59beab8d9a420523'], + }), + ('MarkupSafe', '1.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('packaging', '19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + 'checksums': ['0c98a5d0be38ed775798ece1b9727178c4469d9c3b4ada66e8e6b7849f8732af'], + }), + ('sphinxcontrib-websupport', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], + 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], + 'modulename': 'sphinxcontrib.websupport', + }), + ('Pygments', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], + 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], + }), + ('imagesize', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], + }), + ('docutils', '0.14', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docutils/'], + 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], + }), + ('Babel', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], + }), + ('alabaster', '0.7.12', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], + 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], + }), + ('Sphinx', '1.8.5', { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + 'checksums': ['c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08'], + }), + ('Click', '7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('psutil', '5.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], + }), + ('future', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future'], + 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), ] From f3f759a42f58752e00ffa1dc93a4b1293ff225e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2019 17:09:17 +0100 Subject: [PATCH 0918/5331] drop FIXME from TensorFlow 1.13.1, going forward with installing tensorflow-estimator via .whl (for now) --- .../t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb index 9c524481aa0..05b73431a7c 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb @@ -81,7 +81,6 @@ exts_list = [ 'checksums': ['5e3700117981c2db762e512ed6586638124fac5842170701628088a11aeb51ac'], 'modulename': 'keras_preprocessing', }), - # FIXME new dep, should be installed from source rather using .whl? ('tensorflow-estimator', '1.13.0', { 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow-estimator'], 'source_tmpl': 'tensorflow_estimator-1.13.0-py2.py3-none-any.whl', From 26b6e8c12225dc25ac92e1facf4bb0674209c3db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2019 17:18:52 +0100 Subject: [PATCH 0919/5331] adding easyconfigs: slidingwindow-0.0.13-intel-2018b-Python-2.7.15.eb --- ...window-0.0.13-intel-2018b-Python-2.7.15.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..25a140232a1 --- /dev/null +++ b/easybuild/easyconfigs/s/slidingwindow/slidingwindow-0.0.13-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'slidingwindow' +version = '0.0.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/adamrehn/slidingwindow' +description = """slidingwindow is a simple little Python library for computing a set of windows into a larger dataset, + designed for use with image-processing algorithms that utilise a sliding window to break the processing up + into a series of smaller chunks.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [('Python', '2.7.15')] + +use_pip = True + +exts_list = [ + ('psutil', '5.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], + }), + (name, version, { + 'source_urls': ['https://github.com/adamrehn/slidingwindow/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['8be4df997c1659226201db89610488bb4f85e08811b7cc1775a83e9499b09c82'], + }), +] + +moduleclass = 'data' From e17d7e938414b1d3ffa4e92260f01bb5121f6fe9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2019 17:41:40 +0100 Subject: [PATCH 0920/5331] adding easyconfigs: LIBSVM-3.23-intel-2018b.eb --- .../l/LIBSVM/LIBSVM-3.23-intel-2018b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.23-intel-2018b.eb diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.23-intel-2018b.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.23-intel-2018b.eb new file mode 100644 index 00000000000..24c967ef9e2 --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.23-intel-2018b.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM' +version = '3.23' + +homepage = 'http://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression + (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['257aed630dc0a0163e12cb2a80aea9c7dc988e55f28d69c945a38b9433c0ea4a'] + +files_to_copy = [(['svm-*'], 'bin'), 'tools'] + +sanity_check_paths = { + 'files': ['bin/svm-%s' % x for x in ['predict', 'scale', 'train']], + 'dirs': ['tools'], +} + +moduleclass = 'lib' From b919610ccb776a318890a83084fbf003a719832a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2019 17:44:17 +0100 Subject: [PATCH 0921/5331] adding easyconfigs: scp-0.13.1-intel-2018b-Python-2.7.15.eb --- .../scp-0.13.1-intel-2018b-Python-2.7.15.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..2a31d2d0974 --- /dev/null +++ b/easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'scp' +version = '0.13.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jbardin/scp.py' +description = """The scp.py module uses a paramiko transport to send and recieve files via the scp1 protocol.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4320ad188d3b8216352fb6c3647e0080ca14ced217735afc053256f86cd65159'] + +dependencies = [('Python', '2.7.15')] + +download_dep_fail = True +#use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 9165a1abed9350556893bd1d202f204eb2593565 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 15 Mar 2019 19:19:42 +0200 Subject: [PATCH 0922/5331] adding easyconfigs: Ninja-1.9.0-GCCcore-8.2.0.eb --- .../n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..a49c5ff4a97 --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.9.0' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'vectorize': False} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5d7ec75828f8d3fd1a0c2f31b5b0cea780cdfe1031359228c428c1a48bfcd5b9'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Python', '3.7.2'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +moduleclass = 'tools' From b5914dc8721d96a29e434b87d92847ede86049f0 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 15 Mar 2019 20:09:07 +0200 Subject: [PATCH 0923/5331] Remove unnecessary toolchainopt --- easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb index a49c5ff4a97..887f01adbf6 100644 --- a/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.9.0-GCCcore-8.2.0.eb @@ -7,7 +7,6 @@ homepage = 'https://ninja-build.org/' description = "Ninja is a small build system with a focus on speed." toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -toolchainopts = {'vectorize': False} source_urls = ['https://github.com/ninja-build/ninja/archive/'] sources = ['v%(version)s.tar.gz'] From 8d9418543959a45dc080e456999693a9a9e709cf Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 15 Mar 2019 20:11:23 +0200 Subject: [PATCH 0924/5331] adding easyconfigs: Tk-8.6.9-GCCcore-8.2.0.eb --- .../t/Tk/Tk-8.6.9-GCCcore-8.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.9-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.9-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.9-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..55856934541 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.9-GCCcore-8.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.9' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] +checksums = [ + 'd3f9161e8ba0f107fe8d4df1f6d3a14c30cc3512dfc12a795daa367a27660dac', # tk8.6.9-src.tar.gz + '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d', # Tk-8.6.4_different-prefix-with-tcl.patch +] + +builddependencies = [('binutils', '2.31.1')] +dependencies = [ + ('Tcl', version), + ('X11', '20190311'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' From 67c258a0b049938d14f0b523f65022bf6d080127 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2019 22:22:26 +0100 Subject: [PATCH 0925/5331] enable use_pip in scp 0.13.1 easyconfig --- .../easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb index 2a31d2d0974..f78369388fa 100644 --- a/easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/scp/scp-0.13.1-intel-2018b-Python-2.7.15.eb @@ -16,7 +16,7 @@ checksums = ['4320ad188d3b8216352fb6c3647e0080ca14ced217735afc053256f86cd65159'] dependencies = [('Python', '2.7.15')] download_dep_fail = True -#use_pip = True +use_pip = True sanity_check_paths = { 'files': [], From 39b7165fa350d152cafb69d7deedb62e24abc14a Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 15 Mar 2019 16:18:09 -0700 Subject: [PATCH 0926/5331] GTS 0.7.6 foss-2018b --- .../easyconfigs/g/GTS/GTS-0.7.6-foss-2018b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2018b.eb diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2018b.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2018b.eb new file mode 100644 index 00000000000..a3edf195449 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-foss-2018b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.54.3'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' From 17fb5ca5412af3a55ab701ef2ae0a9b5578780aa Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 16 Mar 2019 01:29:14 +0200 Subject: [PATCH 0927/5331] adding easyconfigs: LLVM-7.0.1-GCCcore-8.2.0.eb --- .../l/LLVM/LLVM-7.0.1-GCCcore-8.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-7.0.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-7.0.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-7.0.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..c112b51426f --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-7.0.1-GCCcore-8.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '7.0.1' + +homepage = "http://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] +checksums = ['a38dfc4db47102ec79dcc2aa61e93722c5f6f06f0a961073bd84b78fb949419b'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), + ('Python', '3.7.2'), +] + +dependencies = [ + ('ncurses', '6.1'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' From 018b6f72c5afb2017500c5dda9a2ce4551b89ab9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 Mar 2019 00:35:07 +0100 Subject: [PATCH 0928/5331] remove outdated 'typing' Python package from Python 3.7.2 easyconfig --- easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb index c0ad9295e62..bb0bef58605 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb @@ -299,10 +299,6 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), - ('typing', '3.6.6', { - 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], - 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], - }), ('Sphinx', '1.8.5', { 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], 'checksums': ['c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08'], From d8543c928e71ce10f2fb7c124a57d891aeee03f7 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 16 Mar 2019 01:35:11 +0200 Subject: [PATCH 0929/5331] adding easyconfigs: libgd-2.2.5-GCCcore-8.2.0.eb --- .../l/libgd/libgd-2.2.5-GCCcore-8.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.2.5-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.2.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.2.5-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..5def4e52511 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.2.5-GCCcore-8.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.2.5' + +homepage = 'https://libgd.github.io/' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a66111c9b4a04e818e9e2a37d7ae8d4aae0939a100a36b0ffb52c706a09074b5'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('fontconfig', '2.13.1'), + ('libjpeg-turbo', '2.0.2'), + ('libpng', '1.6.36'), + ('zlib', '1.2.11'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ["lib/libgd.a", "lib/libgd.%s" % SHLIB_EXT], + 'dirs': ["bin", "include"], +} + +moduleclass = 'lib' From 18fe36270389d7fe0cbffad30644f00dbb39281e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Mar 2019 11:14:27 +0100 Subject: [PATCH 0930/5331] no need to use xargs in post-install command for SqueezeMeta to fix shebang in Perl scripts --- .../s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb index 81d52b96174..caa27abf2c0 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb @@ -57,7 +57,7 @@ postinstallcmds = [ # remove vendored tools that are include as dependencies "rm -r %(installdir)s/bin/*", # fix shebang in Perl scripts - "ls %(installdir)s/scripts/*.pl | xargs sed -i 's@#!/usr/bin/perl@#!/usr/bin/env perl@g'", + "sed -i 's@#!/usr/bin/perl@#!/usr/bin/env perl@g' %(installdir)s/scripts/*.pl", ] sanity_check_paths = { From 39759a047547d36fb4f97546e986d1af1aadd06f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Mar 2019 13:56:31 +0100 Subject: [PATCH 0931/5331] avoid duplicate dependency on MEGAHIT in SqueezeMeta easyconfig --- .../s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb index caa27abf2c0..99b2e9b26ea 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb @@ -46,7 +46,6 @@ dependencies = [ ('Bowtie2', '2.3.4.2'), ('canu', '1.8', '-Perl-%(perlver)s'), ('HMMER', '3.2.1'), - ('MEGAHIT', '1.1.4', versionsuffix), ('MUMmer', '4.0.0beta2'), ('pplacer', '1.1.alpha19', '', True), ] From cdfa6eacdb914b5621d524a9f18d27a858f393a7 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Mon, 18 Mar 2019 10:22:34 -0500 Subject: [PATCH 0932/5331] adding easyconfigs: IntelPython-2.7.15-2019.2.066.eb, IntelPython-3.6.8-2019.2.066.eb --- .../IntelPython-2.7.15-2019.2.066.eb | 42 +++++++++++++++++++ .../IntelPython-3.6.8-2019.2.066.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb create mode 100644 easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb new file mode 100644 index 00000000000..16671346fa8 --- /dev/null +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb @@ -0,0 +1,42 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'IntelPython' +version = '2.7.15' +pysver = version[0] +relver = '2019.2.066' +versionsuffix = '-%s' % relver + +homepage = 'https://software.intel.com/en-us/intel-distribution-for-python' + +description = """ + Intel® Distribution for Python. Powered by Anaconda. + Accelerating Python* performance on modern architectures from Intel. +""" + +# l_pythoni2_p_2019.2.066.tar.gz from the Intel site +sources = ['l_pythoni%s_p_%s.tar.gz' % (pysver, relver)] + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +skipsteps = ['configure', 'build'] + +buildininstalldir = True + +preinstallopts = """ + echo -e "install:\n\t./setup_intel_python.sh" > Makefile +""" + +sanity_check_paths = { + 'dirs': ['intelpython%s/%s' % (pysver, x) for x in ['bin', 'etc', 'include', 'lib']], + 'files': ['intelpython%s/bin/ipython' % pysver], +} + +modextrapaths = { + 'CONDA_PREFIX': 'intelpython%s' % pysver, + 'PATH': 'intelpython%s/bin' % pysver, + 'LD_LIBRARY_PATH': 'intelpython%s/lib' % pysver, +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb new file mode 100644 index 00000000000..808edfa01ec --- /dev/null +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb @@ -0,0 +1,42 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'IntelPython' +version = '3.6.8' +pysver = version[0] +relver = '2019.2.066' +versionsuffix = '-%s' % relver + +homepage = 'https://software.intel.com/en-us/intel-distribution-for-python' + +description = """ + Intel® Distribution for Python. Powered by Anaconda. + Accelerating Python* performance on modern architectures from Intel. +""" + +# l_pythoni3_p_2019.2.066.tar.gz from the Intel site +sources = ['l_pythoni%s_p_%s.tar.gz' % (pysver, relver)] + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +skipsteps = ['configure', 'build'] + +buildininstalldir = True + +preinstallopts = """ + echo -e "install:\n\t./setup_intel_python.sh" > Makefile +""" + +sanity_check_paths = { + 'dirs': ['intelpython%s/%s' % (pysver, x) for x in ['bin', 'etc', 'include', 'lib']], + 'files': ['intelpython%s/bin/ipython' % pysver], +} + +modextrapaths = { + 'CONDA_PREFIX': 'intelpython%s' % pysver, + 'PATH': 'intelpython%s/bin' % pysver, + 'LD_LIBRARY_PATH': 'intelpython%s/lib' % pysver, +} + +moduleclass = 'lang' From b13cf39e96427a4d987ca62b0a588216b764b89b Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Mon, 18 Mar 2019 11:41:43 -0500 Subject: [PATCH 0933/5331] add checksums --- .../easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb | 1 + .../easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb index 16671346fa8..031de9fb5fb 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb @@ -17,6 +17,7 @@ description = """ # l_pythoni2_p_2019.2.066.tar.gz from the Intel site sources = ['l_pythoni%s_p_%s.tar.gz' % (pysver, relver)] +checksums = ['dd0b73db5d0d79c3cdf779d10092eae32780d720b74ed8fde2a2c46e23143de1'] toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb index 808edfa01ec..82da6e376b6 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb @@ -17,6 +17,7 @@ description = """ # l_pythoni3_p_2019.2.066.tar.gz from the Intel site sources = ['l_pythoni%s_p_%s.tar.gz' % (pysver, relver)] +checksums = ['804883fc1413ee72b0ae421a8ac82ab158fc01c8b4631a44a9d2ef1a19324751'] toolchain = {'name': 'dummy', 'version': 'dummy'} From 44c06e2f079cea12d9c23c9ac04e3c476ddf6465 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Mar 2019 17:49:32 +0100 Subject: [PATCH 0934/5331] {lang}[foss/2019a] SciPy-bundle v2019.03 w/ Python 2.7.15 + 3.7.2 (WIP) --- ...bundle-2019.03-foss-2019a-Python-2.7.15.eb | 43 +++++++++++++++++++ ...-bundle-2019.03-foss-2019a-Python-3.7.2.eb | 43 +++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..b0e005bf690 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-2.7.15.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2019.03' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'pic': True} + +dependencies = [('Python', '2.7.15')] + +use_pip = True + +# order is important! +# package versions updated Mar 15th 2019 +exts_list = [ + ('numpy', '1.16.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6c692e3879dde0b67a9dc78f9bfb6f61c666b4562fd8619632d7043fb5b691b0'], + }), + ('scipy', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + 'checksums': ['e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c'], + }), + ('mpi4py', '3.0.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'], + }), + ('pandas', '0.24.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], + }), + ('mpmath', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..ce6a90be0c5 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2019.03' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'pic': True} + +dependencies = [('Python', '3.7.2')] + +use_pip = True + +# order is important! +# package versions updated Mar 15th 2019 +exts_list = [ + ('numpy', '1.16.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6c692e3879dde0b67a9dc78f9bfb6f61c666b4562fd8619632d7043fb5b691b0'], + }), + ('scipy', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + 'checksums': ['e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c'], + }), + ('mpi4py', '3.0.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'], + }), + ('pandas', '0.24.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], + }), + ('mpmath', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), +] + +moduleclass = 'lang' From d4fcfc04737452f54a4ef7e47232d8287498d12c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Mar 2019 17:51:31 +0100 Subject: [PATCH 0935/5331] {lang}[intel/2019a] SciPy-bundle v2019.03 w/ Python 2.7.15 + 3.7.2 (WIP) --- ...undle-2019.03-intel-2019a-Python-2.7.15.eb | 54 +++++++++++++++++++ ...bundle-2019.03-intel-2019a-Python-3.7.2.eb | 54 +++++++++++++++++++ 2 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..4063ccd7a93 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-2.7.15.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2019.03' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True} + +dependencies = [('Python', '2.7.15')] + +use_pip = True + +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +# order is important! +# package versions updated Mar 15th 2019 +exts_list = [ + ('numpy', '1.16.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': [ + 'numpy-1.12.0-mkl.patch', + 'numpy-1.16.1_fix-ifort-V-stderr.patch', + ], + 'checksums': [ + '6c692e3879dde0b67a9dc78f9bfb6f61c666b4562fd8619632d7043fb5b691b0', # numpy-1.16.2.zip + 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch + 'fc7f0c4b910bf3706d43661b94696f07b6e317bfeac062c2c78b3926fde713a7', # numpy-1.16.1_fix-ifort-V-stderr.patch + ], + }), + ('scipy', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + 'checksums': ['e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c'], + }), + ('mpi4py', '3.0.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'], + }), + ('pandas', '0.24.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], + }), + ('mpmath', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..dad4d9f9f71 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2019.03' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True} + +dependencies = [('Python', '3.7.2')] + +use_pip = True + +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +# order is important! +# package versions updated Mar 15th 2019 +exts_list = [ + ('numpy', '1.16.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': [ + 'numpy-1.12.0-mkl.patch', + 'numpy-1.16.1_fix-ifort-V-stderr.patch', + ], + 'checksums': [ + '6c692e3879dde0b67a9dc78f9bfb6f61c666b4562fd8619632d7043fb5b691b0', # numpy-1.16.2.zip + 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch + 'fc7f0c4b910bf3706d43661b94696f07b6e317bfeac062c2c78b3926fde713a7', # numpy-1.16.1_fix-ifort-V-stderr.patch + ], + }), + ('scipy', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + 'checksums': ['e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c'], + }), + ('mpi4py', '3.0.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'], + }), + ('pandas', '0.24.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], + }), + ('mpmath', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), +] + +moduleclass = 'lang' From 32180c787b9eafdbd2c94d4b757c58d47c694400 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 18 Mar 2019 22:00:21 +0200 Subject: [PATCH 0936/5331] adding easyconfigs: SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb --- .../SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..47ff28189db --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,21 @@ +name = 'SWIG' +version = '3.0.12' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7cf9f447ae7ed1c51722efc45e7f14418d15d7a1e143ac9f09a668999f4fc94d'] + +dependencies = [ + ('Python', '3.7.2'), + ('PCRE', '8.43'), +] + +moduleclass = 'devel' From 5085ce180104bd7354ac4e7f094e97db73aa87d0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Mar 2019 09:38:27 +0200 Subject: [PATCH 0937/5331] adding easyconfigs: UCX-1.5.0-GCCcore-7.3.0.eb, UCX-1.5.0-GCCcore-8.2.0.eb --- .../u/UCX/UCX-1.5.0-GCCcore-7.3.0.eb | 42 +++++++++++++++++++ .../u/UCX/UCX-1.5.0-GCCcore-8.2.0.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..91b414d5008 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-7.3.0.eb @@ -0,0 +1,42 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.5.0' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['84f6e4fa5740afebb9b1c8bb405c07206e58c56f83120dcfcd8dc89e4b7d7458'] + +builddependencies = [ + ('binutils', '2.30'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +dependencies = [ + ('numactl', '2.0.11'), +] + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..b0af5919a21 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-8.2.0.eb @@ -0,0 +1,42 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.5.0' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['84f6e4fa5740afebb9b1c8bb405c07206e58c56f83120dcfcd8dc89e4b7d7458'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +dependencies = [ + ('numactl', '2.0.12'), +] + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +moduleclass = 'mpi' From c3341a338c8f18a45edae99d7ac74a6e734769d9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Mar 2019 09:58:27 +0200 Subject: [PATCH 0938/5331] adding easyconfigs: PMIx-3.1.1-GCCcore-6.4.0.eb, PMIx-3.1.1-GCCcore-7.3.0.eb, PMIx-3.1.1-GCCcore-8.2.0.eb --- .../p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb | 51 +++++++++++++++++++ .../p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb | 51 +++++++++++++++++++ .../p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb | 51 +++++++++++++++++++ 3 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..364a569a178 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb @@ -0,0 +1,51 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '3.1.1' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pmix/pmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +patches = ['%(name)s-%(version)s_fix_various_problems.patch'] +checksums = [ + '6d4780e7a198dc72965d6e3c41e1c41edd69ff44ac089f185123c49950cb43ab', # pmix-3.1.1.tar.bz2 + '23a5dd33055ecc3f94116a52d17ac6151dcc730292a825e33fb9140a02f43e92', # PMIx-3.1.1_fix_various_problems.patch +] + +builddependencies = [('binutils', '2.28')] + +dependencies = [ + ('libevent', '2.1.8'), + ('zlib', '1.2.11'), + ('hwloc', '1.11.7'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..5d3139cb8a1 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb @@ -0,0 +1,51 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '3.1.1' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pmix/pmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +patches = ['%(name)s-%(version)s_fix_various_problems.patch'] +checksums = [ + '6d4780e7a198dc72965d6e3c41e1c41edd69ff44ac089f185123c49950cb43ab', # pmix-3.1.1.tar.bz2 + '23a5dd33055ecc3f94116a52d17ac6151dcc730292a825e33fb9140a02f43e92', # PMIx-3.1.1_fix_various_problems.patch +] + +builddependencies = [('binutils', '2.30')] + +dependencies = [ + ('libevent', '2.1.8'), + ('zlib', '1.2.11'), + ('hwloc', '1.11.10'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..9ecc3f847dc --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb @@ -0,0 +1,51 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '3.1.1' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pmix/pmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +patches = ['%(name)s-%(version)s_fix_various_problems.patch'] +checksums = [ + '6d4780e7a198dc72965d6e3c41e1c41edd69ff44ac089f185123c49950cb43ab', # pmix-3.1.1.tar.bz2 + '23a5dd33055ecc3f94116a52d17ac6151dcc730292a825e33fb9140a02f43e92', # PMIx-3.1.1_fix_various_problems.patch +] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('libevent', '2.1.8'), + ('zlib', '1.2.11'), + ('hwloc', '1.11.11'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'mpi' From 8330d41eec15c1cee6ece1abba05d248044dd344 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Mar 2019 10:00:39 +0200 Subject: [PATCH 0939/5331] Add version for GCCcore 6.4.0. --- .../u/UCX/UCX-1.5.0-GCCcore-6.4.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..8c86e5282c2 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.5.0' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['84f6e4fa5740afebb9b1c8bb405c07206e58c56f83120dcfcd8dc89e4b7d7458'] + +builddependencies = [ + ('binutils', '2.28'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +dependencies = [ + ('numactl', '2.0.11'), +] + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +moduleclass = 'mpi' From 369c846c8fd2208e3c9d0c7f1c8cc40188d1e4ce Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 19 Mar 2019 10:39:30 +0200 Subject: [PATCH 0940/5331] Add binutils --- .../easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb index 47ff28189db..e2be0a37bbc 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb @@ -14,6 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['7cf9f447ae7ed1c51722efc45e7f14418d15d7a1e143ac9f09a668999f4fc94d'] dependencies = [ + ('binutils', '2.31.1'), ('Python', '3.7.2'), ('PCRE', '8.43'), ] From 86cef99cbcaf9cf20290234669fe2e63167ba8bd Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 19 Mar 2019 12:28:25 +0200 Subject: [PATCH 0941/5331] Add binutils --- .../s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb index e2be0a37bbc..d300c9ec738 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.12-GCCcore-8.2.0-Python-3.7.2.eb @@ -13,8 +13,9 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['7cf9f447ae7ed1c51722efc45e7f14418d15d7a1e143ac9f09a668999f4fc94d'] +builddependencies = [('binutils', '2.31.1')] + dependencies = [ - ('binutils', '2.31.1'), ('Python', '3.7.2'), ('PCRE', '8.43'), ] From eb73d83d7382bf4b9a0c048fdc9bf7a93bdf4739 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 19 Mar 2019 12:48:54 +0200 Subject: [PATCH 0942/5331] Add missing libevent dependencies and patches. --- .../libevent/libevent-2.1.8-GCCcore-8.2.0.eb | 32 +++ .../PMIx-3.1.1_fix_various_problems.patch | 250 ++++++++++++++++++ 2 files changed, 282 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-3.1.1_fix_various_problems.patch diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..2c5fd0420c7 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.8' + +homepage = 'http://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['965cc5a8bb46ce4199a47e9b2c9e1cae3b137e8356ffdad6d94d3b9069b71dc2'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1_fix_various_problems.patch b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1_fix_various_problems.patch new file mode 100644 index 00000000000..39dffdc8d66 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1_fix_various_problems.patch @@ -0,0 +1,250 @@ +Pull in 3 important commits from v3.1 batch that is missing in 3.1.1 release. + +7224a62d029c2e6225cc2ec08184ac9c185c767c: Fix typo in PMIX_SYSTEM_EVENT macro +ec7da358b39ef33cb94a1790522312644f448866: Forward PMIx MCA params by launchers +ed763d698127497c72c614d65bdc47f1a33617bc: Shift the non-standard macros to pmix_extend.h + +Åke Sandgren, 20190123 +diff --git a/include/pmix_common.h.in b/include/pmix_common.h.in +index e636134..35aecfa 100644 +--- a/include/pmix_common.h.in ++++ b/include/pmix_common.h.in +@@ -836,7 +836,7 @@ typedef int pmix_status_t; + + /* define a macro for identifying system event values */ + #define PMIX_SYSTEM_EVENT(a) \ +- (230 > (a) && -331 < (a)) ++ ((a) <= PMIX_ERR_NODE_DOWN && PMIX_ERR_SYS_OTHER <= (a)) + + /* used by event handlers */ + #define PMIX_EVENT_NO_ACTION_TAKEN -331 +diff --git a/include/pmix_extend.h b/include/pmix_extend.h +index f4bb74f..f6f320a 100644 +--- a/include/pmix_extend.h ++++ b/include/pmix_extend.h +@@ -1,5 +1,5 @@ + /* +- * Copyright (c) 2013-2018 Intel, Inc. All rights reserved. ++ * Copyright (c) 2013-2019 Intel, Inc. All rights reserved. + * Copyright (c) 2015 Artem Y. Polyakov . + * All rights reserved. + * Copyright (c) 2015 Research Organization for Information Science +@@ -42,18 +42,6 @@ + * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * $HEADER$ +- * +- * PMIx provides a "function-shipping" approach to support for +- * implementing the server-side of the protocol. This method allows +- * resource managers to implement the server without being burdened +- * with PMIx internal details. Accordingly, each PMIx API is mirrored +- * here in a function call to be provided by the server. When a +- * request is received from the client, the corresponding server function +- * will be called with the information. +- * +- * Any functions not supported by the RM can be indicated by a NULL for +- * the function pointer. Client calls to such functions will have a +- * "not supported" error returned. + */ + + #ifndef PMIx_EXTEND_H +@@ -63,12 +51,12 @@ + extern "C" { + #endif + +-/* declare a convenience macro for checking keys */ + /* expose some functions that are resolved in the + * PMIx library, but part of a header that + * includes internal functions - we don't +- * want to expose the entire header here. For +- * consistency, we provide macro versions as well ++ * want to expose the entire header here. These ++ * back the associated macros included in the ++ * PMIx Standard + */ + void pmix_value_load(pmix_value_t *v, const void *data, pmix_data_type_t type); + +@@ -96,6 +84,70 @@ pmix_status_t pmix_setenv(const char *name, const char *value, + bool overwrite, char ***env); + + ++/* the following are a set of legacy macros not included in the ++ * PMIx Standard, but used in some codes (e.g., the Slurm plugin). ++ * These should be considered "deprecated" and will be removed ++ * in the next major release of the PRI */ ++#define PMIX_VAL_FIELD_int(x) ((x)->data.integer) ++#define PMIX_VAL_FIELD_uint32_t(x) ((x)->data.uint32) ++#define PMIX_VAL_FIELD_uint16_t(x) ((x)->data.uint16) ++#define PMIX_VAL_FIELD_string(x) ((x)->data.string) ++#define PMIX_VAL_FIELD_float(x) ((x)->data.fval) ++#define PMIX_VAL_FIELD_byte(x) ((x)->data.byte) ++#define PMIX_VAL_FIELD_flag(x) ((x)->data.flag) ++ ++#define PMIX_VAL_TYPE_int PMIX_INT ++#define PMIX_VAL_TYPE_uint32_t PMIX_UINT32 ++#define PMIX_VAL_TYPE_uint16_t PMIX_UINT16 ++#define PMIX_VAL_TYPE_string PMIX_STRING ++#define PMIX_VAL_TYPE_float PMIX_FLOAT ++#define PMIX_VAL_TYPE_byte PMIX_BYTE ++#define PMIX_VAL_TYPE_flag PMIX_BOOL ++ ++#define PMIX_VAL_set_assign(_v, _field, _val ) \ ++ do { \ ++ (_v)->type = PMIX_VAL_TYPE_ ## _field; \ ++ PMIX_VAL_FIELD_ ## _field((_v)) = _val; \ ++ } while (0) ++ ++#define PMIX_VAL_set_strdup(_v, _field, _val ) \ ++ do { \ ++ (_v)->type = PMIX_VAL_TYPE_ ## _field; \ ++ PMIX_VAL_FIELD_ ## _field((_v)) = strdup(_val); \ ++ } while (0) ++ ++#define PMIX_VAL_SET_int PMIX_VAL_set_assign ++#define PMIX_VAL_SET_uint32_t PMIX_VAL_set_assign ++#define PMIX_VAL_SET_uint16_t PMIX_VAL_set_assign ++#define PMIX_VAL_SET_string PMIX_VAL_set_strdup ++#define PMIX_VAL_SET_float PMIX_VAL_set_assign ++#define PMIX_VAL_SET_byte PMIX_VAL_set_assign ++#define PMIX_VAL_SET_flag PMIX_VAL_set_assign ++ ++#define PMIX_VAL_SET(_v, _field, _val ) \ ++ PMIX_VAL_SET_ ## _field(_v, _field, _val) ++ ++#define PMIX_VAL_cmp_val(_val1, _val2) ((_val1) != (_val2)) ++#define PMIX_VAL_cmp_float(_val1, _val2) (((_val1)>(_val2))?(((_val1)-(_val2))>0.000001):(((_val2)-(_val1))>0.000001)) ++#define PMIX_VAL_cmp_ptr(_val1, _val2) strncmp(_val1, _val2, strlen(_val1)+1) ++ ++#define PMIX_VAL_CMP_int PMIX_VAL_cmp_val ++#define PMIX_VAL_CMP_uint32_t PMIX_VAL_cmp_val ++#define PMIX_VAL_CMP_uint16_t PMIX_VAL_cmp_val ++#define PMIX_VAL_CMP_float PMIX_VAL_cmp_float ++#define PMIX_VAL_CMP_string PMIX_VAL_cmp_ptr ++#define PMIX_VAL_CMP_byte PMIX_VAL_cmp_val ++#define PMIX_VAL_CMP_flag PMIX_VAL_cmp_val ++ ++#define PMIX_VAL_ASSIGN(_v, _field, _val) \ ++ PMIX_VAL_set_assign(_v, _field, _val) ++ ++#define PMIX_VAL_CMP(_field, _val1, _val2) \ ++ PMIX_VAL_CMP_ ## _field(_val1, _val2) ++ ++#define PMIX_VAL_FREE(_v) \ ++ PMIx_free_value_data(_v) ++ + #if defined(c_plusplus) || defined(__cplusplus) + } + #endif +diff --git a/src/tool/pmix_tool.c b/src/tool/pmix_tool.c +index 1186626..effa119 100644 +--- a/src/tool/pmix_tool.c ++++ b/src/tool/pmix_tool.c +@@ -63,6 +63,7 @@ + #include "src/runtime/pmix_rte.h" + #include "src/mca/bfrops/base/base.h" + #include "src/mca/gds/base/base.h" ++#include "src/mca/pnet/base/base.h" + #include "src/mca/ptl/base/base.h" + #include "src/mca/psec/psec.h" + #include "src/include/pmix_globals.h" +@@ -619,6 +620,13 @@ PMIX_EXPORT int PMIx_tool_init(pmix_proc_t *proc, + rcv->cbfunc = pmix_server_message_handler; + /* add it to the end of the list of recvs */ + pmix_list_append(&pmix_ptl_globals.posted_recvs, &rcv->super); ++ /* open the pnet framework so we can harvest envars */ ++ rc = pmix_mca_base_framework_open(&pmix_pnet_base_framework, 0); ++ if (PMIX_SUCCESS != rc){ ++ PMIX_RELEASE_THREAD(&pmix_global_lock); ++ return rc; ++ } ++ /* note that we do not select active plugins as we don't need them */ + } + + /* setup IOF */ +@@ -1188,6 +1196,7 @@ PMIX_EXPORT pmix_status_t PMIx_tool_finalize(void) + } + } + ++ (void)pmix_mca_base_framework_close(&pmix_pnet_base_framework); + PMIX_DESTRUCT(&pmix_server_globals.clients); + PMIX_LIST_DESTRUCT(&pmix_server_globals.collectives); + PMIX_LIST_DESTRUCT(&pmix_server_globals.remote_pnd); +diff --git a/test/test_common.h b/test/test_common.h +index 88c7d32..fd25f8b 100644 +--- a/test/test_common.h ++++ b/test/test_common.h +@@ -1,5 +1,5 @@ + /* +- * Copyright (c) 2013-2018 Intel, Inc. All rights reserved. ++ * Copyright (c) 2013-2019 Intel, Inc. All rights reserved. + * Copyright (c) 2015 Artem Y. Polyakov . + * All rights reserved. + * Copyright (c) 2015 Research Organization for Information Science +@@ -346,67 +346,4 @@ typedef struct { + } \ + } while (0) + +-/* Key-Value pair management macros */ +-// TODO: add all possible types/fields here. +- +-#define PMIX_VAL_FIELD_int(x) ((x)->data.integer) +-#define PMIX_VAL_FIELD_uint32_t(x) ((x)->data.uint32) +-#define PMIX_VAL_FIELD_uint16_t(x) ((x)->data.uint16) +-#define PMIX_VAL_FIELD_string(x) ((x)->data.string) +-#define PMIX_VAL_FIELD_float(x) ((x)->data.fval) +-#define PMIX_VAL_FIELD_byte(x) ((x)->data.byte) +-#define PMIX_VAL_FIELD_flag(x) ((x)->data.flag) +- +-#define PMIX_VAL_TYPE_int PMIX_INT +-#define PMIX_VAL_TYPE_uint32_t PMIX_UINT32 +-#define PMIX_VAL_TYPE_uint16_t PMIX_UINT16 +-#define PMIX_VAL_TYPE_string PMIX_STRING +-#define PMIX_VAL_TYPE_float PMIX_FLOAT +-#define PMIX_VAL_TYPE_byte PMIX_BYTE +-#define PMIX_VAL_TYPE_flag PMIX_BOOL +- +-#define PMIX_VAL_set_assign(_v, _field, _val ) \ +- do { \ +- (_v)->type = PMIX_VAL_TYPE_ ## _field; \ +- PMIX_VAL_FIELD_ ## _field((_v)) = _val; \ +- } while (0) +- +-#define PMIX_VAL_set_strdup(_v, _field, _val ) \ +- do { \ +- (_v)->type = PMIX_VAL_TYPE_ ## _field; \ +- PMIX_VAL_FIELD_ ## _field((_v)) = strdup(_val); \ +- } while (0) +- +-#define PMIX_VAL_SET_int PMIX_VAL_set_assign +-#define PMIX_VAL_SET_uint32_t PMIX_VAL_set_assign +-#define PMIX_VAL_SET_uint16_t PMIX_VAL_set_assign +-#define PMIX_VAL_SET_string PMIX_VAL_set_strdup +-#define PMIX_VAL_SET_float PMIX_VAL_set_assign +-#define PMIX_VAL_SET_byte PMIX_VAL_set_assign +-#define PMIX_VAL_SET_flag PMIX_VAL_set_assign +- +-#define PMIX_VAL_SET(_v, _field, _val ) \ +- PMIX_VAL_SET_ ## _field(_v, _field, _val) +- +-#define PMIX_VAL_cmp_val(_val1, _val2) ((_val1) != (_val2)) +-#define PMIX_VAL_cmp_float(_val1, _val2) (((_val1)>(_val2))?(((_val1)-(_val2))>0.000001):(((_val2)-(_val1))>0.000001)) +-#define PMIX_VAL_cmp_ptr(_val1, _val2) strncmp(_val1, _val2, strlen(_val1)+1) +- +-#define PMIX_VAL_CMP_int PMIX_VAL_cmp_val +-#define PMIX_VAL_CMP_uint32_t PMIX_VAL_cmp_val +-#define PMIX_VAL_CMP_uint16_t PMIX_VAL_cmp_val +-#define PMIX_VAL_CMP_float PMIX_VAL_cmp_float +-#define PMIX_VAL_CMP_string PMIX_VAL_cmp_ptr +-#define PMIX_VAL_CMP_byte PMIX_VAL_cmp_val +-#define PMIX_VAL_CMP_flag PMIX_VAL_cmp_val +- +-#define PMIX_VAL_ASSIGN(_v, _field, _val) \ +- PMIX_VAL_set_assign(_v, _field, _val) +- +-#define PMIX_VAL_CMP(_field, _val1, _val2) \ +- PMIX_VAL_CMP_ ## _field(_val1, _val2) +- +-#define PMIX_VAL_FREE(_v) \ +- PMIx_free_value_data(_v) +- + #endif // TEST_COMMON_H From ca97e8280ca73b32b109e2296c7fab1e3b2e4ef9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Mar 2019 10:43:11 +0100 Subject: [PATCH 0943/5331] add missing numpy patch files required by SciPy-bundle using 'intel' toolchain --- .../s/SciPy-bundle/numpy-1.12.0-mkl.patch | 55 +++++++++++++++++++ .../numpy-1.16.1_fix-ifort-V-stderr.patch | 15 +++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.12.0-mkl.patch create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.1_fix-ifort-V-stderr.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.12.0-mkl.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.12.0-mkl.patch new file mode 100644 index 00000000000..3d09924f966 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.12.0-mkl.patch @@ -0,0 +1,55 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) +diff -ru numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py numpy-1.12.0/numpy/distutils/fcompiler/__init__.py +--- numpy-1.12.0.orig/numpy/distutils/fcompiler/__init__.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/fcompiler/__init__.py 2017-03-06 17:19:07.262810683 +0100 +@@ -628,7 +628,10 @@ + return options + + def library_option(self, lib): +- return "-l" + lib ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib + def library_dir_option(self, dir): + return "-L" + dir + +diff -ru numpy-1.12.0.orig/numpy/distutils/system_info.py numpy-1.12.0/numpy/distutils/system_info.py +--- numpy-1.12.0.orig/numpy/distutils/system_info.py 2017-01-15 11:39:18.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/system_info.py 2017-03-06 17:25:38.778143748 +0100 +@@ -675,7 +675,7 @@ + if is_string(default): + return [default] + return default +- return [b for b in [a.strip() for a in libs.split(',')] if b] ++ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): + if hasattr(self, '_lib_names'): +@@ -756,6 +756,9 @@ + # make sure we preserve the order of libs, as it can be important + found_dirs, found_libs = [], [] + for lib in libs: ++ if lib[0] == '-': ++ found_libs.append(lib) ++ continue + for lib_dir in lib_dirs: + found_lib = self._find_lib(lib_dir, lib, exts) + if found_lib: +diff -ru numpy-1.12.0.orig/numpy/distutils/unixccompiler.py numpy-1.12.0/numpy/distutils/unixccompiler.py +--- numpy-1.12.0.orig/numpy/distutils/unixccompiler.py 2016-12-21 16:46:24.000000000 +0100 ++++ numpy-1.12.0/numpy/distutils/unixccompiler.py 2017-03-06 17:19:07.262810683 +0100 +@@ -123,3 +123,12 @@ + + replace_method(UnixCCompiler, 'create_static_lib', + UnixCCompiler_create_static_lib) ++ ++def UnixCCompiler_library_option(self, lib): ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib ++ ++replace_method(UnixCCompiler, 'library_option', ++ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.1_fix-ifort-V-stderr.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.1_fix-ifort-V-stderr.patch new file mode 100644 index 00000000000..b781c2577b7 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.1_fix-ifort-V-stderr.patch @@ -0,0 +1,15 @@ +catch stderr output of 'ifort -V' +see https://github.com/numpy/numpy/issues/10569 and https://github.com/numpy/numpy/pull/12831 +diff --git a/numpy/distutils/ccompiler.py b/numpy/distutils/ccompiler.py +index 100d0d06995..552b9566f77 100644 +--- a/numpy/distutils/ccompiler.py ++++ b/numpy/distutils/ccompiler.py +@@ -639,7 +639,7 @@ def matcher(version_string): + return version + + try: +- output = subprocess.check_output(version_cmd) ++ output = subprocess.check_output(version_cmd, stderr=subprocess.STDOUT) + except subprocess.CalledProcessError as exc: + output = exc.output + status = exc.returncode From 4403c05f83570a509312fa6f2ef2587336be812a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Mar 2019 13:01:26 +0100 Subject: [PATCH 0944/5331] adding easyconfigs: Go-1.12.1-GCCcore-7.3.0.eb --- .../g/Go/Go-1.12.1-GCCcore-7.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..efe696b4984 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb @@ -0,0 +1,28 @@ +# Author: Carlos Fenoy +# F. Hoffmann - La Roche + +name = 'Go' +version = '1.12.1' + +homepage = 'http://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://storage.googleapis.com/golang/'] +sources = ['%(namelower)s%(version)s.src.tar.gz'] +checksums = ['0be127684df4b842a64e58093154f9d15422f1405f1fcff4b2c36ffc6a15818a'] + +builddependencies = [ + ('binutils', '2.30'), + # go requires Go to install from source, see https://golang.org/doc/install/source + ('Go', '1.12', '', True), +] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +moduleclass = 'compiler' From 43ac491ce78b08cf6263f6f5ad1f8b06507b6d21 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 19 Mar 2019 10:36:25 -0500 Subject: [PATCH 0945/5331] switch to Binary easyblock and add source_urls --- .../i/IntelPython/IntelPython-2.7.15-2019.2.066.eb | 12 +++++------- .../i/IntelPython/IntelPython-3.6.8-2019.2.066.eb | 12 +++++------- 2 files changed, 10 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb index 031de9fb5fb..46879b254dd 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb @@ -1,6 +1,6 @@ # Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu -easyblock = 'ConfigureMake' +easyblock = 'Binary' name = 'IntelPython' version = '2.7.15' @@ -15,19 +15,17 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -# l_pythoni2_p_2019.2.066.tar.gz from the Intel site +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15293/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (pysver, relver)] checksums = ['dd0b73db5d0d79c3cdf779d10092eae32780d720b74ed8fde2a2c46e23143de1'] toolchain = {'name': 'dummy', 'version': 'dummy'} -skipsteps = ['configure', 'build'] - buildininstalldir = True -preinstallopts = """ - echo -e "install:\n\t./setup_intel_python.sh" > Makefile -""" +extract_sources = True + +install_cmd = "./setup_intel_python.sh" sanity_check_paths = { 'dirs': ['intelpython%s/%s' % (pysver, x) for x in ['bin', 'etc', 'include', 'lib']], diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb index 82da6e376b6..1b619c8d545 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb @@ -1,6 +1,6 @@ # Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu -easyblock = 'ConfigureMake' +easyblock = 'Binary' name = 'IntelPython' version = '3.6.8' @@ -15,19 +15,17 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -# l_pythoni3_p_2019.2.066.tar.gz from the Intel site +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15293/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (pysver, relver)] checksums = ['804883fc1413ee72b0ae421a8ac82ab158fc01c8b4631a44a9d2ef1a19324751'] toolchain = {'name': 'dummy', 'version': 'dummy'} -skipsteps = ['configure', 'build'] - buildininstalldir = True -preinstallopts = """ - echo -e "install:\n\t./setup_intel_python.sh" > Makefile -""" +extract_sources = True + +install_cmd = "./setup_intel_python.sh" sanity_check_paths = { 'dirs': ['intelpython%s/%s' % (pysver, x) for x in ['bin', 'etc', 'include', 'lib']], From c0098cc415a0e7861dd83f4bc182fa8a8c21f1dd Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 19 Mar 2019 16:56:19 +0100 Subject: [PATCH 0946/5331] adding easyconfigs: ACT-18.0.2-Java-11.eb, Java-11.eb --- .../easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb | 26 +++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-11.eb | 18 +++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-11.eb diff --git a/easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb b/easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb new file mode 100644 index 00000000000..20c4c52dec2 --- /dev/null +++ b/easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb @@ -0,0 +1,26 @@ +easyblock = 'PackedBinary' + +name = 'ACT' +version = '18.0.2' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sanger-pathogens.github.io/Artemis/ACT/' +description = """ ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. + It can be used to identify and analyse regions of similarity and difference between genomes + and to explore conservation of synteny, in the context of the entire sequences and their annotation. + It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/sanger-pathogens/Artemis/releases/download/v%(version)s/'] +sources = ['artemis-unix-release-%(version)s.tar.gz'] +checksums = ['1cb9f36af4c96ae3bde4fa849e01e66c830d4b968867e7842abbab9195b57e60'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['act', 'art'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/Java/Java-11.eb b/easybuild/easyconfigs/j/Java/Java-11.eb new file mode 100644 index 00000000000..6c4c3689409 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-11.eb @@ -0,0 +1,18 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# updated to version 202 + +easyblock = 'ModuleRC' + +name = 'Java' +version = '11' + +homepage = 'http://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [('Java', '%(version)s.0.2')] + +moduleclass = 'lang' From 9860254916ac726fd2a9c0472f4a43de7bfe7f6c Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 19 Mar 2019 18:16:26 +0200 Subject: [PATCH 0947/5331] adding easyconfigs: Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb --- .../Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..5dc7acd5873 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] + +builddependencies = [('binutils', '2.31.1')] +dependencies = [('Python', '3.7.2')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], +} + +moduleclass = 'devel' From 16f710b6a5fb70b1accfaa23cb53f12bfa34d78f Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 19 Mar 2019 18:50:55 +0200 Subject: [PATCH 0948/5331] configure with --without-docbook to avoid dependency to docbook2X --- easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb index 70707a37a44..347dc48e678 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb @@ -18,6 +18,11 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_BZ2] checksums = ['17b43c2716d521369f82fc2dc70f359860e90fa440bea65b3b85f0b246ea81f2'] +# since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf +# docbook2X needs XML-Parser and XML-Parser needs expat +# so circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + builddependencies = [ ('binutils', '2.31.1'), ] From e19fc7806cf8573c157134b9a116824ac6a578c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Mar 2019 18:04:08 +0100 Subject: [PATCH 0949/5331] don't symlink SAMtools install dir while building MetaBAT, copy it instead --- .../m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb index ef0c0f0fd99..beb661b0ec1 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb @@ -26,7 +26,7 @@ dependencies = [ ('SAMtools', '1.9'), ] -prebuildopts = "ln -s $EBROOTSAMTOOLS samtools && " +prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], From f066618f307ba596fd9e38c4bc9459197f1a462a Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 19 Mar 2019 19:40:49 +0200 Subject: [PATCH 0950/5331] use_pip and download_dep_fail --- .../m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb index 5dc7acd5873..dacf4ccb704 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb @@ -13,6 +13,9 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] +download_dep_fail = True +use_pip = True + builddependencies = [('binutils', '2.31.1')] dependencies = [('Python', '3.7.2')] From 4c4a5b2c94082069be067ef03324d0cd88a97871 Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Mon, 25 Feb 2019 12:39:37 +0200 Subject: [PATCH 0951/5331] HPCX: add configs to build OSS part of HPCX --- .../h/HPCX/HPCX-2.3.0-foss-2018b.eb | 18 ++++++++ .../h/HPCX/HPCX_OMPI-4.0.0-foss-2018b.eb | 35 ++++++++++++++++ .../h/HPCX/HPCX_UCX-1.5.0-foss-2018b.eb | 42 +++++++++++++++++++ 3 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb create mode 100644 easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.0-foss-2018b.eb create mode 100644 easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb b/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb new file mode 100644 index 00000000000..1b3a0e2db7b --- /dev/null +++ b/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb @@ -0,0 +1,18 @@ +easyblock = 'Bundle' + +name = 'HPCX' +version = '2.3.0' + +homepage = 'http://www.mellanox.com/page/products_dyn?product_family=189&mtag=hpc-x' +description = """The Mellanox HPC-X Toolkit +is a comprehensive MPI and SHMEM/PGAS software suite +for high performance computing environments""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('HPCX_UCX', '1.5.0'), + ('HPCX_OMPI', '4.0.0') +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.0-foss-2018b.eb b/easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.0-foss-2018b.eb new file mode 100644 index 00000000000..d3d711a25e4 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.0-foss-2018b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'HPCX_OMPI' +version = '4.0.0' + +homepage = 'http://www.open-mpi.org/' +description = """Mellanox flavored Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://download.open-mpi.org/release/open-mpi/v4.0'] +sources = ['openmpi-4.0.0.tar.gz'] +checksums = ['36f10daa3f1b1d37530f686bf7f70966b2a13c0bc6e2e05aebc7e85e3d21b10d'] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +dependencies = [ + ('zlib', '1.2.11'), + ('HPCX_UCX', '1.5.0') +] + +configopts = '--with-libevent=internal --enable-mpi1-compatibility ' +configopts = '--with-slurm --with-platform=contrib/platform/mellanox/optimized ' +configopts += '--with-ucx=$EBROOTUCX ' + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0-foss-2018b.eb b/easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0-foss-2018b.eb new file mode 100644 index 00000000000..d3c4be5409a --- /dev/null +++ b/easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0-foss-2018b.eb @@ -0,0 +1,42 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'HPCX_UCX' +version = '1.5.0' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['ucx-%(version)s.tar.gz'] +checksums = ['84f6e4fa5740afebb9b1c8bb405c07206e58c56f83120dcfcd8dc89e4b7d7458'] + +builddependencies = [ + ('binutils', '2.30'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +dependencies = [ + ('numactl', '2.0.11'), +] + +configopts = '--enable-optimizations --enable-optimizations --disable-logging ' +configopts += '--disable-debug --disable-assertions --disable-params-check ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +moduleclass = 'mpi' From 0f14bf47ea3717e58295b3b5aeeba38343b0fb4a Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Thu, 28 Feb 2019 10:47:27 +0200 Subject: [PATCH 0952/5331] HPCX: update configs to match HPCX v2.3 --- .../easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb | 4 ++-- ...oss-2018b.eb => HPCX_OMPI-4.0.x-foss-2018b.eb} | 15 +++++++++++---- ...s-2018b.eb => HPCX_UCX-1.5.0rc1-foss-2018b.eb} | 8 ++++---- 3 files changed, 17 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/h/HPCX/{HPCX_OMPI-4.0.0-foss-2018b.eb => HPCX_OMPI-4.0.x-foss-2018b.eb} (76%) rename easybuild/easyconfigs/h/HPCX/{HPCX_UCX-1.5.0-foss-2018b.eb => HPCX_UCX-1.5.0rc1-foss-2018b.eb} (87%) diff --git a/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb b/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb index 1b3a0e2db7b..cb19dcd1485 100644 --- a/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb +++ b/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb @@ -11,8 +11,8 @@ for high performance computing environments""" toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [ - ('HPCX_UCX', '1.5.0'), - ('HPCX_OMPI', '4.0.0') + ('HPCX_UCX', '1.5.0rc1'), + ('HPCX_OMPI', '4.0.x') ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.0-foss-2018b.eb b/easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.x-foss-2018b.eb similarity index 76% rename from easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.0-foss-2018b.eb rename to easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.x-foss-2018b.eb index d3d711a25e4..3253a2e30b5 100644 --- a/easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.0-foss-2018b.eb +++ b/easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.x-foss-2018b.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'HPCX_OMPI' -version = '4.0.0' +version = '4.0.x' homepage = 'http://www.open-mpi.org/' description = """Mellanox flavored Open MPI Project is an open source MPI-3 implementation.""" @@ -9,15 +9,22 @@ description = """Mellanox flavored Open MPI Project is an open source MPI-3 impl toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://download.open-mpi.org/release/open-mpi/v4.0'] -sources = ['openmpi-4.0.0.tar.gz'] -checksums = ['36f10daa3f1b1d37530f686bf7f70966b2a13c0bc6e2e05aebc7e85e3d21b10d'] +sources = [{ + 'filename': 'openmpi-4.0.x.tar.gz', + 'git_config': { + 'url': 'https://github.com/open-mpi', + 'repo_name': 'ompi', + 'commit': '03cf3e4', + }, +}] +checksums = ['5986f36b91a0b9ffc7d0c7d5f11a832000d0c7bef1d26c11a476dc98bdf3cc09'] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] dependencies = [ ('zlib', '1.2.11'), - ('HPCX_UCX', '1.5.0') + ('HPCX_UCX', '1.5.0rc1') ] configopts = '--with-libevent=internal --enable-mpi1-compatibility ' diff --git a/easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0-foss-2018b.eb b/easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0rc1-foss-2018b.eb similarity index 87% rename from easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0-foss-2018b.eb rename to easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0rc1-foss-2018b.eb index d3c4be5409a..cc49e2bc6e6 100644 --- a/easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0-foss-2018b.eb +++ b/easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0rc1-foss-2018b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HPCX_UCX' -version = '1.5.0' +version = '1.5.0rc1' homepage = 'http://www.openucx.org/' description = """Unified Communication X @@ -13,9 +13,9 @@ and high-performance applications toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] -checksums = ['84f6e4fa5740afebb9b1c8bb405c07206e58c56f83120dcfcd8dc89e4b7d7458'] +source_urls = ['https://github.com/openucx/ucx/releases/download/v1.5.0-rc1'] +sources = ['ucx-1.5.0.tar.gz'] +checksums = ['ae5dfa59c54627a11d8cb1c7fdd0b0319e5e8633a6aebd42a07e54a6a4a32181'] builddependencies = [ ('binutils', '2.30'), From ea8246ea4dfb5cec01551f0a34fa23be59bd4c25 Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Wed, 20 Mar 2019 04:11:41 +0200 Subject: [PATCH 0953/5331] UCX: rename HPCX_UCX into UCX-hpcx --- .../UCX/UCX-1.5.0rc1-GCCcore-6.4.0-hpcx.eb} | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/{h/HPCX/HPCX_UCX-1.5.0rc1-foss-2018b.eb => u/UCX/UCX-1.5.0rc1-GCCcore-6.4.0-hpcx.eb} (88%) diff --git a/easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0rc1-foss-2018b.eb b/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-6.4.0-hpcx.eb similarity index 88% rename from easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0rc1-foss-2018b.eb rename to easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-6.4.0-hpcx.eb index cc49e2bc6e6..a83323cd347 100644 --- a/easybuild/easyconfigs/h/HPCX/HPCX_UCX-1.5.0rc1-foss-2018b.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-6.4.0-hpcx.eb @@ -2,8 +2,9 @@ # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild easyblock = 'ConfigureMake' -name = 'HPCX_UCX' +name = 'UCX' version = '1.5.0rc1' +versionsuffix = '-hpcx' homepage = 'http://www.openucx.org/' description = """Unified Communication X @@ -11,14 +12,15 @@ An open-source production grade communication framework for data centric and high-performance applications """ -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v1.5.0-rc1'] sources = ['ucx-1.5.0.tar.gz'] checksums = ['ae5dfa59c54627a11d8cb1c7fdd0b0319e5e8633a6aebd42a07e54a6a4a32181'] builddependencies = [ - ('binutils', '2.30'), + ('binutils', '2.28'), ('pkg-config', '0.29.2'), ] From 0a9537a1e64b48f73b3c15edb33849b772358103 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Mar 2019 08:35:35 +0200 Subject: [PATCH 0954/5331] UCX should be in module class lib, not mpi --- easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-8.2.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-6.4.0.eb index 8c86e5282c2..d9e983ff814 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-6.4.0.eb @@ -39,4 +39,4 @@ sanity_check_paths = { 'dirs': ['include', 'lib', 'share'] } -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-7.3.0.eb index 91b414d5008..646b3a07d3f 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-7.3.0.eb @@ -39,4 +39,4 @@ sanity_check_paths = { 'dirs': ['include', 'lib', 'share'] } -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-8.2.0.eb index b0af5919a21..d8bc1862ebe 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.5.0-GCCcore-8.2.0.eb @@ -39,4 +39,4 @@ sanity_check_paths = { 'dirs': ['include', 'lib', 'share'] } -moduleclass = 'mpi' +moduleclass = 'lib' From e94d9cf9b0bf693342456cd25ab1e19f20a7ce62 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Mar 2019 08:37:56 +0200 Subject: [PATCH 0955/5331] PMIx should be in module class lib, not mpi. --- easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb index 364a569a178..11d83d89022 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb @@ -48,4 +48,4 @@ sanity_check_paths = { 'dirs': ['etc', 'include', 'lib', 'share'] } -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb index 5d3139cb8a1..c0058825264 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb @@ -48,4 +48,4 @@ sanity_check_paths = { 'dirs': ['etc', 'include', 'lib', 'share'] } -moduleclass = 'mpi' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb index 9ecc3f847dc..731b002f2f7 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb @@ -48,4 +48,4 @@ sanity_check_paths = { 'dirs': ['etc', 'include', 'lib', 'share'] } -moduleclass = 'mpi' +moduleclass = 'lib' From add5016f8d5856742beb3d88de2a6a9f55d90367 Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Wed, 20 Mar 2019 11:10:37 +0200 Subject: [PATCH 0956/5331] OMPI: rename HPCX_OMPI into OpenMPI-hpcx --- .../OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/{h/HPCX/HPCX_OMPI-4.0.x-foss-2018b.eb => o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb} (81%) diff --git a/easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.x-foss-2018b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb similarity index 81% rename from easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.x-foss-2018b.eb rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb index 3253a2e30b5..3882f8911fa 100644 --- a/easybuild/easyconfigs/h/HPCX/HPCX_OMPI-4.0.x-foss-2018b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb @@ -1,14 +1,14 @@ easyblock = 'ConfigureMake' -name = 'HPCX_OMPI' +name = 'OpenMPI' version = '4.0.x' +versionsuffix = '-hpcx' homepage = 'http://www.open-mpi.org/' description = """Mellanox flavored Open MPI Project is an open source MPI-3 implementation.""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = ['https://download.open-mpi.org/release/open-mpi/v4.0'] sources = [{ 'filename': 'openmpi-4.0.x.tar.gz', 'git_config': { @@ -17,14 +17,14 @@ sources = [{ 'commit': '03cf3e4', }, }] -checksums = ['5986f36b91a0b9ffc7d0c7d5f11a832000d0c7bef1d26c11a476dc98bdf3cc09'] +checksums = ['ef53605823b01499e09844a610614a555724603c72a1bb9a5ca59b35389f67ec'] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] dependencies = [ ('zlib', '1.2.11'), - ('HPCX_UCX', '1.5.0rc1') + ('UCX', '1.5.0rc1', '-hpcx', ('GCCcore', '6.4.0')) ] configopts = '--with-libevent=internal --enable-mpi1-compatibility ' From 6eab44fabf3c378d90fd1851b55a67abe08a842f Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Wed, 20 Mar 2019 11:51:07 +0200 Subject: [PATCH 0957/5331] UCX: upgrade to GCCcore 8.2.0 --- ...ore-6.4.0-hpcx.eb => UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/u/UCX/{UCX-1.5.0rc1-GCCcore-6.4.0-hpcx.eb => UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb} (91%) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-6.4.0-hpcx.eb b/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb similarity index 91% rename from easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-6.4.0-hpcx.eb rename to easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb index a83323cd347..b87360810c0 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-6.4.0-hpcx.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb @@ -12,7 +12,7 @@ An open-source production grade communication framework for data centric and high-performance applications """ -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v1.5.0-rc1'] @@ -20,14 +20,14 @@ sources = ['ucx-1.5.0.tar.gz'] checksums = ['ae5dfa59c54627a11d8cb1c7fdd0b0319e5e8633a6aebd42a07e54a6a4a32181'] builddependencies = [ - ('binutils', '2.28'), + ('binutils', '2.31.1'), ('pkg-config', '0.29.2'), ] osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] dependencies = [ - ('numactl', '2.0.11'), + ('numactl', '2.0.12'), ] configopts = '--enable-optimizations --enable-optimizations --disable-logging ' From 10f599e5741eb248cbe8d4c3815a0712224d6567 Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Wed, 20 Mar 2019 11:51:50 +0200 Subject: [PATCH 0958/5331] OMPI: add preconfigure action --- .../o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb index 3882f8911fa..9e532ba4c71 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb @@ -24,9 +24,10 @@ osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] dependencies = [ ('zlib', '1.2.11'), - ('UCX', '1.5.0rc1', '-hpcx', ('GCCcore', '6.4.0')) + ('UCX', '1.5.0rc1', '-hpcx', ('GCCcore', '8.2.0')) ] +preconfigopts = "./autogen.pl && " configopts = '--with-libevent=internal --enable-mpi1-compatibility ' configopts = '--with-slurm --with-platform=contrib/platform/mellanox/optimized ' configopts += '--with-ucx=$EBROOTUCX ' From 2e2d01b8d60d83dfabebdce2f68a82e02e671cba Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Wed, 20 Mar 2019 11:55:28 +0200 Subject: [PATCH 0959/5331] HPCX: update toolchain and dependencies --- ...X-2.3.0-foss-2018b.eb => HPCX-2.3.0-GCC-8.2.0-2.31.1.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/h/HPCX/{HPCX-2.3.0-foss-2018b.eb => HPCX-2.3.0-GCC-8.2.0-2.31.1.eb} (65%) diff --git a/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb b/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb similarity index 65% rename from easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb rename to easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb index cb19dcd1485..34a544c36bf 100644 --- a/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-foss-2018b.eb +++ b/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb @@ -8,11 +8,11 @@ description = """The Mellanox HPC-X Toolkit is a comprehensive MPI and SHMEM/PGAS software suite for high performance computing environments""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} dependencies = [ - ('HPCX_UCX', '1.5.0rc1'), - ('HPCX_OMPI', '4.0.x') + ('UCX', '1.5.0rc1', '-hpcx', ('GCCcore', '8.2.0')), + ('OpenMPI', '4.0.x', '-hpcx', ('GCC', '8.2.0-2.31.1')) ] moduleclass = 'mpi' From 782322061bd7ff7b6b0a48b5f49d458f4195fc56 Mon Sep 17 00:00:00 2001 From: wapoelma Date: Wed, 20 Mar 2019 12:15:03 +0100 Subject: [PATCH 0960/5331] adding easyconfigs: tesseract-4.0.0-GCCcore-7.3.0.eb, Leptonica-1.77.0-GCCcore-7.3.0.eb --- .../Leptonica-1.77.0-GCCcore-7.3.0.eb | 30 +++++++++++ .../tesseract-4.0.0-GCCcore-7.3.0.eb | 52 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/t/tesseract/tesseract-4.0.0-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..2cf54816fad --- /dev/null +++ b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Leptonica' +version = '1.77.0' + +homepage = 'http://www.leptonica.org' +description = """Leptonica is a pedagogically-oriented open source site containing software + that is broadly useful for image processing and image analysis applications.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/DanBloomberg/leptonica/releases/download/%(version)s/'] +checksums = ['161d0b368091986b6c60990edf257460bdc7da8dd18d48d4179e297bcdca5eb7'] + +dependencies = [ + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), + ('libjpeg-turbo', '2.0.0'), + ('giflib', '5.1.4'), + ('libwebp', '1.0.2'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/convertformat', 'lib/liblept.%s' % SHLIB_EXT], + 'dirs': ['include/leptonica', 'lib/pkgconfig'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-4.0.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-4.0.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..367fcad031b --- /dev/null +++ b/easybuild/easyconfigs/t/tesseract/tesseract-4.0.0-GCCcore-7.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'tesseract' +version = '4.0.0' + +homepage = 'https://github.com/tesseract-ocr/tesseract' +description = """Tesseract is an optical character recognition engine""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +github_account = 'tesseract-ocr' +source_urls = [GITHUB_SOURCE] +sources = [ + '%(version)s.tar.gz', + { + 'source_urls': ['https://github.com/tesseract-ocr/tessdata/archive/'], + 'download_filename': '%(version)s.tar.gz', + 'filename': 'tessdata-%(version)s.tar.gz', + }, +] +checksums = [ + 'a1f5422ca49a32e5f35c54dee5112b11b99928fc9f4ee6695cdc6768d69f61dd', # 4.0.0.tar.gz + '38c637d3a1763f6c3d32e8f1d979f045668676ec5feb8ee1869ee77cedd31b08', # tessdata-4.0.0.tar.gz +] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), + ('libjpeg-turbo', '2.0.0'), + ('zlib', '1.2.11'), + ('Leptonica', '1.77.0'), +] + +separate_build_dir = True + +postinstallcmds = [ + 'mkdir %(installdir)s/tessdata', + 'mv %(builddir)s/tessdata-%(version)s/* %(installdir)s/tessdata' +] + +modextrapaths = { + 'TESSDATA_PREFIX': 'tessdata', +} + +sanity_check_paths = { + 'files': ['bin/tesseract', 'lib/libtesseract.%s' % SHLIB_EXT], + 'dirs': ['tessdata', 'include/tesseract'] +} + +moduleclass = 'vis' From 90f3d8d59199ef943d24b35034c4b1c061143dad Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 20 Mar 2019 12:48:15 +0100 Subject: [PATCH 0961/5331] Add binutils builddep --- .../l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb | 2 ++ .../easyconfigs/t/tesseract/tesseract-4.0.0-GCCcore-7.3.0.eb | 5 ++++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb index 2cf54816fad..cb338d1c679 100644 --- a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb @@ -13,6 +13,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://github.com/DanBloomberg/leptonica/releases/download/%(version)s/'] checksums = ['161d0b368091986b6c60990edf257460bdc7da8dd18d48d4179e297bcdca5eb7'] +builddependencies = [('binutils', '2.30')] + dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-4.0.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-4.0.0-GCCcore-7.3.0.eb index 367fcad031b..e56ecd9f4b8 100644 --- a/easybuild/easyconfigs/t/tesseract/tesseract-4.0.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/t/tesseract/tesseract-4.0.0-GCCcore-7.3.0.eb @@ -23,7 +23,10 @@ checksums = [ '38c637d3a1763f6c3d32e8f1d979f045668676ec5feb8ee1869ee77cedd31b08', # tessdata-4.0.0.tar.gz ] -builddependencies = [('CMake', '3.12.1')] +builddependencies = [ + ('CMake', '3.12.1'), + ('binutils', '2.30'), +] dependencies = [ ('libpng', '1.6.34'), From 0d233e8a347d24eefdb3bffc313be31aef8d02c5 Mon Sep 17 00:00:00 2001 From: wapoelma Date: Wed, 20 Mar 2019 14:15:51 +0100 Subject: [PATCH 0962/5331] adding easyconfigs: R-tesseract-4.0-foss-2018b-R-3.5.1.eb --- .../R-tesseract-4.0-foss-2018b-R-3.5.1.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-tesseract/R-tesseract-4.0-foss-2018b-R-3.5.1.eb diff --git a/easybuild/easyconfigs/r/R-tesseract/R-tesseract-4.0-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-4.0-foss-2018b-R-3.5.1.eb new file mode 100644 index 00000000000..28cb5231cee --- /dev/null +++ b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-4.0-foss-2018b-R-3.5.1.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'R-tesseract' +version = '4.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/package=tesseract' +description = "The R extension for using tesseract" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('R', '3.5.1'), + ('poppler', '0.70.1'), + ('tesseract', '4.0.0'), +] + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/tesseract', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('sys', '3.1', { + 'checksums': ['98088e01e7682077569ed8a5f767c59b34172d6240af3c7462270fa83ce3432a'], + }), + ('askpass', '1.1', { + 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], + }), + ('qpdf', '1.1', { + 'checksums': ['71f106925aeffcf3cae500aad5f9306b64a9ed963540ec1d77a161c49975960e'], + }), + ('pdftools', '2.2', { + 'checksums': ['14cccc891a0a491ab8be6709620918aa9319415be8016c4e3b39812ec7c875b3'], + }), + ('rappdirs', '0.3.1', { + 'checksums': ['2fd891ec16d28862f65bb57e4a78f77a597930abb59380e757afd8b6c6d3264a'], + }), + ('tesseract', version, { + 'preinstallopts': 'INCLUDE_DIR="$EBROOTTESSERACT/include/tesseract -I$EBROOTLEPTONICA/include/leptonica"' + + ' LIB_DIR=$EBROOTTESSERACT/lib', + 'checksums': ['30267d7f41f5ec4ce163796f4d285703538aaa8eb076c0322179a307f0c84db5'], + }), +] + +sanity_check_paths = { + 'files': ['tesseract/libs/tesseract.%s' % SHLIB_EXT, 'tesseract/R/tesseract'], + 'dirs': ['sys', 'askpass', 'qpdf', 'pdftools', 'rappdirs'], +} + +modextrapaths = {'R_LIBS': ''} + +moduleclass = 'vis' From c4314262a72eaa28c7fde4bde510aab8578af109 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 20 Mar 2019 09:12:09 -0500 Subject: [PATCH 0963/5331] update source_urls --- .../easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb | 2 +- .../easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb index 46879b254dd..eb9c1846954 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb @@ -15,7 +15,7 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15293/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (pysver, relver)] checksums = ['dd0b73db5d0d79c3cdf779d10092eae32780d720b74ed8fde2a2c46e23143de1'] diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb index 1b619c8d545..d63c1f055fe 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb @@ -15,7 +15,7 @@ description = """ Accelerating Python* performance on modern architectures from Intel. """ -source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15293/'] +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15115/'] sources = ['l_pythoni%s_p_%s.tar.gz' % (pysver, relver)] checksums = ['804883fc1413ee72b0ae421a8ac82ab158fc01c8b4631a44a9d2ef1a19324751'] From 20209d5d64fa97b8483967bf9986b73f6055fbf3 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 20 Mar 2019 09:52:21 -0500 Subject: [PATCH 0964/5331] adding easyconfigs: rclone-1.42-amd64.eb --- .../easyconfigs/r/rclone/rclone-1.42-amd64.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.42-amd64.eb diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.42-amd64.eb b/easybuild/easyconfigs/r/rclone/rclone-1.42-amd64.eb new file mode 100644 index 00000000000..8adaf4b58ad --- /dev/null +++ b/easybuild/easyconfigs/r/rclone/rclone-1.42-amd64.eb @@ -0,0 +1,35 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'CmdCp' + +name = 'rclone' +version = '1.42' +versionsuffix = '-amd64' + +homepage = 'https://rclone.org/' + +description = """ + Rclone is a command line program to sync files and directories to and from + a variety of online storage services +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://downloads.%(name)s.org/v%(version)s/'] +sources = ['%(name)s-v%(version)s-linux%(versionsuffix)s.zip'] +checksums = ['7a623f60a5995f33cca3ed285210d8701c830f6f34d4dc50d74d75edd6a5bfa6'] + +cmds_map = [('', '')] + +files_to_copy = [ + (['rclone'], 'bin'), + (['rclone.1'], 'share/man/man1'), + (['README.*'], 'share/doc'), +] + +sanity_check_paths = { + 'files': ['bin/rclone', 'share/doc/README.txt', 'share/man/man1/rclone.1'], + 'dirs': [] +} + +moduleclass = 'tools' From 5938058c2b2e4132c92f407b7bbc8260483a9446 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Mar 2019 16:42:14 +0100 Subject: [PATCH 0965/5331] add parsedate extension to R 3.5.1 easyconfigs --- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 3 +++ easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index b0157208052..ecf472fe005 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -2105,6 +2105,9 @@ exts_list = [ ('GenSA', '1.1.7', { 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], }), + ('parsedate', '1.1.3', { + 'checksums': ['020005634099a057207a614928ced57900acd4952f147bebe6718034ea82e755'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 4860a03bc25..9e93f03acd2 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -2103,6 +2103,9 @@ exts_list = [ ('GenSA', '1.1.7', { 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], }), + ('parsedate', '1.1.3', { + 'checksums': ['020005634099a057207a614928ced57900acd4952f147bebe6718034ea82e755'], + }), ] moduleclass = 'lang' From ea4ef31966d82f83d20c223f4df7f885df2e966a Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 20 Mar 2019 11:11:01 -0500 Subject: [PATCH 0966/5331] adding easyconfigs: BCEL-5.2.eb --- easybuild/easyconfigs/b/BCEL/BCEL-5.2.eb | 27 ++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCEL/BCEL-5.2.eb diff --git a/easybuild/easyconfigs/b/BCEL/BCEL-5.2.eb b/easybuild/easyconfigs/b/BCEL/BCEL-5.2.eb new file mode 100644 index 00000000000..055a12dc3ce --- /dev/null +++ b/easybuild/easyconfigs/b/BCEL/BCEL-5.2.eb @@ -0,0 +1,27 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'PackedBinary' + +name = 'BCEL' +version = '5.2' + +homepage = 'http://commons.apache.org/proper/commons-bcel/' + +description = """ + The Byte Code Engineering Library (Apache Commons BCEL™) is intended to give + users a convenient way to analyze, create, and manipulate (binary) Java class + files (those ending with .class). +""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [('http://archive.apache.org/dist/jakarta/bcel/binaries/')] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['669e96c3553e2c4f41842f8837c544b8fb00c58cc45e1904964d52a74cb3f78e'] + +sanity_check_paths = { + 'files': ['%(namelower)s-%(version)s.jar'], + 'dirs': [], +} + +moduleclass = 'lang' From 59751ada02be12632ea4c4a8496cecc979ad8923 Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Thu, 21 Mar 2019 06:28:45 +0200 Subject: [PATCH 0967/5331] OMPI: fix version --- .../o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb index 9e532ba4c71..10b5cb4d487 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' -version = '4.0.x' +version = '4.0.0' versionsuffix = '-hpcx' homepage = 'http://www.open-mpi.org/' From c6c236317c1bdb6c344fa0320cfd49ace2e04a7c Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Thu, 21 Mar 2019 10:57:22 +0200 Subject: [PATCH 0968/5331] OMPI: fix version --- ....0-2.31.1-hpcx.eb => OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb => OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb} (98%) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb similarity index 98% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb index 10b5cb4d487..9e532ba4c71 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' -version = '4.0.0' +version = '4.0.x' versionsuffix = '-hpcx' homepage = 'http://www.open-mpi.org/' From 549b953d2d6b3a9bb12bd76a0577ab9174dfc77d Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Thu, 21 Mar 2019 11:19:49 +0200 Subject: [PATCH 0969/5331] Address review comments --- easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb | 4 ++-- .../o/OpenMPI/OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb index 34a544c36bf..03cca0222b8 100644 --- a/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb @@ -11,8 +11,8 @@ for high performance computing environments""" toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} dependencies = [ - ('UCX', '1.5.0rc1', '-hpcx', ('GCCcore', '8.2.0')), - ('OpenMPI', '4.0.x', '-hpcx', ('GCC', '8.2.0-2.31.1')) + ('UCX', '1.5.0rc1', '-hpcx'), + ('OpenMPI', '4.0.x', '-hpcx') ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb index 9e532ba4c71..5b2066cbb05 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb @@ -24,7 +24,7 @@ osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] dependencies = [ ('zlib', '1.2.11'), - ('UCX', '1.5.0rc1', '-hpcx', ('GCCcore', '8.2.0')) + ('UCX', '1.5.0rc1', '-hpcx') ] preconfigopts = "./autogen.pl && " From b63f4aa107ddecbaf785f879e30be736d5620efe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Mar 2019 12:27:53 +0100 Subject: [PATCH 0970/5331] fix MetaBAT patch file to also link with -llzma and -lbz2, as required by SAMtools's htslib.a --- ...MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb | 4 +++- .../MetaBAT-2.12.1_fix-prepend-PATH.patch | 23 +++++++++++++++++-- 2 files changed, 24 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb index beb661b0ec1..8f1a12ff8c5 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1-foss-2018b-Python-2.7.15.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-%(version)s_fix-prepend-PATH.patch'] checksums = [ 'e3aca0656f56f815135521360dc56667ec26af25143c3a31d645fef1a96abbc2', # v2.12.1.tar.gz - '5735d2661f1b890688029ccccf24d278c71ece9d6c603ced442327010de1287b', # MetaBAT-2.12.1_fix-prepend-PATH.patch + '2e5f84ad7090e7853c506278adf2d09a8af57b90d7003c5c01a62fa58c9f4931', # MetaBAT-2.12.1_fix-prepend-PATH.patch ] builddependencies = [('SCons', '3.0.4', versionsuffix)] @@ -24,6 +24,8 @@ dependencies = [ ('Boost', '1.67.0'), ('zlib', '1.2.11'), ('SAMtools', '1.9'), + ('XZ', '5.2.4'), + ('bzip2', '1.0.6'), ] prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1_fix-prepend-PATH.patch b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1_fix-prepend-PATH.patch index 0f0d328931e..01759452942 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1_fix-prepend-PATH.patch +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.12.1_fix-prepend-PATH.patch @@ -1,8 +1,9 @@ -prepend to $PATH rather than append, to avoid picking up system compiler (g++) +prepend to $PATH rather than append, to avoid picking up system compiler (g++); +add missing -llzma -lbz2 link options, required when linking to libhts.a author: Kenneth Hoste (HPC-UGent) see also https://bitbucket.org/berkeleylab/metabat/issues/52 --- berkeleylab-metabat-37db58fe3fda/SConstruct.orig 2017-09-01 07:28:02.000000000 +0200 -+++ berkeleylab-metabat-37db58fe3fda/SConstruct 2019-02-26 16:13:03.150132631 +0100 ++++ berkeleylab-metabat-37db58fe3fda/SConstruct 2019-03-21 12:24:35.516202521 +0100 @@ -7,7 +7,7 @@ def ENV_update(tgt_ENV, src_ENV): for K in src_ENV.keys(): @@ -12,3 +13,21 @@ see also https://bitbucket.org/berkeleylab/metabat/issues/52 else: tgt_ENV[K]=src_ENV[K] +@@ -184,7 +184,7 @@ + sources, + CCFLAGS=ccflags, + CPPPATH=[hts_inc, boost_inc], +- LIBS=['pthread', 'z'], ++ LIBS=['pthread', 'z', 'lzma', 'bz2'], + LINKFLAGS=linkflags + ) + +@@ -204,7 +204,7 @@ + CPPPATH=[hts_inc, boost_inc], + LINKPATH=[hts_lib, boost_lib], + LINKFLAGS=linkflags, +- LIBS=['z'] ++ LIBS=['z', 'lzma', 'bz2'] + ) + + test_sum = env.Alias('test_sum', [jgi_summarize_bam_contig_depths], ' '.join([jgi_summarize_bam_contig_depths[0].abspath, '--outputDepth', test_depth, test_bam]) ) From 12b6f3e6bbe10436b99abc522da14ee713132950 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 21 Mar 2019 14:15:14 +0100 Subject: [PATCH 0971/5331] adding easyconfigs: VAtools-3.0.1-foss-2018b-Python-3.6.6.eb --- .../VAtools-3.0.1-foss-2018b-Python-3.6.6.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/v/VAtools/VAtools-3.0.1-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/v/VAtools/VAtools-3.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/v/VAtools/VAtools-3.0.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..a708679e99b --- /dev/null +++ b/easybuild/easyconfigs/v/VAtools/VAtools-3.0.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'VAtools' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://vatools.readthedocs.io/en/latest/' +description = """ VAtools is a python package that includes several tools to annotate VCF files + with data from other tools. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('Pysam', '0.15.1', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('vcfpy', '0.12.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcfpy'], + 'checksums': ['2ce36cdad9b7853e0be056070336d6f664d8b6e17f51125d25d0cc172219e6e0'], + }), + ('gtfparse', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gtfparse'], + 'checksums': ['2f27aa2b87eb43d613edabf27f9c11147dc595c8683b440ac1d88e9acdb85873'], + }), + ('testfixtures', '6.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/testfixtures'], + 'checksums': ['1ff15abd7c93a25c25e707e15bc245fb3d5723e43ce114e8fd6f72cff17926c8'], + }), + (name, version, { + 'source_tmpl': 'vatools-%(version)s-py3-none-any.whl', + 'source_urls': ['https://pypi.python.org/packages/source/v/vatools/'], + 'unpack_sources': False, + 'checksums': ['d26f775df7e7ee8d84eb0857ac1a1226200ce92ecda9ad8d7dd2cb13d3b19de4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ( + 'vcf-expression-annotator', 'vcf-info-annotator', 'vcf-readcount-annotator', 'vep-annotation-reporter')], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'vcf-expression-annotator -h', + 'vcf-info-annotator -h', + 'vcf-readcount-annotator -h', + 'vep-annotation-reporter -h', +] + +moduleclass = 'bio' From ed5f24a5cd9dc66687fcbc14822678bf2dde27f5 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 21 Mar 2019 15:34:12 +0200 Subject: [PATCH 0972/5331] Add fix to prevent segfaulting in the gds/ds21 component. --- .../p/PMIx/PMIx-2.2.1_fix_seg_hdr_problem.patch | 17 +++++++++++++++++ .../p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb | 6 +++++- .../p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb | 6 +++++- .../p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb | 6 +++++- 4 files changed, 32 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-2.2.1_fix_seg_hdr_problem.patch diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-2.2.1_fix_seg_hdr_problem.patch b/easybuild/easyconfigs/p/PMIx/PMIx-2.2.1_fix_seg_hdr_problem.patch new file mode 100644 index 00000000000..f63e5155c33 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-2.2.1_fix_seg_hdr_problem.patch @@ -0,0 +1,17 @@ +gds/ds21: update the pointer of `seg_hdr` when segment re-attached + +Taken from PMIX https://github.com/pmix/pmix/pull/1156 + +Åke Sandgren, 20190321 +diff --git a/src/mca/gds/ds21/gds_ds21_lock_pthread.c b/src/mca/gds/ds21/gds_ds21_lock_pthread.c +index 5e8b7be..9b2e075 100644 +--- a/src/mca/gds/ds21/gds_ds21_lock_pthread.c ++++ b/src/mca/gds/ds21/gds_ds21_lock_pthread.c +@@ -234,6 +234,7 @@ pmix_status_t pmix_gds_ds21_lock_init(pmix_common_dstor_lock_ctx_t *ctx, const c + rc = PMIX_ERR_NOT_FOUND; + goto error; + } ++ seg_hdr = (segment_hdr_t*)lock_item->seg_desc->seg_info.seg_base_addr; + } + + lock_item->num_locks = seg_hdr->num_locks; diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb index 11d83d89022..ae1799ef243 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-6.4.0.eb @@ -23,10 +23,14 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/pmix/pmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -patches = ['%(name)s-%(version)s_fix_various_problems.patch'] +patches = [ + '%(name)s-%(version)s_fix_various_problems.patch', + '%(name)s-2.2.1_fix_seg_hdr_problem.patch', +] checksums = [ '6d4780e7a198dc72965d6e3c41e1c41edd69ff44ac089f185123c49950cb43ab', # pmix-3.1.1.tar.bz2 '23a5dd33055ecc3f94116a52d17ac6151dcc730292a825e33fb9140a02f43e92', # PMIx-3.1.1_fix_various_problems.patch + 'cf4ec59d68b938904fa8881eeb6e0a318a8690e0716c132192b3bcb6ed45f2e8', # PMIx-2.2.1_fix_seg_hdr_problem.patch ] builddependencies = [('binutils', '2.28')] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb index c0058825264..a1f829a5a72 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-7.3.0.eb @@ -23,10 +23,14 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/pmix/pmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -patches = ['%(name)s-%(version)s_fix_various_problems.patch'] +patches = [ + '%(name)s-%(version)s_fix_various_problems.patch', + '%(name)s-2.2.1_fix_seg_hdr_problem.patch', +] checksums = [ '6d4780e7a198dc72965d6e3c41e1c41edd69ff44ac089f185123c49950cb43ab', # pmix-3.1.1.tar.bz2 '23a5dd33055ecc3f94116a52d17ac6151dcc730292a825e33fb9140a02f43e92', # PMIx-3.1.1_fix_various_problems.patch + 'cf4ec59d68b938904fa8881eeb6e0a318a8690e0716c132192b3bcb6ed45f2e8', # PMIx-2.2.1_fix_seg_hdr_problem.patch ] builddependencies = [('binutils', '2.30')] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb index 731b002f2f7..b61e9a0cbb5 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.1-GCCcore-8.2.0.eb @@ -23,10 +23,14 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/pmix/pmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -patches = ['%(name)s-%(version)s_fix_various_problems.patch'] +patches = [ + '%(name)s-%(version)s_fix_various_problems.patch', + '%(name)s-2.2.1_fix_seg_hdr_problem.patch', +] checksums = [ '6d4780e7a198dc72965d6e3c41e1c41edd69ff44ac089f185123c49950cb43ab', # pmix-3.1.1.tar.bz2 '23a5dd33055ecc3f94116a52d17ac6151dcc730292a825e33fb9140a02f43e92', # PMIx-3.1.1_fix_various_problems.patch + 'cf4ec59d68b938904fa8881eeb6e0a318a8690e0716c132192b3bcb6ed45f2e8', # PMIx-2.2.1_fix_seg_hdr_problem.patch ] builddependencies = [('binutils', '2.31.1')] From 00b03108600c0e6745a375da1be6c95ae33d1002 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Mar 2019 19:49:22 +0100 Subject: [PATCH 0973/5331] also install ANTs scripts (and set $ANTSPATH as required by those scripts) --- .../a/ANTs/ANTs-2.3.1-foss-2018b-Python-3.6.6.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.1-foss-2018b-Python-3.6.6.eb index 4ea80cc18dc..0ad26a8b7c9 100644 --- a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.1-foss-2018b-Python-3.6.6.eb @@ -34,12 +34,17 @@ configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON ' configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF' skipsteps = ['install'] + # need to ensure user has write permissions on all files, to avoid permission denied problems when copying buildopts = ' && mkdir -p %(installdir)s && chmod -R u+w . && cp -a * %(installdir)s/' +postinstallcmds = ["cp -a %(builddir)s/ANTs-%(version)s/Scripts/* %(installdir)s/bin/"] + sanity_check_paths = { - 'files': ['bin/ANTS'], + 'files': ['bin/ANTS', 'bin/antsBrainExtraction.sh'], 'dirs': ['lib'], } +modextravars = {'ANTSPATH': '%(installdir)s/bin'} + moduleclass = 'data' From e1e5518ff6eb1cda2cb4c3f94fbe045151de2472 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 21 Mar 2019 13:16:58 -0700 Subject: [PATCH 0974/5331] update Xerces-C++ 3.2.0-GCCcore-7.3.0 --- .../Xerces-C++-3.2.0-GCCcore-7.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.0-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..68a5d3eaa3b --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.0-GCCcore-7.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'Xerces-C++' +version = '3.2.0' + +homepage = 'http://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [ + 'http://archive.apache.org/dist/xerces/c/%(version_major)s/sources/' +] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['d3162910ada85612f5b8cc89cdab84d0ad9a852a49577691e54bc7e9fc304e15'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.30'), +] + +dependencies = [ + ('cURL', '7.60.0'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +sanity_check_paths = { + 'files': ['bin/XInclude', + 'include/xercesc/xinclude/XIncludeUtils.hpp', + 'lib/libxerces-c-3.2.so'], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' From d01eacd7ec5fa7b27f40c947734fb649664b9b41 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 21 Mar 2019 16:48:30 -0500 Subject: [PATCH 0975/5331] remove the GDB intel versions, we always run into compiler problems --- .../GDB-8.0.1-intel-2017b-Python-2.7.14.eb | 38 ------------------- .../GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb | 38 ------------------- 2 files changed, 76 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb delete mode 100644 easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb deleted file mode 100644 index 352651afdfa..00000000000 --- a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-2.7.14.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDB' -version = '8.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.gnu.org/software/gdb/gdb.html' -description = "The GNU Project Debugger" - -toolchain = {'name': 'intel', 'version': '2017b'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['3dbd5f93e36ba2815ad0efab030dcd0c7b211d7b353a40a53f4c02d7d56295e3'] - -builddependencies = [ - ('texinfo', '6.5'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('libreadline', '7.0'), - ('ncurses', '6.0'), - ('expat', '2.2.5'), - ('Python', '2.7.14'), -] - -configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' -configopts += '--with-system-readline --enable-tui --enable-plugins' - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/gdb', 'bin/gdbserver'], - 'dirs': [], -} - -moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb deleted file mode 100644 index 67d0d3b585f..00000000000 --- a/easybuild/easyconfigs/g/GDB/GDB-8.0.1-intel-2017b-Python-3.6.3.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDB' -version = '8.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.gnu.org/software/gdb/gdb.html' -description = "The GNU Project Debugger" - -toolchain = {'name': 'intel', 'version': '2017b'} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['3dbd5f93e36ba2815ad0efab030dcd0c7b211d7b353a40a53f4c02d7d56295e3'] - -builddependencies = [ - ('texinfo', '6.5'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('libreadline', '7.0'), - ('ncurses', '6.0'), - ('expat', '2.2.5'), - ('Python', '3.6.3'), -] - -configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' -configopts += '--with-system-readline --enable-tui --enable-plugins' - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/gdb', 'bin/gdbserver'], - 'dirs': [], -} - -moduleclass = 'debugger' From dc0de235d198054a51640f49c8053ed2643cd3ba Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 22 Mar 2019 14:56:47 +0000 Subject: [PATCH 0976/5331] moving fosscuda configs into a separate pr --- ...Torch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 238 ------------------ 1 file changed, 238 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb deleted file mode 100644 index 2efcf66a3c1..00000000000 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,238 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyTorch' -version = '1.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://pytorch.org/' -description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. -PyTorch is a deep learning framework that puts Python first.""" - -toolchain = {'name': 'fosscuda', 'version': '2018b'} - -pytorchdir = 'pytorch-%(version)s' -extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' -mklml_extract_cmd = "mkdir -p %s/%s && tar -C %s/%s --strip-components=1 -xzf %%s" - -source_urls = ['https://github.com/pytorch/pytorch/archive'] -# PyTorch pulls in a bunch of submodules which don't have releases. -# We download the submodule revisions from their repos. -# determine commit of additional sources via https://github.com/pytorch/pytorch/tree/v1.0.1/third_party -sources = [ - 'v%(version)s.tar.gz', # PyTorch - { - 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], - 'download_filename': '670b4d4aa46886cc66874e2a4dc846f5cfc2a285.tar.gz', - 'filename': 'gloo-20190201.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/gloo'), - }, - { - 'source_urls': ['https://github.com/google/googletest/archive'], - 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', - 'filename': 'googletest-20180831.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/googletest'), - }, - { - 'source_urls': ['https://github.com/pybind/pybind11/archive'], - 'download_filename': '5c8746ff135abb390bf95944be593e895a586a50.tar.gz', - 'filename': 'pybind11-20180911.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pybind11'), - }, - { - 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], - 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', - 'filename': 'clang-cindex-python3-20170330.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pybind11/tools/clang'), - }, - { - 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], - 'download_filename': '89fe1695edf9ee14c22f815f24bac45577a4f135.tar.gz', - 'filename': 'cpuinfo-20190117.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/cpuinfo'), - }, - { - 'source_urls': ['https://github.com/onnx/onnx/archive'], - 'download_filename': '42804705bdbf179d1a98394008417e1392013547.tar.gz', - 'filename': 'onnx-20181204.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/onnx'), - }, - { - 'source_urls': ['https://github.com/google/protobuf/archive'], - 'download_filename': '2761122b810fe8861004ae785cc3ab39f384d342.tar.gz', - 'filename': 'protobuf-20171113.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/protobuf'), - }, - { - 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], - 'download_filename': '13da0b4c21d17f94150713366420baaf1b5a46f4.tar.gz', - 'filename': 'pthreadpool-20181008.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pthreadpool'), - }, - { - 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], - 'download_filename': 'b742d1143724d646cd0f914646f1240eacf5bd73.tar.gz', - 'filename': 'FXdiv-20181016.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/FXdiv'), - }, - { - 'source_urls': ['https://github.com/Maratyszcza/psimd/archive'], - 'download_filename': '90a938f30ba414ada2f4b00674ee9631d7d85e19.tar.gz', - 'filename': 'psimd-20180906.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/psimd'), - }, - { - 'source_urls': ['https://github.com/Maratyszcza/FP16/archive'], - 'download_filename': '34d4bf01bbf7376f2baa71b8fa148b18524d45cf.tar.gz', - 'filename': 'FP16-20181011.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/FP16'), - }, - { - 'source_urls': ['https://github.com/Maratyszcza/NNPACK/archive'], - 'download_filename': '1e005b0c2777f39972a4ac15bea03e0e315a3d92.tar.gz', - 'filename': 'NNPACK-20180903.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/NNPACK'), - }, - { - 'source_urls': ['https://github.com/shibatch/sleef/archive'], - 'download_filename': '6ff7a135a1e31979d1e1844a2e7171dfbd34f54f.tar.gz', - 'filename': 'sleef-20180509.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/sleef'), - }, - { - 'source_urls': ['https://github.com/Maratyszcza/PeachPy/archive'], - 'download_filename': '07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz', - 'filename': 'PeachPy-20180219.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/python-peachpy'), - }, - { - 'source_urls': ['https://github.com/pytorch/QNNPACK/archive'], - 'download_filename': 'ef05e87cef6b8e719989ce875b5e1c9fdb304c05.tar.gz', - 'filename': 'QNNPACK-20181205.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/QNNPACK'), - }, - { - 'source_urls': ['https://github.com/pytorch/fbgemm/archive'], - 'download_filename': '79333308f5e2fc242727879dcd3de3536b6ffc39.tar.gz', - 'filename': 'fbgemm-20190123.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/fbgemm'), - }, - { - 'source_urls': ['https://github.com/google/benchmark/archive'], - 'download_filename': '505be96ab23056580a3a2315abba048f4428b04e.tar.gz', - 'filename': 'benchmark-20180606.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/benchmark'), - }, - { - 'source_urls': ['https://github.com/eigenteam/eigen-git-mirror/archive'], - 'download_filename': 'f59336cee358f92b959de6a0daf07c4ab2318022.tar.gz', - 'filename': 'eigen-20180908.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/eigen'), - }, - { - 'source_urls': ['https://github.com/google/gemmlowp/archive'], - 'download_filename': '8416bab644641a5c0a81ecf91a5cda804af0aee1.tar.gz', - 'filename': 'gemmlowp-20180828.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/gemmlowp/gemmlowp'), - }, - { - 'source_urls': ['https://github.com/NVIDIA/nccl/archive'], - 'download_filename': '3c6e25210bb1b544748937e5db74db0b9679b95e.tar.gz', - 'filename': 'nccl-20181109.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/nccl/nccl'), - }, - { - 'source_urls': ['https://github.com/NVlabs/cub/archive'], - 'download_filename': '285aeebaa34b0e8a7670867a2e66c1a52d998d6a.tar.gz', - 'filename': 'cub-20170829.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/cub'), - }, - { - 'source_urls': ['https://github.com/intel/ideep/archive'], - 'download_filename': '7b8f9d025a675522305a1c5d1328d83f11f205e8.tar.gz', - 'filename': 'ideep-20181224.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/ideep'), - }, - { - 'source_urls': ['https://github.com/intel/mkl-dnn/archive'], - 'download_filename': '0c3cb94999919d33e4875177fdef662bd9413dd4.tar.gz', - 'filename': 'mkl-dnn-20190131.tar.gz', - 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/ideep/mkl-dnn'), - }, - # mkl-dnn requires Intel MKL, so download minimal Intel MKL version - # actually using imkl as a dependency would be messy due to underlying icc/ifort compilers & impi MPI lib - { - 'source_urls': ['https://github.com/intel/mkl-dnn/releases/download/v0.17.3'], - 'filename': 'mklml_lnx_2019.0.1.20180928.tgz', - 'extract_cmd': mklml_extract_cmd % - (pytorchdir, 'third_party/ideep/mkl-dnn/external/mklml_lnx_2019.0.1.20180928', - pytorchdir, 'third_party/ideep/mkl-dnn/external/mklml_lnx_2019.0.1.20180928'), - }, -] -patches = [ - '%(name)s-%(version)s-fix-findAVX.patch', - '%(name)s-%(version)s-fix-for-intel.patch', -] -checksums = [ - '210561583378132d07287518710251bcf861f9b7d625eb67258ed2e9d567cea1', # v1.0.1.tar.gz - '0e98a4fdb6e27add72b4bb0e63a5ed20a9271139c3d0ccc2c15c502e3366bca3', # gloo-20190201.tar.gz - 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz - 'ffe077d0fccc34aa95c2aba7a3abadbdc2a480c44a238879381733d38322e921', # pybind11-20180911.tar.gz - '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz - 'b84c49b4bdc12b0e8f1bff365dcefd50e5a2a25eeef8c928aeb2dab9fda4d599', # cpuinfo-20190117.tar.gz - 'b9520d6ce9f8b9928bf517696ea62fd03308fd21dafdebfec7aeb8894b3813ab', # onnx-20181204.tar.gz - 'd293a86f4c82a31990b89be2b9787df045e3f6b86378e9950e5e1145d4a08e6a', # protobuf-20171113.tar.gz - '90ab4f60ae0e99c0172dd5201dccc6de6c8f384a21b3d959588f4c1e00beec0f', # pthreadpool-20181008.tar.gz - '07625551202a1f35fe5e826669ad495962b26f6a139290e90b321c5996f002ef', # FXdiv-20181016.tar.gz - 'afd27417c6df1c85f79a68361055dd3adc292174913c39c1f58b698b9cfd7926', # psimd-20180906.tar.gz - 'dacd927f345c40163532e65ed3ea796d190f4efdd125838401a35e8147e55313', # FP16-20181011.tar.gz - '02d278559609982f2dbd973f265caf674274ac7a61ddd867c4956176252d940e', # NNPACK-20180903.tar.gz - 'f822489cbbf3cd09db578ea7ac9af40a9d3184f8ff95cb98e8b33b71ed5d89f8', # sleef-20180509.tar.gz - '13100c3deed300bbf16f87d8af3539f432462bfef9d38f0c7e3e387dc2e88676', # PeachPy-20180219.tar.gz - 'dc0c9ca760bb1bf858dd1aebaf1471b8437c1b2ef9a9b6acaf302fa14b04194f', # QNNPACK-20181205.tar.gz - 'd2dabcd172db8fb91dfa75422a5eb6f55f55f22d047d9f1b02eb6a3be88a09cd', # fbgemm-20190123.tar.gz - '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz - 'fd9e9f0d6ef407a162f5f283c52d3c271efc1092377274abe1e30dff83dbc1a4', # eigen-20180908.tar.gz - 'e12e096e986221d96d55185e870397b3717b625d6c5d155fbd9a7be314bed06a', # gemmlowp-20180828.tar.gz - '72b4835362d8586e315bdf5c30eea99f2efcf14f19162f00ac0675e8b1b22e61', # nccl-20181109.tar.gz - '7224b03af4acbc54525105bb42e3ecd75c66a3a5b47e8a725ab008467c4109f9', # cub-20170829.tar.gz - 'c7418025bd57b3143e651433d0874a39629fce6cc96b43e3f8d5861a8ad23ffb', # ideep-20181224.tar.gz - 'f98d2c297353acfab1ecff2054bee65efd2367b4c621e762cf26f50e037a9728', # mkl-dnn-20190131.tar.gz - 'f00dc3b142a5be399bdeebd7e7ea369545a35d4fb84c86f98b6b048d72685295', # mklml_lnx_2019.0.1.20180928.tgz - 'c8dabee9fd710976c6073a81d2cad2735f95c063819cf8effc001e1940f63283', # PyTorch-1.0.1-fix-findAVX.patch - '569333e194d6a1d716972e17ad2ca1cd72e92a8845cee2f02ab2d5f541f013e9', # PyTorch-1.0.1-fix-for-intel.patch -] - -builddependencies = [('CMake', '3.12.1')] - -dependencies = [ - ('Python', '3.6.6'), - ('PyYAML', '3.13', versionsuffix), - ('hypothesis', '4.5.0', versionsuffix), - ('cuDNN', '7.1.4.18'), - ('Ninja', '1.8.2'), - ('magma', '2.5.0'), -] - -download_dep_fail = True - -# This environment is needed to prevent setup.py from invoking git to determine version. -prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' - -# you can choice here: either give a list of CUDA cc version or tell it All -# by default it does autodetect of the GPU on the local machine -# https://en.wikipedia.org/wiki/CUDA#GPUs_supported -# register error with 5.2, 5.3, 6.2 -prebuildopts += ' TORCH_CUDA_ARCH_LIST="3.0 3.2 3.5 3.7 5.0 6.0 6.1 7.0 7.2"' - -runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' -# skip test subsuites that include hanging/failing tests for now -runtest += '&& python test/run_test.py --exclude autograd cpp_extensions c10d torch --verbose' - -options = {'modulename': 'torch'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'devel' From 676807faf7a0626fc8eab9f3f3a1bb2d3809bec4 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 22 Mar 2019 14:56:58 +0000 Subject: [PATCH 0977/5331] moving fosscuda configs into a separate pr --- ...hesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb deleted file mode 100644 index 7bde035e223..00000000000 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,33 +0,0 @@ -# This easyconfig was created by the BEAR Software team at the University of Birmingham. -easyblock = 'PythonBundle' - -name = 'hypothesis' -version = '4.5.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = "https://github.com/HypothesisWorks/hypothesis" -description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized - by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets - you find more bugs in your code with less work.""" - -toolchain = {'name': 'fosscuda', 'version': '2018b'} - -dependencies = [ - ('Python', '3.6.6'), -] - -use_pip = True - -exts_list = [ - ('attrs', '18.2.0', { - 'modulename': 'attr', - 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], - 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/h/hypothesis/'], - 'checksums': ['2187928e96bab144b89c6c19d08d61dc247bb1623e58e31bec1da7f71381fa9e'], - }), -] - -moduleclass = 'tools' From 420af52e5d4afc558bead338ff67f29f267cbda5 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 22 Mar 2019 14:57:45 +0000 Subject: [PATCH 0978/5331] moving fosscuda configs into a separate pr --- .../m/magma/magma-2.5.0-fix-makefile.patch | 39 ------------------- 1 file changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch b/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch deleted file mode 100644 index 8bd8e446258..00000000000 --- a/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch +++ /dev/null @@ -1,39 +0,0 @@ -# Fix the makefile to use EB values for everything -# Based off magma-2.3.0-fix-makefile.patch by wpoely86@gmail.com -# and updated for 2.5.0 ---- magma-2.5.0/Makefile.orig 2019-03-08 12:33:11.872321116 +0000 -+++ magma-2.5.0/Makefile 2019-03-08 12:35:58.463432082 +0000 -@@ -10,7 +10,7 @@ - CC ?= cc - CXX ?= c++ - NVCC ?= nvcc --FORT ?= -+FORT ?= $(FC) - ifeq ($(FORT),) - $(warning No Fortran compiler was given in FORT in make.inc. Some testers will not be able to check their results.) - endif -@@ -23,17 +23,17 @@ - #FPIC = -fPIC - - # may want -std=c99 for CFLAGS, -std=c++11 for CXXFLAGS --CFLAGS ?= -O3 $(FPIC) -DADD_ -Wall -MMD --CXXFLAGS ?= $(CFLAGS) -std=c++11 --NVCCFLAGS ?= -O3 -DADD_ -Xcompiler "$(FPIC) -Wall -Wno-unused-function" -std=c++11 --FFLAGS ?= -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument --F90FLAGS ?= -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument --LDFLAGS ?= -O3 $(FPIC) -+CFLAGS := $(FPIC) -DADD_ -Wall -MMD $(CFLAGS) -+CXXFLAGS := $(CFLAGS) -+NVCCFLAGS := -DADD_ -Xcompiler "$(FPIC) -Wall -Wno-unused-function $(CFLAGS)" -+FFLAGS := $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument $(FCFLAGS) -+F90FLAGS := $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument $(F90FLAGS) -+LDFLAGS := $(FPIC) -fopenmp $(LDFLAGS) - - INC ?= -I$(CUDADIR)/include - - LIBDIR ?= -L$(CUDADIR)/lib64 --LIB ?= -lcudart -lcudadevrt -lcublas -lcusparse -llapack -lblas -lpthread -lm -+LIB := $(LIBLAPACK) -lcudart -lcudadevrt -lcublas -lcusparse -lpthread -lm $(LIBS) - - GPU_TARGET ?= Kepler Maxwell Pascal - From ee8ca34a16e1803fe18be9a07c037a700f9ead99 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 22 Mar 2019 14:57:58 +0000 Subject: [PATCH 0979/5331] moving fosscuda configs into a separate pr --- .../m/magma/magma-2.5.0-fosscuda-2018b.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb deleted file mode 100644 index 4ad082ef129..00000000000 --- a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = "ConfigureMake" - -name = 'magma' -version = '2.5.0' - -homepage = 'http://icl.cs.utk.edu/magma/' -description = """The MAGMA project aims to develop a dense linear algebra library similar to - LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" - -toolchain = {'name': 'fosscuda', 'version': '2018b'} -toolchainopts = {'pic': True, 'openmp': True} - -source_urls = ['http://icl.cs.utk.edu/projectsfiles/magma/downloads/'] -sources = [SOURCE_TAR_GZ] -patches = [('%(name)s-%(version)s-fix-makefile.patch')] -checksums = [ - '4fd45c7e46bd9d9124253e7838bbfb9e6003c64c2c67ffcff02e6c36d2bcfa33', # magma-2.5.0.tar.gz - '2839e33a17134e686ccd9fde7e008b40495e4e8bafb3ae1bd49cb0e39852e7ac', # magma-2.5.0-fix-makefile.patch -] - -skipsteps = ['configure'] - -prebuildopts = 'touch make.inc && ' -# magma 2.5.0 does not build on sm_30 - so remove Kepler and specify sm_35 -# http://icl.cs.utk.edu/magma/forum/viewtopic.php?f=2&t=1906&sid=7048fadfd48a0d00c3c4294ddef6a096 -prebuildopts += 'GPU_TARGET="sm_35 Maxwell Pascal Volta" ' - -installopts = 'prefix=%(installdir)s' - -sanity_check_paths = { - 'files': ['lib/libmagma.so', 'lib/libmagma.a'], - 'dirs': ['include'], -} - -moduleclass = 'math' From 364a303859c4251b86186b070cbe2a8ba0f49dd7 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 22 Mar 2019 14:58:47 +0000 Subject: [PATCH 0980/5331] Update PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb --- .../p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb index 88e1c54f167..f9f38c56be6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb @@ -216,6 +216,7 @@ download_dep_fail = True # This environment is needed to prevent setup.py from invoking git to determine version. prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' +prebuildopts += ' CFLAGS="-ldl"' runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' # skip test subsuites that include hanging/failing tests for now From 5b58cb7b7999b521f0080cc7f23c13b87b3e0662 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 22 Mar 2019 15:33:57 +0000 Subject: [PATCH 0981/5331] PyTorch 1.0.1 for fosscuda 2018b --- ...hesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb | 33 +++ .../m/magma/magma-2.5.0-fix-makefile.patch | 39 +++ .../m/magma/magma-2.5.0-fosscuda-2018b.eb | 35 +++ ...Torch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 239 ++++++++++++++++++ 4 files changed, 346 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch create mode 100644 easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..7bde035e223 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.5.0-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,33 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'hypothesis' +version = '4.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), +] + +use_pip = True + +exts_list = [ + ('attrs', '18.2.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], + 'checksums': ['10cbf6e27dbce8c30807caf056c8eb50917e0eaafe86347671b57254006c3e69'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/h/hypothesis/'], + 'checksums': ['2187928e96bab144b89c6c19d08d61dc247bb1623e58e31bec1da7f71381fa9e'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch b/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch new file mode 100644 index 00000000000..8bd8e446258 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.5.0-fix-makefile.patch @@ -0,0 +1,39 @@ +# Fix the makefile to use EB values for everything +# Based off magma-2.3.0-fix-makefile.patch by wpoely86@gmail.com +# and updated for 2.5.0 +--- magma-2.5.0/Makefile.orig 2019-03-08 12:33:11.872321116 +0000 ++++ magma-2.5.0/Makefile 2019-03-08 12:35:58.463432082 +0000 +@@ -10,7 +10,7 @@ + CC ?= cc + CXX ?= c++ + NVCC ?= nvcc +-FORT ?= ++FORT ?= $(FC) + ifeq ($(FORT),) + $(warning No Fortran compiler was given in FORT in make.inc. Some testers will not be able to check their results.) + endif +@@ -23,17 +23,17 @@ + #FPIC = -fPIC + + # may want -std=c99 for CFLAGS, -std=c++11 for CXXFLAGS +-CFLAGS ?= -O3 $(FPIC) -DADD_ -Wall -MMD +-CXXFLAGS ?= $(CFLAGS) -std=c++11 +-NVCCFLAGS ?= -O3 -DADD_ -Xcompiler "$(FPIC) -Wall -Wno-unused-function" -std=c++11 +-FFLAGS ?= -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument +-F90FLAGS ?= -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument +-LDFLAGS ?= -O3 $(FPIC) ++CFLAGS := $(FPIC) -DADD_ -Wall -MMD $(CFLAGS) ++CXXFLAGS := $(CFLAGS) ++NVCCFLAGS := -DADD_ -Xcompiler "$(FPIC) -Wall -Wno-unused-function $(CFLAGS)" ++FFLAGS := $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument $(FCFLAGS) ++F90FLAGS := $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument $(F90FLAGS) ++LDFLAGS := $(FPIC) -fopenmp $(LDFLAGS) + + INC ?= -I$(CUDADIR)/include + + LIBDIR ?= -L$(CUDADIR)/lib64 +-LIB ?= -lcudart -lcudadevrt -lcublas -lcusparse -llapack -lblas -lpthread -lm ++LIB := $(LIBLAPACK) -lcudart -lcudadevrt -lcublas -lcusparse -lpthread -lm $(LIBS) + + GPU_TARGET ?= Kepler Maxwell Pascal + diff --git a/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb new file mode 100644 index 00000000000..4ad082ef129 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.5.0-fosscuda-2018b.eb @@ -0,0 +1,35 @@ +easyblock = "ConfigureMake" + +name = 'magma' +version = '2.5.0' + +homepage = 'http://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['http://icl.cs.utk.edu/projectsfiles/magma/downloads/'] +sources = [SOURCE_TAR_GZ] +patches = [('%(name)s-%(version)s-fix-makefile.patch')] +checksums = [ + '4fd45c7e46bd9d9124253e7838bbfb9e6003c64c2c67ffcff02e6c36d2bcfa33', # magma-2.5.0.tar.gz + '2839e33a17134e686ccd9fde7e008b40495e4e8bafb3ae1bd49cb0e39852e7ac', # magma-2.5.0-fix-makefile.patch +] + +skipsteps = ['configure'] + +prebuildopts = 'touch make.inc && ' +# magma 2.5.0 does not build on sm_30 - so remove Kepler and specify sm_35 +# http://icl.cs.utk.edu/magma/forum/viewtopic.php?f=2&t=1906&sid=7048fadfd48a0d00c3c4294ddef6a096 +prebuildopts += 'GPU_TARGET="sm_35 Maxwell Pascal Volta" ' + +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libmagma.so', 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..2e19fdd3fa5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,239 @@ +easyblock = 'PythonPackage' + +name = 'PyTorch' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +pytorchdir = 'pytorch-%(version)s' +extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' +mklml_extract_cmd = "mkdir -p %s/%s && tar -C %s/%s --strip-components=1 -xzf %%s" + +source_urls = ['https://github.com/pytorch/pytorch/archive'] +# PyTorch pulls in a bunch of submodules which don't have releases. +# We download the submodule revisions from their repos. +# determine commit of additional sources via https://github.com/pytorch/pytorch/tree/v1.0.1/third_party +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], + 'download_filename': '670b4d4aa46886cc66874e2a4dc846f5cfc2a285.tar.gz', + 'filename': 'gloo-20190201.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/gloo'), + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/googletest'), + }, + { + 'source_urls': ['https://github.com/pybind/pybind11/archive'], + 'download_filename': '5c8746ff135abb390bf95944be593e895a586a50.tar.gz', + 'filename': 'pybind11-20180911.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pybind11'), + }, + { + 'source_urls': ['https://github.com/wjakob/clang-cindex-python3/archive'], + 'download_filename': '6a00cbc4a9b8e68b71caf7f774b3f9c753ae84d5.tar.gz', + 'filename': 'clang-cindex-python3-20170330.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pybind11/tools/clang'), + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': '89fe1695edf9ee14c22f815f24bac45577a4f135.tar.gz', + 'filename': 'cpuinfo-20190117.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/cpuinfo'), + }, + { + 'source_urls': ['https://github.com/onnx/onnx/archive'], + 'download_filename': '42804705bdbf179d1a98394008417e1392013547.tar.gz', + 'filename': 'onnx-20181204.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/onnx'), + }, + { + 'source_urls': ['https://github.com/google/protobuf/archive'], + 'download_filename': '2761122b810fe8861004ae785cc3ab39f384d342.tar.gz', + 'filename': 'protobuf-20171113.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/protobuf'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], + 'download_filename': '13da0b4c21d17f94150713366420baaf1b5a46f4.tar.gz', + 'filename': 'pthreadpool-20181008.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/pthreadpool'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], + 'download_filename': 'b742d1143724d646cd0f914646f1240eacf5bd73.tar.gz', + 'filename': 'FXdiv-20181016.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/FXdiv'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/psimd/archive'], + 'download_filename': '90a938f30ba414ada2f4b00674ee9631d7d85e19.tar.gz', + 'filename': 'psimd-20180906.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/psimd'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FP16/archive'], + 'download_filename': '34d4bf01bbf7376f2baa71b8fa148b18524d45cf.tar.gz', + 'filename': 'FP16-20181011.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/FP16'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/NNPACK/archive'], + 'download_filename': '1e005b0c2777f39972a4ac15bea03e0e315a3d92.tar.gz', + 'filename': 'NNPACK-20180903.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/NNPACK'), + }, + { + 'source_urls': ['https://github.com/shibatch/sleef/archive'], + 'download_filename': '6ff7a135a1e31979d1e1844a2e7171dfbd34f54f.tar.gz', + 'filename': 'sleef-20180509.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/sleef'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/PeachPy/archive'], + 'download_filename': '07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz', + 'filename': 'PeachPy-20180219.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/python-peachpy'), + }, + { + 'source_urls': ['https://github.com/pytorch/QNNPACK/archive'], + 'download_filename': 'ef05e87cef6b8e719989ce875b5e1c9fdb304c05.tar.gz', + 'filename': 'QNNPACK-20181205.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/QNNPACK'), + }, + { + 'source_urls': ['https://github.com/pytorch/fbgemm/archive'], + 'download_filename': '79333308f5e2fc242727879dcd3de3536b6ffc39.tar.gz', + 'filename': 'fbgemm-20190123.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/fbgemm'), + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': '505be96ab23056580a3a2315abba048f4428b04e.tar.gz', + 'filename': 'benchmark-20180606.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/benchmark'), + }, + { + 'source_urls': ['https://github.com/eigenteam/eigen-git-mirror/archive'], + 'download_filename': 'f59336cee358f92b959de6a0daf07c4ab2318022.tar.gz', + 'filename': 'eigen-20180908.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/eigen'), + }, + { + 'source_urls': ['https://github.com/google/gemmlowp/archive'], + 'download_filename': '8416bab644641a5c0a81ecf91a5cda804af0aee1.tar.gz', + 'filename': 'gemmlowp-20180828.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/gemmlowp/gemmlowp'), + }, + { + 'source_urls': ['https://github.com/NVIDIA/nccl/archive'], + 'download_filename': '3c6e25210bb1b544748937e5db74db0b9679b95e.tar.gz', + 'filename': 'nccl-20181109.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/nccl/nccl'), + }, + { + 'source_urls': ['https://github.com/NVlabs/cub/archive'], + 'download_filename': '285aeebaa34b0e8a7670867a2e66c1a52d998d6a.tar.gz', + 'filename': 'cub-20170829.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/cub'), + }, + { + 'source_urls': ['https://github.com/intel/ideep/archive'], + 'download_filename': '7b8f9d025a675522305a1c5d1328d83f11f205e8.tar.gz', + 'filename': 'ideep-20181224.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/ideep'), + }, + { + 'source_urls': ['https://github.com/intel/mkl-dnn/archive'], + 'download_filename': '0c3cb94999919d33e4875177fdef662bd9413dd4.tar.gz', + 'filename': 'mkl-dnn-20190131.tar.gz', + 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/ideep/mkl-dnn'), + }, + # mkl-dnn requires Intel MKL, so download minimal Intel MKL version + # actually using imkl as a dependency would be messy due to underlying icc/ifort compilers & impi MPI lib + { + 'source_urls': ['https://github.com/intel/mkl-dnn/releases/download/v0.17.3'], + 'filename': 'mklml_lnx_2019.0.1.20180928.tgz', + 'extract_cmd': mklml_extract_cmd % + (pytorchdir, 'third_party/ideep/mkl-dnn/external/mklml_lnx_2019.0.1.20180928', + pytorchdir, 'third_party/ideep/mkl-dnn/external/mklml_lnx_2019.0.1.20180928'), + }, +] +patches = [ + '%(name)s-%(version)s-fix-findAVX.patch', + '%(name)s-%(version)s-fix-for-intel.patch', +] +checksums = [ + '210561583378132d07287518710251bcf861f9b7d625eb67258ed2e9d567cea1', # v1.0.1.tar.gz + '0e98a4fdb6e27add72b4bb0e63a5ed20a9271139c3d0ccc2c15c502e3366bca3', # gloo-20190201.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + 'ffe077d0fccc34aa95c2aba7a3abadbdc2a480c44a238879381733d38322e921', # pybind11-20180911.tar.gz + '828e0d6238e2129a9e08071750dc16ba10e38eacf96f21b8a71e501c2085b282', # clang-cindex-python3-20170330.tar.gz + 'b84c49b4bdc12b0e8f1bff365dcefd50e5a2a25eeef8c928aeb2dab9fda4d599', # cpuinfo-20190117.tar.gz + 'b9520d6ce9f8b9928bf517696ea62fd03308fd21dafdebfec7aeb8894b3813ab', # onnx-20181204.tar.gz + 'd293a86f4c82a31990b89be2b9787df045e3f6b86378e9950e5e1145d4a08e6a', # protobuf-20171113.tar.gz + '90ab4f60ae0e99c0172dd5201dccc6de6c8f384a21b3d959588f4c1e00beec0f', # pthreadpool-20181008.tar.gz + '07625551202a1f35fe5e826669ad495962b26f6a139290e90b321c5996f002ef', # FXdiv-20181016.tar.gz + 'afd27417c6df1c85f79a68361055dd3adc292174913c39c1f58b698b9cfd7926', # psimd-20180906.tar.gz + 'dacd927f345c40163532e65ed3ea796d190f4efdd125838401a35e8147e55313', # FP16-20181011.tar.gz + '02d278559609982f2dbd973f265caf674274ac7a61ddd867c4956176252d940e', # NNPACK-20180903.tar.gz + 'f822489cbbf3cd09db578ea7ac9af40a9d3184f8ff95cb98e8b33b71ed5d89f8', # sleef-20180509.tar.gz + '13100c3deed300bbf16f87d8af3539f432462bfef9d38f0c7e3e387dc2e88676', # PeachPy-20180219.tar.gz + 'dc0c9ca760bb1bf858dd1aebaf1471b8437c1b2ef9a9b6acaf302fa14b04194f', # QNNPACK-20181205.tar.gz + 'd2dabcd172db8fb91dfa75422a5eb6f55f55f22d047d9f1b02eb6a3be88a09cd', # fbgemm-20190123.tar.gz + '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz + 'fd9e9f0d6ef407a162f5f283c52d3c271efc1092377274abe1e30dff83dbc1a4', # eigen-20180908.tar.gz + 'e12e096e986221d96d55185e870397b3717b625d6c5d155fbd9a7be314bed06a', # gemmlowp-20180828.tar.gz + '72b4835362d8586e315bdf5c30eea99f2efcf14f19162f00ac0675e8b1b22e61', # nccl-20181109.tar.gz + '7224b03af4acbc54525105bb42e3ecd75c66a3a5b47e8a725ab008467c4109f9', # cub-20170829.tar.gz + 'c7418025bd57b3143e651433d0874a39629fce6cc96b43e3f8d5861a8ad23ffb', # ideep-20181224.tar.gz + 'f98d2c297353acfab1ecff2054bee65efd2367b4c621e762cf26f50e037a9728', # mkl-dnn-20190131.tar.gz + 'f00dc3b142a5be399bdeebd7e7ea369545a35d4fb84c86f98b6b048d72685295', # mklml_lnx_2019.0.1.20180928.tgz + 'c8dabee9fd710976c6073a81d2cad2735f95c063819cf8effc001e1940f63283', # PyTorch-1.0.1-fix-findAVX.patch + '569333e194d6a1d716972e17ad2ca1cd72e92a8845cee2f02ab2d5f541f013e9', # PyTorch-1.0.1-fix-for-intel.patch +] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '3.6.6'), + ('PyYAML', '3.13', versionsuffix), + ('hypothesis', '4.5.0', versionsuffix), + ('cuDNN', '7.1.4.18'), + ('Ninja', '1.8.2'), + ('magma', '2.5.0'), +] + +download_dep_fail = True + +# This environment is needed to prevent setup.py from invoking git to determine version. +prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' +prebuildopts += ' CFLAGS="-ldl"' + +# you can choice here: either give a list of CUDA cc version or tell it All +# by default it does autodetect of the GPU on the local machine +# https://en.wikipedia.org/wiki/CUDA#GPUs_supported +# register error with 5.2, 5.3, 6.2 +prebuildopts += ' TORCH_CUDA_ARCH_LIST="3.0 3.2 3.5 3.7 5.0 6.0 6.1 7.0 7.2"' + +runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' +# skip test subsuites that include hanging/failing tests for now +runtest += '&& python test/run_test.py --exclude autograd cpp_extensions c10d torch --verbose' + +options = {'modulename': 'torch'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'devel' From 25c144e1815bc047d09d79bdccc6f018a40d8e39 Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Sun, 24 Mar 2019 08:58:41 +0200 Subject: [PATCH 0982/5331] UCX: download to unambiguous file name --- .../easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb b/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb index b87360810c0..97d890f4a5b 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb @@ -15,8 +15,11 @@ and high-performance applications toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} +sources = [{ + 'filename': 'ucx-1.5.0rc1.tar.gz', + 'download_filename': 'ucx-1.5.0.tar.gz' +}] source_urls = ['https://github.com/openucx/ucx/releases/download/v1.5.0-rc1'] -sources = ['ucx-1.5.0.tar.gz'] checksums = ['ae5dfa59c54627a11d8cb1c7fdd0b0319e5e8633a6aebd42a07e54a6a4a32181'] builddependencies = [ From a3a1a32c7a3c09dc43f3e7ebf3a98d6e6ce08e06 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 24 Mar 2019 13:58:28 +0200 Subject: [PATCH 0983/5331] adding easyconfigs: Mesa-19.0.0-GCCcore-8.2.0.eb, libunwind-1.3.1-GCCcore-8.2.0.eb, libGLU-9.0.0-GCCcore-8.2.0.eb --- .../l/libGLU/libGLU-9.0.0-GCCcore-8.2.0.eb | 27 +++++++ .../libunwind-1.3.1-GCCcore-8.2.0.eb | 33 ++++++++ .../m/Mesa/Mesa-19.0.0-GCCcore-8.2.0.eb | 75 +++++++++++++++++++ 3 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-19.0.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..d02e3bb817d --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-8.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.0' + +homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] +sources = ['glu-%(version)s.tar.bz2'] +checksums = ['1f7ad0d379a722fcbd303aa5650c6d7d5544fde83196b42a73d1193568a4df12'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('Mesa', '18.1.1'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..a556600f95b --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.3.1' + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['43997a3939b6ccdf2f669b50fdb8a4d3205374728c2923ddc2354c65260214f8'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('XZ', '5.2.4'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..bccaac10e6b --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.0-GCCcore-8.2.0.eb @@ -0,0 +1,75 @@ +# Automatically converted from Mesa-17.2.4-intel-2017b.eb +# Original message: +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '19.0.0' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. +toolchainopts = {'optarch': False} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] +sources = [SOURCELOWER_TAR_XZ] +patches = ['Mesa-17.3.6_fix-strip-llvm-flags.patch'] +checksums = [ + '5a549dfb40ec31e5c36c47aadac04554cb2e2a8d144a046a378fc16da57e38f8', # mesa-19.0.0.tar.xz + '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.3.6_fix-strip-llvm-flags.patch +] + +builddependencies = [ + ('binutils', '2.31.1'), + ('flex', '2.6.4'), + ('Bison', '3.0.5'), + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), + ('Mako', '1.0.7', '-Python-3.7.2'), + ('libxml2', '2.9.8'), + ('expat', '2.2.6'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('nettle', '3.4.1'), + ('libdrm', '2.4.97'), + ('LLVM', '7.0.1'), + ('X11', '20190311'), + ('libunwind', '1.3.1'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' From bb7c8210fa05dc70f2792074f2959737bb136ef7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 24 Mar 2019 20:05:43 +0100 Subject: [PATCH 0984/5331] prefer https:// over ftp:// for source_urls in recent GROMACS easyconfigs --- .../easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb | 5 ++++- .../g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb | 5 ++++- easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb | 5 ++++- .../g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb | 5 ++++- easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb | 5 ++++- easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-foss-2017b.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2016.4-fosscuda-2017b.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2016.4-giolf-2017b.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2016.4-goolfc-2017.02.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2016.4-intel-2017a.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2016.4-intel-2017b.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2016.4-intelcuda-2017b.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2016.5-intel-2018a.eb | 5 ++++- easybuild/easyconfigs/g/GROMACS/GROMACS-2018-foss-2018a.eb | 5 ++++- .../g/GROMACS/GROMACS-2018.1-foss-2018b-PLUMED.eb | 5 ++++- easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2018b.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2018b.eb | 5 ++++- easybuild/easyconfigs/g/GROMACS/GROMACS-2018.3-foss-2018b.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2018.3-fosscuda-2018b.eb | 5 ++++- .../g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED-2.5.0.eb | 5 ++++- .../g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED-2.5.0.eb | 5 ++++- easybuild/easyconfigs/g/GROMACS/GROMACS-2019-foss-2018b.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2019-fosscuda-2018b.eb | 5 ++++- 26 files changed, 104 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb index ce6e9ad3099..c41c6859e55 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-hybrid.eb @@ -23,7 +23,10 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['aa0a27cd13050a4b70aacfbd169ddce2fe507c7e668f460ecf6cf32afcac5771'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb index ca2552c92cc..138db042126 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016-foss-2016b-mt.eb @@ -23,7 +23,10 @@ description = """GROMACS is a versatile package to perform molecular dynamics, toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'openmp': True, 'usempi': False} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['aa0a27cd13050a4b70aacfbd169ddce2fe507c7e668f460ecf6cf32afcac5771'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb index 3bb98cc3026..d1ea82fc5a2 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.1-foss-2017a-PLUMED.eb @@ -26,7 +26,10 @@ This is CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['9e7d2892a903777b982bc9ab4306de969d92cb45b51a562f523ec5fe58db41e3'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb index 77ace3b36a4..7eb9c02ce17 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.2-foss-2017a.eb @@ -25,7 +25,10 @@ This is CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['b6ac3632b848ab0c19f8f319dd5b58fcd09b8e2005ee7509478606613e5409a5'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb index a04e23b103b..6c8583a872f 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2016b-GPU-enabled.eb @@ -26,7 +26,10 @@ This is a GPU enabled build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-%(version)s_fix_search_for_nvml_include.patch', diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb index dcf957194b8..bfb198b34bc 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-foss-2017a.eb @@ -25,7 +25,10 @@ This is CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb index fa4a0cb0ad4..24b855d6793 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-goolfc-2017.01.eb @@ -25,7 +25,10 @@ This is a GPU enabled build, containing both MPI and threadMPI builds. toolchain = {'name': 'goolfc', 'version': '2017.01'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-%(version)s_fix_search_for_nvml_include.patch', diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb index daab58130fe..5297f5cbfd4 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.3-intel-2017a.eb @@ -25,7 +25,10 @@ This is CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-foss-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-foss-2017b.eb index acc18f2e955..088922690d9 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-foss-2017b.eb @@ -26,7 +26,10 @@ This is CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-fosscuda-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-fosscuda-2017b.eb index 2bf75d36d3a..8f968d1b69c 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-fosscuda-2017b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-fosscuda-2017b.eb @@ -26,7 +26,10 @@ This is a GPU enabled build, containing both MPI and threadMPI binaries. toolchain = {'name': 'fosscuda', 'version': '2017b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-2018_fix_search_for_nvml_include.patch', diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-giolf-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-giolf-2017b.eb index 6f938c06dea..eeac7538ea6 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-giolf-2017b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-giolf-2017b.eb @@ -26,7 +26,10 @@ This is CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'giolf', 'version': '2017b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-goolfc-2017.02.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-goolfc-2017.02.eb index 408819d8b81..ac279b68665 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-goolfc-2017.02.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-goolfc-2017.02.eb @@ -26,7 +26,10 @@ This is a GPU enabled build, containing both MPI and threadMPI builds. toolchain = {'name': 'goolfc', 'version': '2017.02'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = ['GROMACS-%(version)s_fix_search_for_nvml_include.patch'] checksums = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intel-2017a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intel-2017a.eb index 95eea390cde..dd6dcd8583d 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intel-2017a.eb @@ -25,7 +25,10 @@ This is CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intel-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intel-2017b.eb index 8a2fb65d0e5..9f204518355 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intel-2017b.eb @@ -26,7 +26,10 @@ This is CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intelcuda-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intelcuda-2017b.eb index 6971b6044f7..2f20b8f764c 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intelcuda-2017b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.4-intelcuda-2017b.eb @@ -26,7 +26,10 @@ This is a GPU enabled build, containing both MPI and threadMPI binaries. toolchain = {'name': 'intelcuda', 'version': '2017b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-2018_fix_search_for_nvml_include.patch', diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.5-intel-2018a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.5-intel-2018a.eb index 21a3e554488..f40ae9349f4 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.5-intel-2018a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2016.5-intel-2018a.eb @@ -25,7 +25,10 @@ This is CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'intel', 'version': '2018a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['57db26c6d9af84710a1e0c47a1f5bf63a22641456448dcd2eeb556ebd14e0b7c'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018-foss-2018a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018-foss-2018a.eb index a3490bf32af..a55d7411deb 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018-foss-2018a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018-foss-2018a.eb @@ -11,7 +11,10 @@ This is CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2018a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['deb5d0b749a52a0c6083367b5f50a99e08003208d81954fb49e7009e1b1fd0e9'] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.1-foss-2018b-PLUMED.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.1-foss-2018b-PLUMED.eb index 51926e118cc..422ab5918a3 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.1-foss-2018b-PLUMED.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.1-foss-2018b-PLUMED.eb @@ -27,7 +27,10 @@ This is a CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = ['GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch'] checksums = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2018b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2018b.eb index c04f54387fa..8a34c0496bb 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2018b.eb @@ -26,7 +26,10 @@ This is a CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = [ '4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857', # gromacs-2018.2.tar.gz diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2018b.eb index 9bc9173e5c8..fb969c70d08 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2018b.eb @@ -26,7 +26,10 @@ This is a GPU enabled build, containing both MPI and threadMPI binaries. toolchain = {'name': 'fosscuda', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = [ '4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857', # gromacs-2018.2.tar.gz diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.3-foss-2018b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.3-foss-2018b.eb index ba8c709dab7..9f5b7790f46 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.3-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.3-foss-2018b.eb @@ -26,7 +26,10 @@ This is a CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = ['GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch'] checksums = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.3-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.3-fosscuda-2018b.eb index 183741d462d..73db64b7584 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.3-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.3-fosscuda-2018b.eb @@ -26,7 +26,10 @@ This is a GPU enabled build, containing both MPI and threadMPI binaries. toolchain = {'name': 'fosscuda', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-2018_fix_search_for_nvml_include.patch', diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED-2.5.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED-2.5.0.eb index f16e20dffa3..13c5c5bfd2e 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED-2.5.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-foss-2018b-PLUMED-2.5.0.eb @@ -28,7 +28,10 @@ This is a CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = ['GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch'] checksums = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED-2.5.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED-2.5.0.eb index ba0826248ca..090207fcd83 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED-2.5.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.4-fosscuda-2018b-PLUMED-2.5.0.eb @@ -28,7 +28,10 @@ This is a GPU enabled build, containing both MPI and threadMPI binaries. toolchain = {'name': 'fosscuda', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-2018_fix_search_for_nvml_include.patch', diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019-foss-2018b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019-foss-2018b.eb index 5512f8aae25..d04428f7f6e 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019-foss-2018b.eb @@ -26,7 +26,10 @@ This is a CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch', diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019-fosscuda-2018b.eb index b579e1ceb08..172dd1255b3 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019-fosscuda-2018b.eb @@ -26,7 +26,10 @@ This is a GPU enabled build, containing both MPI and threadMPI binaries. toolchain = {'name': 'fosscuda', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', From b994ba74fce0973256fe34533e51030e070ec71c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 25 Mar 2019 11:00:40 +0100 Subject: [PATCH 0985/5331] adding easyconfigs: libconfig-1.7.1-GCCcore-7.3.0.eb --- .../libconfig-1.7.1-GCCcore-7.3.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libconfig/libconfig-1.7.1-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/l/libconfig/libconfig-1.7.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.1-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..33666c54053 --- /dev/null +++ b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.1-GCCcore-7.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libconfig' +version = '1.7.1' + +homepage = 'https://hyperrealm.github.io/libconfig' +description = "Libconfig is a simple library for processing structured configuration files" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://hyperrealm.github.io/libconfig/dist/'] +sources = [SOURCE_TAR_GZ] +checksums = ['7b5b63f5ea046704481ce2e4c1d8cf28c13c3ca3387b84fd06901d2c4e6c037d'] + +builddependencies = [('binutils', '2.30')] + +sanity_check_paths = { + 'files': ['include/libconfig.h', 'include/libconfig.h++', 'lib/libconfig.a', 'lib/libconfig++.a', + 'lib/libconfig.%s' % SHLIB_EXT, 'lib/libconfig++.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' From 4af268efbd8d3849f9ba21e2c69a837369cd1ccb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 25 Mar 2019 11:11:00 +0100 Subject: [PATCH 0986/5331] bump libconfig version to latest 1.7.2 --- ....7.1-GCCcore-7.3.0.eb => libconfig-1.7.2-GCCcore-7.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/l/libconfig/{libconfig-1.7.1-GCCcore-7.3.0.eb => libconfig-1.7.2-GCCcore-7.3.0.eb} (86%) diff --git a/easybuild/easyconfigs/l/libconfig/libconfig-1.7.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.2-GCCcore-7.3.0.eb similarity index 86% rename from easybuild/easyconfigs/l/libconfig/libconfig-1.7.1-GCCcore-7.3.0.eb rename to easybuild/easyconfigs/l/libconfig/libconfig-1.7.2-GCCcore-7.3.0.eb index 33666c54053..0eab6a0cfd7 100644 --- a/easybuild/easyconfigs/l/libconfig/libconfig-1.7.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.2-GCCcore-7.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libconfig' -version = '1.7.1' +version = '1.7.2' homepage = 'https://hyperrealm.github.io/libconfig' description = "Libconfig is a simple library for processing structured configuration files" @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = ['https://hyperrealm.github.io/libconfig/dist/'] sources = [SOURCE_TAR_GZ] -checksums = ['7b5b63f5ea046704481ce2e4c1d8cf28c13c3ca3387b84fd06901d2c4e6c037d'] +checksums = ['7c3c7a9c73ff3302084386e96f903eb62ce06953bb1666235fac74363a16fad9'] builddependencies = [('binutils', '2.30')] From 790f3d64ef1e35eb3e587563c8d8d0fd8b27fbe0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 25 Mar 2019 11:43:08 +0100 Subject: [PATCH 0987/5331] adding easyconfigs: Cheetah-2.4.4-intel-2018b.eb --- .../c/Cheetah/Cheetah-2.4.4-intel-2018b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b.eb diff --git a/easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b.eb b/easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b.eb new file mode 100644 index 00000000000..460dc2e6f99 --- /dev/null +++ b/easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Cheetah' +version = '2.4.4' + +homepage = 'http://cheetahtemplate.org' +description = "Cheetah is an open source template engine and code generation tool." + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [('Python', '2.7.15')] + +#use_pip = True + +exts_list = [ + ('Markdown', '3.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], + 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/C/Cheetah'], + 'checksums': ['be308229f0c1e5e5af4f27d7ee06d90bb19e6af3059794e5fd536a6f29a9b550'], + 'modulename': name, + }), +] + +sanity_check_paths = { + 'files': ['bin/cheetah'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From b3f24183f4e3706c5e23e06f2450f327a7afd025 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Mon, 25 Mar 2019 09:13:25 -0500 Subject: [PATCH 0988/5331] add Java dep, switch to JAR easyblock --- .../easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb diff --git a/easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb b/easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb new file mode 100644 index 00000000000..7aa176c1285 --- /dev/null +++ b/easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb @@ -0,0 +1,33 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'JAR' + +name = 'BCEL' +version = '5.2' +javaver = '1.8' +versionsuffix = '-Java-%s' % javaver + +homepage = 'http://commons.apache.org/proper/commons-bcel/' + +description = """ + The Byte Code Engineering Library (Apache Commons BCEL™) is intended to give + users a convenient way to analyze, create, and manipulate (binary) Java class + files (those ending with .class). +""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [('http://archive.apache.org/dist/jakarta/bcel/binaries/')] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['669e96c3553e2c4f41842f8837c544b8fb00c58cc45e1904964d52a74cb3f78e'] + +extract_sources = True + +dependencies = [('Java', javaver)] + +sanity_check_paths = { + 'files': ['%(namelower)s-%(version)s.jar'], + 'dirs': [], +} + +moduleclass = 'lang' From 72de06784e93c2e9ada491911fc699df5361d751 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 25 Mar 2019 18:19:23 +0100 Subject: [PATCH 0989/5331] add missing versionsuffix for Cheetah + use pip --- ...tel-2018b.eb => Cheetah-2.4.4-intel-2018b-Python-2.7.15.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/c/Cheetah/{Cheetah-2.4.4-intel-2018b.eb => Cheetah-2.4.4-intel-2018b-Python-2.7.15.eb} (94%) diff --git a/easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b.eb b/easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b-Python-2.7.15.eb similarity index 94% rename from easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b.eb rename to easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b-Python-2.7.15.eb index 460dc2e6f99..a7dd12ec211 100644 --- a/easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b.eb +++ b/easybuild/easyconfigs/c/Cheetah/Cheetah-2.4.4-intel-2018b-Python-2.7.15.eb @@ -2,6 +2,7 @@ easyblock = 'PythonBundle' name = 'Cheetah' version = '2.4.4' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://cheetahtemplate.org' description = "Cheetah is an open source template engine and code generation tool." @@ -10,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} dependencies = [('Python', '2.7.15')] -#use_pip = True +use_pip = True exts_list = [ ('Markdown', '3.0.1', { From 0689df940547a4c26ddec0428b3a96164b9ce9f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 25 Mar 2019 18:53:14 +0100 Subject: [PATCH 0990/5331] collapse SciPy-bundle easyconfigs using foss/2019a for both Python 2.7.15 + 3.7.2 into a single easyconfig using multi_deps --- ...bundle-2019.03-foss-2019a-Python-2.7.15.eb | 43 ------------------- ....eb => SciPy-bundle-2019.03-foss-2019a.eb} | 5 +-- 2 files changed, 2 insertions(+), 46 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-2.7.15.eb rename easybuild/easyconfigs/s/SciPy-bundle/{SciPy-bundle-2019.03-foss-2019a-Python-3.7.2.eb => SciPy-bundle-2019.03-foss-2019a.eb} (93%) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-2.7.15.eb deleted file mode 100644 index b0e005bf690..00000000000 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-2.7.15.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'SciPy-bundle' -version = '2019.03' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://python.org/' -description = "Bundle of Python packages for scientific software" - -toolchain = {'name': 'foss', 'version': '2019a'} -toolchainopts = {'pic': True} - -dependencies = [('Python', '2.7.15')] - -use_pip = True - -# order is important! -# package versions updated Mar 15th 2019 -exts_list = [ - ('numpy', '1.16.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['6c692e3879dde0b67a9dc78f9bfb6f61c666b4562fd8619632d7043fb5b691b0'], - }), - ('scipy', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], - 'checksums': ['e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c'], - }), - ('mpi4py', '3.0.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - 'checksums': ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'], - }), - ('pandas', '0.24.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], - 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], - }), - ('mpmath', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], - 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a.eb similarity index 93% rename from easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-3.7.2.eb rename to easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a.eb index ce6a90be0c5..ed9e91412d2 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-foss-2019a.eb @@ -2,15 +2,14 @@ easyblock = 'PythonBundle' name = 'SciPy-bundle' version = '2019.03' -versionsuffix = '-Python-%(pyver)s' homepage = 'http://python.org/' description = "Bundle of Python packages for scientific software" toolchain = {'name': 'foss', 'version': '2019a'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'lowopt': True} -dependencies = [('Python', '3.7.2')] +multi_deps = {'Python': ['3.7.2', '2.7.15']} use_pip = True From 0aa0cf17939e3b39b21d858c9b804f0a3dad37d3 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 25 Mar 2019 19:01:29 +0100 Subject: [PATCH 0991/5331] Create OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb OpenCV 4.0.1 easyconfig for use with Python 3.6.6 --- .../OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..0aa61fe1e65 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,45 @@ +name = 'OpenCV' +version = '4.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [ + 'https://github.com/opencv/opencv/archive/', + # the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake + 'https://raw.githubusercontent.com/opencv/opencv_3rdparty/32e315a5b106a7b89dbed51c28f8120a48b368b4/ippicv', +] +sources = [ + '%(version)s.zip', + {'filename': 'ippicv_2019_lnx_intel64_general_20180723.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + 'b79ccdc4797a959c5ab17249a8a302c066248ae070e4d7010e2d77a625fdb30a', # 4.0.1.zip + 'fc167cb60deb8924339a7050f3da168bb02e221b2d6b8c00139d1fa7eace0c7d', # ippicv_2019_lnx_intel64_general_20180723.tgz +] + +builddependencies = [ + ('CMake', '3.12.1'), +] + +dependencies = [ + ('Python', '3.6.6'), + ('zlib', '1.2.11'), + ('FFmpeg', '4.1'), + ('libjpeg-turbo', '2.0.0'), + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), + ('JasPer', '2.0.14'), + ('Java', '1.8', '', True), + ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('GLib', '2.54.3'), + ('GTK+', '2.24.32'), +] + +moduleclass = 'vis' From d14d0caf5e1504d1ef64d1a9531d4b283bad0c8c Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Tue, 26 Mar 2019 08:31:11 +0200 Subject: [PATCH 0992/5331] Address review comments --- easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb b/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb index 97d890f4a5b..4c8fe8f4c5b 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.5.0rc1-GCCcore-8.2.0-hpcx.eb @@ -15,11 +15,11 @@ and high-performance applications toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} +source_urls = ['https://github.com/openucx/ucx/releases/download/v1.5.0-rc1'] sources = [{ 'filename': 'ucx-1.5.0rc1.tar.gz', 'download_filename': 'ucx-1.5.0.tar.gz' }] -source_urls = ['https://github.com/openucx/ucx/releases/download/v1.5.0-rc1'] checksums = ['ae5dfa59c54627a11d8cb1c7fdd0b0319e5e8633a6aebd42a07e54a6a4a32181'] builddependencies = [ From 93b562fe1b1efc4b62ccd34bc738979dc8d3acac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Mar 2019 09:38:46 +0100 Subject: [PATCH 0993/5331] adding easyconfigs: PAPI-5.7.0-GCCcore-7.3.0.eb --- .../p/PAPI/PAPI-5.7.0-GCCcore-7.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.7.0-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.7.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.7.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..1b5b6fe9206 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.7.0-GCCcore-7.3.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.7.0' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d1a3bb848e292c805bc9f29e09c27870e2ff4cda6c2fba3b7da8b4bba6547589'] + +builddependencies = [ + ('binutils', '2.30'), +] + +start_dir = 'src' + +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' From 358a7c73bd192583faf0d4d926f1e44e62f2f5e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Mar 2019 09:56:26 +0100 Subject: [PATCH 0994/5331] adding easyconfigs: KyotoCabinet-1.2.77-GCCcore-7.3.0.eb --- .../KyotoCabinet-1.2.77-GCCcore-7.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/k/KyotoCabinet/KyotoCabinet-1.2.77-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/k/KyotoCabinet/KyotoCabinet-1.2.77-GCCcore-7.3.0.eb b/easybuild/easyconfigs/k/KyotoCabinet/KyotoCabinet-1.2.77-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..dddf990adae --- /dev/null +++ b/easybuild/easyconfigs/k/KyotoCabinet/KyotoCabinet-1.2.77-GCCcore-7.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'KyotoCabinet' +version = '1.2.77' + +homepage = 'https://fallabs.com/kyotocabinet' +description = "Kyoto Cabinet is a library of routines for managing a database." + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://fallabs.com/kyotocabinet/pkg/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56899329384cc6f0f1f8aa3f1b41001071ca99c1d79225086a7f3575c0209de6'] + +builddependencies = [('binutils', '2.30')] + +sanity_check_paths = { + 'files': ['bin/kcdirmgr', 'bin/kcdirtest', 'bin/kcstashtest', 'bin/kcpolymgr', 'bin/kcpolytest'], + 'dirs': [], +} + +moduleclass = 'lib' From 8a691be227166f71d4ccd92a978b7f36fa06764e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Mar 2019 10:13:57 +0100 Subject: [PATCH 0995/5331] adding easyconfigs: LevelDB-1.20-GCCcore-7.3.0.eb --- .../l/LevelDB/LevelDB-1.20-GCCcore-7.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/LevelDB/LevelDB-1.20-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.20-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.20-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..8d8cffd9296 --- /dev/null +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.20-GCCcore-7.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'LevelDB' +version = '1.20' + +homepage = 'https://github.com/google/leveldb' +description = """LevelDB is a fast key-value storage library written at Google that provides an + ordered mapping from string keys to string values.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://github.com/google/leveldb/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f5abe8b5b209c2f36560b75f32ce61412f39a2922f7045ae764a2c23335b6664'] + +dependencies = [('binutils', '2.30')] + +files_to_copy = [ + (['out-shared/libleveldb.%s*' % SHLIB_EXT, 'out-static/libleveldb.a'], 'lib'), + (['include/leveldb/*.h'], 'include/leveldb') +] + +sanity_check_paths = { + 'files': ['include/leveldb/cache.h', 'include/leveldb/table.h', 'lib/libleveldb.a', + 'lib/libleveldb.%s' % SHLIB_EXT, 'lib/libleveldb.%s.%%(version_major)s' % SHLIB_EXT, + 'lib/libleveldb.%s.%%(version_major_minor)s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From 416b11dca73bf13a13af81ed28498a3c70df2409 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 26 Mar 2019 06:59:24 -0500 Subject: [PATCH 0996/5331] adding easyconfigs: HMMER-3.1b2-iccifort-2017.4.196-GCC-6.4.0-2.28.eb, HMMER-3.1b2-GCC-6.4.0-2.28.eb, RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb, RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb --- .../h/HMMER/HMMER-3.1b2-GCC-6.4.0-2.28.eb | 44 +++++++++++++++++++ ....1b2-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 44 +++++++++++++++++++ ...-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb | 21 +++++++++ ....4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb | 21 +++++++++ 4 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-iccifort-2017.4.196-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb create mode 100644 easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..e221527de3a --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-GCC-6.4.0-2.28.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.1b2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs of protein sequences, + and for making protein sequence alignments. It implements methods using probabilistic models + called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other + sequence alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote homologs + because of the strength of its underlying mathematical models. In the past, this strength + came at significant computational expense, but in the new HMMER3 project, HMMER is now + essentially as fast as BLAST.""" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536'] + +runtest = 'check' + +installopts = ' && cd easel && make install' + +sanity_check_paths = { + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan', + 'lib/libeasel.a', 'lib/libhmmer.a'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..3c2bf283564 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.1b2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs of protein sequences, + and for making protein sequence alignments. It implements methods using probabilistic models + called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other + sequence alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote homologs + because of the strength of its underlying mathematical models. In the past, this strength + came at significant computational expense, but in the new HMMER3 project, HMMER is now + essentially as fast as BLAST.""" + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536'] + +runtest = 'check' + +installopts = ' && cd easel && make install' + +sanity_check_paths = { + 'files': ['bin/esl-alimap', 'bin/esl-cluster', 'bin/esl-mask', 'bin/hmmemit', 'bin/hmmsearch', 'bin/hmmscan', + 'lib/libeasel.a', 'lib/libhmmer.a'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb new file mode 100644 index 00000000000..e8ef0ee102f --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb @@ -0,0 +1,21 @@ +name = 'RepeatMasker' +version = '4.0.8' +versionsuffix = '-Perl-%(perlver)s-HMMER' + +homepage = 'http://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = ['http://www.repeatmasker.org/'] +sources = ['RepeatMasker-open-%s.tar.gz' % '-'.join(version.split('.'))] +checksums = ['e294396f49ec236626c47020ce3c893ba08a50bce204e1d51a074978d215b558'] + +dependencies = [ + ('Perl', '5.26.0'), + ('TRF', '4.09', '-linux64', True), + ('HMMER', '3.1b2'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb new file mode 100644 index 00000000000..52f3b80f931 --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb @@ -0,0 +1,21 @@ +name = 'RepeatMasker' +version = '4.0.8' +versionsuffix = '-Perl-%(perlver)s-HMMER' + +homepage = 'http://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +source_urls = ['http://www.repeatmasker.org/'] +sources = ['RepeatMasker-open-%s.tar.gz' % '-'.join(version.split('.'))] +checksums = ['e294396f49ec236626c47020ce3c893ba08a50bce204e1d51a074978d215b558'] + +dependencies = [ + ('Perl', '5.26.0'), + ('TRF', '4.09', '-linux64', True), + ('HMMER', '3.1b2'), +] + +moduleclass = 'bio' From f2b870eb40efc46d2eb7d4515940b6d2f98567b9 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 26 Mar 2019 07:07:02 -0500 Subject: [PATCH 0997/5331] adding easyconfigs: BLAST-2.8.1-Linux_x86_64.eb --- .../b/BLAST/BLAST-2.8.1-Linux_x86_64.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb new file mode 100644 index 00000000000..74a447d6bbd --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb @@ -0,0 +1,26 @@ +# +# Author: Fenglai Liu +# fenglai@accre.vanderbilt.edu +# Vanderbilt University +# +easyblock = 'Tarball' + +name = 'BLAST' +version = '2.8.1' +versionsuffix = "-Linux_x86_64" + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST'] +sources = ['ncbi-%(namelower)s-%(version)s+-x64-linux.tar.gz'] +checksums = ['6c8216ba652d0af1c11b7e368c988fad58f2cb7ff66c2f2a05c826eac69728a6'] + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastx", "bin/tblastn"], + 'dirs': [] +} + +moduleclass = 'bio' From 8696c05b78882c799d407afd9824314f7d6a3a1d Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 26 Mar 2019 07:10:16 -0500 Subject: [PATCH 0998/5331] adding easyconfigs: snap-2013-11-29-GCC-6.4.0-2.28.eb, snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb and patches: snap_makefile_correction.patch --- .../s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb | 39 +++++++++++ ...1-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 39 +++++++++++ .../s/snap/snap_makefile_correction.patch | 65 +++++++++++++++++++ 3 files changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/s/snap/snap_makefile_correction.patch diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..fd3ee7732e8 --- /dev/null +++ b/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb @@ -0,0 +1,39 @@ +# +# Author: Fenglai Liu +# fenglai@accre.vanderbilt.edu +# Vanderbilt University +# +easyblock = 'MakeCp' + +name = 'snap' +version = '2013-11-29' + +homepage = 'http://korflab.ucdavis.edu/software.html' +description = """SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.""" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = ['http://korflab.ucdavis.edu/Software'] +sources = [SOURCE_TAR_GZ] +patches = ['snap_makefile_correction.patch'] +checksums = [ + 'e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a', # snap-2013-11-29.tar.gz + '02ea6dc6006ca5a5173dd2fc6a01b679a0910a68e0b51d00b7b9f732e4f79dcc', # snap_makefile_correction.patch +] + +files_to_copy = [ + (["cds-trainer.pl", "hmm-assembler.pl", "noncoding-trainer.pl", "patch-hmm.pl", + "zff2gff3.pl", "exonpairs","fathom","forge","hmm-info","snap","Zoe/zoe-loop"], "bin"), + "DNA", + "HMM", + "Zoe" +] + +sanity_check_paths = { + 'files': ["bin/snap", "bin/forge", "bin/zoe-loop"], + 'dirs': [""], +} + +modextravars = {'ZOE': '%(installdir)s/Zoe'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..1e5e39175e7 --- /dev/null +++ b/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,39 @@ +# +# Author: Fenglai Liu +# fenglai@accre.vanderbilt.edu +# Vanderbilt University +# +easyblock = 'MakeCp' + +name = 'snap' +version = '2013-11-29' + +homepage = 'http://korflab.ucdavis.edu/software.html' +description = """SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.""" + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +source_urls = ['http://korflab.ucdavis.edu/Software'] +sources = [SOURCE_TAR_GZ] +patches = ['snap_makefile_correction.patch'] +checksums = [ + 'e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a', # snap-2013-11-29.tar.gz + '02ea6dc6006ca5a5173dd2fc6a01b679a0910a68e0b51d00b7b9f732e4f79dcc', # snap_makefile_correction.patch +] + +files_to_copy = [ + (["cds-trainer.pl", "hmm-assembler.pl", "noncoding-trainer.pl", "patch-hmm.pl", + "zff2gff3.pl", "exonpairs","fathom","forge","hmm-info","snap","Zoe/zoe-loop"], "bin"), + "DNA", + "HMM", + "Zoe" +] + +sanity_check_paths = { + 'files': ["bin/snap", "bin/forge", "bin/zoe-loop"], + 'dirs': [""], +} + +modextravars = {'ZOE': '%(installdir)s/Zoe'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snap/snap_makefile_correction.patch b/easybuild/easyconfigs/s/snap/snap_makefile_correction.patch new file mode 100644 index 00000000000..7e8a1b068c4 --- /dev/null +++ b/easybuild/easyconfigs/s/snap/snap_makefile_correction.patch @@ -0,0 +1,65 @@ +drop the hard coded "gcc", also remove the -Werror since there are warining with GCC +author: fenglai liu (fenglai@accre.vanderbilt.edu) + +diff -Naur snap_ori/Makefile snap/Makefile +--- snap_ori/Makefile 2019-03-20 12:14:03.152600843 -0500 ++++ snap/Makefile 2019-03-20 13:54:45.172606540 -0500 +@@ -77,7 +77,7 @@ + cd Zoe; make clean + + depend: $(OBJECTS:.o=.c) +- gcc $(INC) -MM $^ > $@ ++ $(CC) $(INC) -MM $^ > $@ + + tar: + rm -rf /tmp/$(APP) +@@ -94,11 +94,11 @@ + + gcc: + cd Zoe; make; +- make $(APP) CC="gcc" CFLAGS="-O2 -Wall -Werror" +- make $(APP2) CC="gcc" CFLAGS="-O2 -Wall -Werror" +- make $(APP3) CC="gcc" CFLAGS="-O2 -Wall -Werror" +- make $(APP4) CC="gcc" CFLAGS="-O2 -Wall -Werror" +- make $(APP5) CC="gcc" CFLAGS="-O2 -Wall -Werror" ++ make $(APP) CFLAGS="-O2 -Wall " ++ make $(APP2) CFLAGS="-O2 -Wall " ++ make $(APP3) CFLAGS="-O2 -Wall " ++ make $(APP4) CFLAGS="-O2 -Wall " ++ make $(APP5) CFLAGS="-O2 -Wall " + + + ################### +diff -Naur snap_ori/Zoe/Makefile snap/Zoe/Makefile +--- snap_ori/Zoe/Makefile 2019-03-20 12:14:03.148600924 -0500 ++++ snap/Zoe/Makefile 2019-03-20 13:55:51.632260071 -0500 +@@ -76,7 +76,7 @@ + rm -f *.o $(APP) $(APP2) $(APP3) $(APP4) $(APP5) + + depend: $(OBJECTS:.o=.c) +- gcc -MM $^ > $@ ++ $(CC) -MM $^ > $@ + + tar: + rm -rf /tmp/$(APP) +@@ -92,14 +92,14 @@ + ################# + + gcc: +- make $(APP) CC="gcc" CFLAGS="-O2 -Wall -Werror" ++ make $(APP) CFLAGS="-O2 -Wall " + + all: +- make $(APP) CC="gcc" CFLAGS="-O2 -Wall -Werror" +- make $(APP2) CC="gcc" CFLAGS="-O2 -Wall -Werror" +- make $(APP3) CC="gcc" CFLAGS="-O2 -Wall -Werror" +- make $(APP4) CC="gcc" CFLAGS="-O2 -Wall -Werror" +- make $(APP5) CC="gcc" CFLAGS="-O2 -Wall -Werror" ++ make $(APP) CFLAGS="-O2 -Wall " ++ make $(APP2) CFLAGS="-O2 -Wall " ++ make $(APP3) CFLAGS="-O2 -Wall " ++ make $(APP4) CFLAGS="-O2 -Wall " ++ make $(APP5) CFLAGS="-O2 -Wall " + + + ################### From 5bec6f74a5d93d58a7f727363553d237b9100924 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 26 Mar 2019 07:43:34 -0500 Subject: [PATCH 0999/5331] use built-in javaver tag --- easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb b/easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb index 7aa176c1285..4a078913f57 100644 --- a/easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb +++ b/easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb @@ -4,8 +4,7 @@ easyblock = 'JAR' name = 'BCEL' version = '5.2' -javaver = '1.8' -versionsuffix = '-Java-%s' % javaver +versionsuffix = '-Java-%(javaver)s' homepage = 'http://commons.apache.org/proper/commons-bcel/' @@ -23,7 +22,7 @@ checksums = ['669e96c3553e2c4f41842f8837c544b8fb00c58cc45e1904964d52a74cb3f78e'] extract_sources = True -dependencies = [('Java', javaver)] +dependencies = [('Java', '1.8')] sanity_check_paths = { 'files': ['%(namelower)s-%(version)s.jar'], From 0732c42cc0d0e417c84df483b53884cde23fc05b Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 26 Mar 2019 07:46:35 -0500 Subject: [PATCH 1000/5331] Delete BCEL-5.2.eb lacked Java-%(javaver)s tag --- easybuild/easyconfigs/b/BCEL/BCEL-5.2.eb | 27 ------------------------ 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BCEL/BCEL-5.2.eb diff --git a/easybuild/easyconfigs/b/BCEL/BCEL-5.2.eb b/easybuild/easyconfigs/b/BCEL/BCEL-5.2.eb deleted file mode 100644 index 055a12dc3ce..00000000000 --- a/easybuild/easyconfigs/b/BCEL/BCEL-5.2.eb +++ /dev/null @@ -1,27 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu - -easyblock = 'PackedBinary' - -name = 'BCEL' -version = '5.2' - -homepage = 'http://commons.apache.org/proper/commons-bcel/' - -description = """ - The Byte Code Engineering Library (Apache Commons BCEL™) is intended to give - users a convenient way to analyze, create, and manipulate (binary) Java class - files (those ending with .class). -""" - -toolchain = {'name': 'dummy', 'version': ''} - -source_urls = [('http://archive.apache.org/dist/jakarta/bcel/binaries/')] -sources = ['%(namelower)s-%(version)s.tar.gz'] -checksums = ['669e96c3553e2c4f41842f8837c544b8fb00c58cc45e1904964d52a74cb3f78e'] - -sanity_check_paths = { - 'files': ['%(namelower)s-%(version)s.jar'], - 'dirs': [], -} - -moduleclass = 'lang' From 7917d081e04a44973c5991bdf187719c8af6b7e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Mar 2019 13:54:43 +0100 Subject: [PATCH 1001/5331] also fix hardcoded path in 'masurca' script --- .../m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb index 9693f0d6499..48ab80bad8f 100644 --- a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb @@ -39,11 +39,16 @@ dependencies = [ buildopts = "install-special" start_dir = "global-1" -# escaping single quotes within single quotes is tricky, so we use $'...' to use ANSI C-like escaping -postinstallcmds = ["sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA"] +postinstallcmds = [ + # fix location of 'bin' in install prefix in runCA script + # escaping single quotes within single quotes is tricky, so we use $'...' to use ANSI C-like escaping + "sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA", + # fix hardcoded path in masurca script, just point back to 'bin' subdirectory instead + "sed -i 's@../CA8/Linux-amd64/bin@../bin@g' %(installdir)s/bin/masurca", +] sanity_check_paths = { - 'files': ['bin/masurca'], + 'files': ['bin/masurca', 'bin/runCA'], 'dirs': ['include', 'lib'], } From 81d296df37fe03fac20dda22f71eb0c995b42fad Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 26 Mar 2019 09:32:20 -0500 Subject: [PATCH 1002/5331] correct the style for description part --- easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb index 74a447d6bbd..22a6c7cda85 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb @@ -10,7 +10,8 @@ version = '2.8.1' versionsuffix = "-Linux_x86_64" homepage = 'http://blast.ncbi.nlm.nih.gov/' -description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.""" +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological +sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.""" toolchain = {'name': 'dummy', 'version': 'dummy'} From 17b42b0ad332e7d2e28989d5541c792a71909f3f Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 26 Mar 2019 09:46:15 -0500 Subject: [PATCH 1003/5331] correct the style --- .../easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb | 7 ++++--- .../snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 7 ++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb index fd3ee7732e8..54a9fb3994a 100644 --- a/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb @@ -9,7 +9,8 @@ name = 'snap' version = '2013-11-29' homepage = 'http://korflab.ucdavis.edu/software.html' -description = """SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.""" +description = """SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. +SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.""" toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} @@ -22,8 +23,8 @@ checksums = [ ] files_to_copy = [ - (["cds-trainer.pl", "hmm-assembler.pl", "noncoding-trainer.pl", "patch-hmm.pl", - "zff2gff3.pl", "exonpairs","fathom","forge","hmm-info","snap","Zoe/zoe-loop"], "bin"), + (["cds-trainer.pl", "hmm-assembler.pl", "noncoding-trainer.pl", "patch-hmm.pl", "zff2gff3.pl", + "exonpairs", "fathom", "forge", "hmm-info", "snap", "Zoe/zoe-loop"], "bin"), "DNA", "HMM", "Zoe" diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 1e5e39175e7..dff22109e19 100644 --- a/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -9,7 +9,8 @@ name = 'snap' version = '2013-11-29' homepage = 'http://korflab.ucdavis.edu/software.html' -description = """SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.""" +description = """SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. +SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.""" toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} @@ -22,8 +23,8 @@ checksums = [ ] files_to_copy = [ - (["cds-trainer.pl", "hmm-assembler.pl", "noncoding-trainer.pl", "patch-hmm.pl", - "zff2gff3.pl", "exonpairs","fathom","forge","hmm-info","snap","Zoe/zoe-loop"], "bin"), + (["cds-trainer.pl", "hmm-assembler.pl", "noncoding-trainer.pl", "patch-hmm.pl", "zff2gff3.pl", + "exonpairs", "fathom", "forge", "hmm-info", "snap", "Zoe/zoe-loop"], "bin"), "DNA", "HMM", "Zoe" From 6ce9a7995e57e8dbbf33c9874e66ee4fcd513e7e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 26 Mar 2019 16:50:40 +0200 Subject: [PATCH 1004/5331] adding easyconfigs: dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb --- ...dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb | 96 +++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/d/dask/dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/d/dask/dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..29a5a9da8b9 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-1.1.4-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,96 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '1.1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), + ('PyYAML', '3.13', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('futures', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/f/futures'], + 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], + 'modulename': 'concurrent.futures', + }), + ('toolz', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], + 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], + }), + ('HeapDict', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/h/HeapDict'], + 'checksums': ['40c9e3680616cfdf942f77429a3a9e0a76f31ce965d62f4ffbe63a83a5ef1b5a'], + }), + ('zict', '0.1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], + 'checksums': ['a7838b2f21bc06b7e3db5c64ffa6642255a5f7c01841660b3388a9840e101f99'], + }), + ('tornado', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], + }), + ('tblib', '1.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], + 'checksums': ['436e4200e63d92316551179dc540906652878df4ff39b43db30fcf6400444fe7'], + }), + ('sortedcontainers', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], + 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], + }), + ('psutil', '5.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], + }), + ('msgpack-python', '0.5.6', { + 'modulename': 'msgpack', + 'source_urls': ['https://pypi.python.org/packages/source/s/msgpack-python'], + 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], + }), + ('msgpack', '0.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'], + 'checksums': ['4008c72f5ef2b7936447dcb83db41d97e9791c83221be13d5e19db0796df1972'], + }), + ('cloudpickle', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], + 'checksums': ['3ea6fd33b7521855a97819b3d645f92d51c8763d3ab5df35197cd8e96c19ba6f'], + }), + ('Click', '7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], + 'checksums': ['7e9a3c053d8f503483d7357d5b8486c70250c4975b08b3d29f91ab7fc97736c3'], + }), + ('distributed', '1.26.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], + 'checksums': ['b9ffc4c28eb7a6639b15fbb84cea847693b6f9ce7e71f3e2a3e3272467b5b0b8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'remote', 'scheduler', 'ssh', 'submit', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'data' From 540076f336bbaee4e3723f94fc9d78171cc0ae01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Mar 2019 19:49:54 +0100 Subject: [PATCH 1005/5331] collapse SciPy-bundle easyconfigs using intel/2019a for both Python 2.7.15 + 3.7.2 into a single easyconfig using multi_deps --- ...undle-2019.03-intel-2019a-Python-2.7.15.eb | 54 ------------------- ...eb => SciPy-bundle-2019.03-intel-2019a.eb} | 3 +- 2 files changed, 1 insertion(+), 56 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-2.7.15.eb rename easybuild/easyconfigs/s/SciPy-bundle/{SciPy-bundle-2019.03-intel-2019a-Python-3.7.2.eb => SciPy-bundle-2019.03-intel-2019a.eb} (96%) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-2.7.15.eb deleted file mode 100644 index 4063ccd7a93..00000000000 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-2.7.15.eb +++ /dev/null @@ -1,54 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'SciPy-bundle' -version = '2019.03' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://python.org/' -description = "Bundle of Python packages for scientific software" - -toolchain = {'name': 'intel', 'version': '2019a'} -toolchainopts = {'pic': True} - -dependencies = [('Python', '2.7.15')] - -use_pip = True - -# required because we're building Python packages using Intel compilers on top of Python built with GCC -check_ldshared = True - -# order is important! -# package versions updated Mar 15th 2019 -exts_list = [ - ('numpy', '1.16.2', { - 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], - 'source_tmpl': '%(name)s-%(version)s.zip', - 'patches': [ - 'numpy-1.12.0-mkl.patch', - 'numpy-1.16.1_fix-ifort-V-stderr.patch', - ], - 'checksums': [ - '6c692e3879dde0b67a9dc78f9bfb6f61c666b4562fd8619632d7043fb5b691b0', # numpy-1.16.2.zip - 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch - 'fc7f0c4b910bf3706d43661b94696f07b6e317bfeac062c2c78b3926fde713a7', # numpy-1.16.1_fix-ifort-V-stderr.patch - ], - }), - ('scipy', '1.2.1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], - 'checksums': ['e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c'], - }), - ('mpi4py', '3.0.1', { - 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], - 'checksums': ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'], - }), - ('pandas', '0.24.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], - 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], - }), - ('mpmath', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], - 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], - }), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a.eb similarity index 96% rename from easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-3.7.2.eb rename to easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a.eb index dad4d9f9f71..d4eeb11b53d 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intel-2019a.eb @@ -2,7 +2,6 @@ easyblock = 'PythonBundle' name = 'SciPy-bundle' version = '2019.03' -versionsuffix = '-Python-%(pyver)s' homepage = 'http://python.org/' description = "Bundle of Python packages for scientific software" @@ -10,7 +9,7 @@ description = "Bundle of Python packages for scientific software" toolchain = {'name': 'intel', 'version': '2019a'} toolchainopts = {'pic': True} -dependencies = [('Python', '3.7.2')] +multi_deps = {'Python': ['3.7.2', '2.7.15']} use_pip = True From 532c4836a5a436567ea6d5d438bcf85a3ee27152 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Mar 2019 20:47:29 +0100 Subject: [PATCH 1006/5331] binutils is a *build* dependency for LevelDB --- easybuild/easyconfigs/l/LevelDB/LevelDB-1.20-GCCcore-7.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.20-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.20-GCCcore-7.3.0.eb index 8d8cffd9296..e2f9c39986d 100644 --- a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.20-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.20-GCCcore-7.3.0.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/google/leveldb/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['f5abe8b5b209c2f36560b75f32ce61412f39a2922f7045ae764a2c23335b6664'] -dependencies = [('binutils', '2.30')] +builddependencies = [('binutils', '2.30')] files_to_copy = [ (['out-shared/libleveldb.%s*' % SHLIB_EXT, 'out-static/libleveldb.a'], 'lib'), From daeeaaf0a080e022b1a0ef24d1305d7f0b6e1c29 Mon Sep 17 00:00:00 2001 From: Gert Hulselmans Date: Tue, 26 Mar 2019 14:48:41 +0100 Subject: [PATCH 1007/5331] Fix "source_urls" and homepage for mawk. The "source_urls" for mawk changed from: "ftp://ftp.invisible-island.net/mawk/" To: "ftp://ftp.invisible-island.net/mawk/" but "ftp://ftp.invisible-island.net/mawk/" is a symlink, so easybuild is unable to retreive the source archive. cURL has problems with it too: $ curl -v ftp://ftp.invisible-island.net/mawk/ * About to connect() to ftp.invisible-island.net port 21 (#0) * Trying 216.194.196.78... * Connected to ftp.invisible-island.net (216.194.196.78) port 21 (#0) < 220 ProFTPD Server (ftp.invisible-island.net) [216.194.196.78] > USER anonymous < 331 Anonymous login ok, send your complete email address as your password > PASS ftp@example.com < 230 Anonymous access granted, restrictions apply > PWD < 257 "/" is the current directory * Entry path is '/' > CWD mawk * ftp_perform ends with SECONDARY: 0 < 550 mawk: No such file or directory * Server denied you to change to the given directory * Connection #0 to host ftp.invisible-island.net left intact curl: (9) Server denied you to change to the given directory Giving the real path without symlinks works: "ftp://ftp.invisible-island.net/pub/mawk/" --- .../easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb | 5 +++-- .../easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb index 752b5a4a617..5ad0853468b 100644 --- a/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb +++ b/easybuild/easyconfigs/m/Mawk/Mawk-1.3.4-goolf-1.4.10-20150503.eb @@ -9,13 +9,14 @@ name = 'Mawk' version = '1.3.4' versionsuffix = '-20150503' -homepage = 'http://invisible-island.net/mawk/' +homepage = 'https://invisible-island.net/mawk/' description = """mawk is an interpreter for the AWK Programming Language.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['ftp://invisible-island.net/mawk/'] +source_urls = ['ftp://ftp.invisible-island.net/pub/mawk'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] +checksums = ['461673c7c4572e1e67e69e7bf7582e02d3c175b814485f2aa52c2c28099b3c6f'] parallel = 1 diff --git a/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb index dd90e4fccd3..a93713acc85 100644 --- a/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20141206-GCC-4.9.2.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'mawk' version = '1.3.4-20141206' -homepage = 'http://invisible-island.net/mawk/mawk.html' +homepage = 'https://invisible-island.net/mawk/mawk.html' description = """mawk is an interpreter for the AWK Programming Language.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCELOWER_TGZ] -source_urls = ['ftp://invisible-island.net/mawk'] +source_urls = ['ftp://ftp.invisible-island.net/pub/mawk'] +checksums = ['efa092ec3ea5dfd54571e8ba3b0327073f1fa51b8efa0953c2cadd87a87389c8'] sanity_check_paths = { 'files': ['bin/mawk'], From 823a65e64a57c6a0327706bed7e4cf1633927d27 Mon Sep 17 00:00:00 2001 From: Gert Hulselmans Date: Tue, 26 Mar 2019 15:59:11 +0100 Subject: [PATCH 1008/5331] Add easyconfigs for mawk 1.3.4-20171017 Add easyconfigs for mawk 1.3.4-20171017 --- .../m/mawk/mawk-1.3.4-20171017-foss-2018a.eb | 20 +++++++++++++++++++ .../m/mawk/mawk-1.3.4-20171017-foss-2018b.eb | 20 +++++++++++++++++++ .../m/mawk/mawk-1.3.4-20171017-foss-2019a.eb | 20 +++++++++++++++++++ .../m/mawk/mawk-1.3.4-20171017-intel-2018a.eb | 20 +++++++++++++++++++ .../m/mawk/mawk-1.3.4-20171017-intel-2018b.eb | 20 +++++++++++++++++++ .../m/mawk/mawk-1.3.4-20171017-intel-2019a.eb | 20 +++++++++++++++++++ 6 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2018a.eb create mode 100644 easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2018b.eb create mode 100644 easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2019a.eb create mode 100644 easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2018a.eb create mode 100644 easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2018b.eb create mode 100644 easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2019a.eb diff --git a/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2018a.eb b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2018a.eb new file mode 100644 index 00000000000..907c88e2ced --- /dev/null +++ b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2018a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'mawk' +version = '1.3.4-20171017' + +homepage = 'https://invisible-island.net/mawk/' +description = """mawk is an interpreter for the AWK Programming Language.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['ftp://ftp.invisible-island.net/pub/mawk'] +sources = ['%(namelower)s-%(version)s.tgz'] +checksums = ['db17115d1ed18ed1607c8b93291db9ccd4fe5e0f30d2928c3c5d127b23ec9e5b'] + +sanity_check_paths = { + 'files': ['bin/mawk'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2018b.eb b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2018b.eb new file mode 100644 index 00000000000..0935e235c3a --- /dev/null +++ b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2018b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'mawk' +version = '1.3.4-20171017' + +homepage = 'https://invisible-island.net/mawk/' +description = """mawk is an interpreter for the AWK Programming Language.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['ftp://ftp.invisible-island.net/pub/mawk'] +sources = ['%(namelower)s-%(version)s.tgz'] +checksums = ['db17115d1ed18ed1607c8b93291db9ccd4fe5e0f30d2928c3c5d127b23ec9e5b'] + +sanity_check_paths = { + 'files': ['bin/mawk'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2019a.eb b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2019a.eb new file mode 100644 index 00000000000..8e9b8ca145a --- /dev/null +++ b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-foss-2019a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'mawk' +version = '1.3.4-20171017' + +homepage = 'https://invisible-island.net/mawk/' +description = """mawk is an interpreter for the AWK Programming Language.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['ftp://ftp.invisible-island.net/pub/mawk'] +sources = ['%(namelower)s-%(version)s.tgz'] +checksums = ['db17115d1ed18ed1607c8b93291db9ccd4fe5e0f30d2928c3c5d127b23ec9e5b'] + +sanity_check_paths = { + 'files': ['bin/mawk'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2018a.eb b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2018a.eb new file mode 100644 index 00000000000..75db875ed84 --- /dev/null +++ b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2018a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'mawk' +version = '1.3.4-20171017' + +homepage = 'https://invisible-island.net/mawk/' +description = """mawk is an interpreter for the AWK Programming Language.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['ftp://ftp.invisible-island.net/pub/mawk'] +sources = ['%(namelower)s-%(version)s.tgz'] +checksums = ['db17115d1ed18ed1607c8b93291db9ccd4fe5e0f30d2928c3c5d127b23ec9e5b'] + +sanity_check_paths = { + 'files': ['bin/mawk'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2018b.eb b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2018b.eb new file mode 100644 index 00000000000..ab218bd40a7 --- /dev/null +++ b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2018b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'mawk' +version = '1.3.4-20171017' + +homepage = 'https://invisible-island.net/mawk/' +description = """mawk is an interpreter for the AWK Programming Language.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['ftp://ftp.invisible-island.net/pub/mawk'] +sources = ['%(namelower)s-%(version)s.tgz'] +checksums = ['db17115d1ed18ed1607c8b93291db9ccd4fe5e0f30d2928c3c5d127b23ec9e5b'] + +sanity_check_paths = { + 'files': ['bin/mawk'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2019a.eb b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2019a.eb new file mode 100644 index 00000000000..0a309b3953a --- /dev/null +++ b/easybuild/easyconfigs/m/mawk/mawk-1.3.4-20171017-intel-2019a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'mawk' +version = '1.3.4-20171017' + +homepage = 'https://invisible-island.net/mawk/' +description = """mawk is an interpreter for the AWK Programming Language.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = ['ftp://ftp.invisible-island.net/pub/mawk'] +sources = ['%(namelower)s-%(version)s.tgz'] +checksums = ['db17115d1ed18ed1607c8b93291db9ccd4fe5e0f30d2928c3c5d127b23ec9e5b'] + +sanity_check_paths = { + 'files': ['bin/mawk'], + 'dirs': [] +} + +moduleclass = 'tools' From 4fe2fc63c6b46127b8954510e3a286c03405eaa3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Mar 2019 09:33:04 +0100 Subject: [PATCH 1009/5331] adding easyconfigs: Autotools-20180311-GCCcore-8.3.0.eb, Autoconf-2.69-GCCcore-8.3.0.eb, Automake-1.16.1-GCCcore-8.3.0.eb, libtool-2.4.6-GCCcore-8.3.0.eb --- .../a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb | 38 +++++++++++++++++ .../Automake/Automake-1.16.1-GCCcore-8.3.0.eb | 41 +++++++++++++++++++ .../Autotools-20180311-GCCcore-8.3.0.eb | 24 +++++++++++ .../l/libtool/libtool-2.4.6-GCCcore-8.3.0.eb | 32 +++++++++++++++ 4 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..2dc65b675b7 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-8.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..cf2b65896b1 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.1-GCCcore-8.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.1' + +homepage = 'http://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('Autoconf', '2.69'), +] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..09db41a9643 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20180311-GCCcore-8.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20180311' # date of the most recent change + +homepage = 'http://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.16.1'), # 20180311 + ('libtool', '2.4.6'), # 20150215 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..455464b29da --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-8.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' From bbb4403c1bd6e5963ff5f19ab8bc8bccd444fd1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Mar 2019 09:35:55 +0100 Subject: [PATCH 1010/5331] adding easyconfigs: OpenMPI-4.0.1-GCC-8.3.0-2.32.eb, hwloc-2.0.3-GCCcore-8.3.0.eb, numactl-2.0.12-GCCcore-8.3.0.eb, libxml2-2.9.9-GCCcore-8.3.0.eb, XZ-5.2.4-GCCcore-8.3.0.eb, libpciaccess-0.14-GCCcore-8.3.0.eb, xorg-macros-1.19.2-GCCcore-8.3.0.eb --- .../h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb | 48 +++++++++++++++++++ .../libpciaccess-0.14-GCCcore-8.3.0.eb | 26 ++++++++++ .../l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb | 28 +++++++++++ .../n/numactl/numactl-2.0.12-GCCcore-8.3.0.eb | 34 +++++++++++++ .../o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb | 38 +++++++++++++++ .../x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb | 34 +++++++++++++ .../xorg-macros-1.19.2-GCCcore-8.3.0.eb | 27 +++++++++++ 7 files changed, 235 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.14-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.12-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..daac466bc8f --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.0.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +# need to build with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake +# cfr. https://github.com/open-mpi/hwloc/issues/315 +toolchainopts = {'vectorize': False} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['64def246aaa5b3a6e411ce10932a22e2146c3031b735c8f94739534f06ad071c'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('numactl', '2.0.12'), + ('libxml2', '2.9.9'), + ('libpciaccess', '0.14'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.14-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.14-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..ac7e9c262ca --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.14-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.14' + +homepage = 'http://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8d86e64893917be3dfb1c5e837888d1275399c818783474002203d751312b03c'] + +builddependencies = [ + ('binutils', '2.32'), + ('Autotools', '20180311'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..7f8f41a3902 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.9' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['94fb70890143e3c6549f265cee93ec064c80a84c42ad0f23e85ee1fd6540a871'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('XZ', '5.2.4'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.12-GCCcore-8.3.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.12-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..cddca35f9c4 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.12-GCCcore-8.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.12' + +homepage = 'http://oss.sgi.com/projects/libnuma/' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7c3e819c2bdeb883de68bafe88776a01356f7ef565e75ba866c4b49a087c6bdf'] + +builddependencies = [ + ('binutils', '2.32'), + ('Autotools', '20180311'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb new file mode 100644 index 00000000000..dc19fcb2d8b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '4.0.1' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0-2.32'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e55e213fe09a214ab9f2c722acfd8bf7b39bbc1800e4b7a464d38df15e707f59'] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.0.3') +] + +configopts = '--enable-shared --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..cd9e93e00e0 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.4' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['XZ-5.2.2_compat-libs.patch'] +checksums = [ + '3313fd2a95f43d88e44264e6b015e7d03053e681860b0d5d3f9baca79c57b7bf', # xz-5.2.4.tar.bz2 + '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch +] + +builddependencies = [ + # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.19.8.1', '', True), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.32'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ["bin/xz", "bin/lzmainfo"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..fec1d50a969 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-8.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.2' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] +checksums = ['5d6e62803c9f20830b28ad8a9800c97a9987635089229e3e380ef3848c84d2a6'] + +builddependencies = [ + ('binutils', '2.32'), + ('Autotools', '20180311'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From a8eb4536d123d7720ab0d3c9e93a8ef5f8d8665a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Mar 2019 15:05:20 +0100 Subject: [PATCH 1011/5331] adding easyconfigs: argtable-2.13-intel-2018b.eb, Clustal-Omega-1.2.4-intel-2018b.eb --- .../a/argtable/argtable-2.13-intel-2018b.eb | 28 ++++++++++++++++ .../Clustal-Omega-1.2.4-intel-2018b.eb | 32 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018b.eb create mode 100644 easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-intel-2018b.eb diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018b.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018b.eb new file mode 100644 index 00000000000..0c9bb3bc28e --- /dev/null +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018b.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'argtable' +version = '2.13' + +homepage = 'http://argtable.sourceforge.net/' +description = """ Argtable is an ANSI C library for parsing GNU style + command line options with a minimum of fuss. """ + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))] +checksums = ['8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf'] + +sanity_check_paths = { + 'files': ['lib/libargtable2.%s' % SHLIB_EXT, 'lib/libargtable2.la'], + 'dirs': ['include', 'lib', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-intel-2018b.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-intel-2018b.eb new file mode 100644 index 00000000000..9f62b64aefc --- /dev/null +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-intel-2018b.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by Adam Huffman +# Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Clustal-Omega' +version = '1.2.4' + +homepage = 'http://www.clustal.org/omega/' +description = """ Clustal Omega is a multiple sequence alignment + program for proteins. It produces biologically meaningful multiple + sequence alignments of divergent sequences. Evolutionary relationships + can be seen via viewing Cladograms or Phylograms """ + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee'] + +dependencies = [('argtable', '2.13')] + +sanity_check_paths = { + 'files': ['bin/clustalo'], + 'dirs': [], +} + +moduleclass = 'bio' From 4abb754b04e45779f6079aeefb62f3cd27fb3a91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Mar 2019 15:05:53 +0100 Subject: [PATCH 1012/5331] adding easyconfigs: FastTree-2.1.10-intel-2018b.eb --- .../f/FastTree/FastTree-2.1.10-intel-2018b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.10-intel-2018b.eb diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.10-intel-2018b.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.10-intel-2018b.eb new file mode 100644 index 00000000000..8d74c530345 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.10-intel-2018b.eb @@ -0,0 +1,29 @@ +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.10' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = ['%(name)s-%(version)s.c'] +checksums = ['54cb89fc1728a974a59eae7a7ee6309cdd3cddda9a4c55b700a71219fc6e926d'] + +skipsteps = ['source'] + +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +moduleclass = 'bio' From 2e0368a3bac87a607b1dddb75b3abd787eafa94a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 28 Mar 2019 16:15:00 +0100 Subject: [PATCH 1013/5331] adding easyconfigs: GDAL-2.2.3-intel-2018b-Python-3.6.6.eb, PROJ-5.0.0-intel-2018b.eb, libgeotiff-1.4.2-intel-2018b.eb --- .../GDAL-2.2.3-intel-2018b-Python-3.6.6.eb | 51 +++++++++++++++++++ .../libgeotiff-1.4.2-intel-2018b.eb | 33 ++++++++++++ .../p/PROJ/PROJ-5.0.0-intel-2018b.eb | 31 +++++++++++ 3 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.4.2-intel-2018b.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-5.0.0-intel-2018b.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..2523cf04fa3 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['a328d63d476b3653f5a25b5f7971e87a15cdf8860ab0729d4b1157ba988b8d0b'] + +dependencies = [ + ('Python', '3.6.6'), + ('netCDF', '4.6.1'), + ('expat', '2.2.5'), + ('GEOS', '3.6.2', '-Python-%(pyver)s'), + ('SQLite', '3.24.0'), + ('libxml2', '2.9.8'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '2.0.0'), + ('JasPer', '2.0.14'), + ('LibTIFF', '4.0.9'), + ('zlib', '1.2.11'), + ('cURL', '7.60.0'), + ('PCRE', '8.41'), + ('PROJ', '5.0.0'), + ('libgeotiff', '1.4.2'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.4.2-intel-2018b.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.4.2-intel-2018b.eb new file mode 100644 index 00000000000..151946174fd --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.4.2-intel-2018b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.4.2' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = "Library for reading and writing coordinate system information from/to GeoTIFF files" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [ + 'http://download.osgeo.org/geotiff/libgeotiff/', + 'ftp://ftp.remotesensing.org/pub/libgeotiff/', +] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['ad87048adb91167b07f34974a8e53e4ec356494c29f1748de95252e8f81a5e6e'] + +dependencies = [ + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.9'), + ('PROJ', '5.0.0'), + ('libjpeg-turbo', '2.0.0'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-5.0.0-intel-2018b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-5.0.0-intel-2018b.eb new file mode 100644 index 00000000000..95bdc197845 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-5.0.0-intel-2018b.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '5.0.0' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b30df08d736e69744cb255828721abb545b494d6032c13a96520f3219a444cd2'] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' From 5587c460631e965b35a2247f3fa2c593bc914e23 Mon Sep 17 00:00:00 2001 From: jdemeul Date: Thu, 28 Mar 2019 15:49:38 +0000 Subject: [PATCH 1014/5331] {bio}[foss/2018b] CD-HIT v4.8.1 --- .../c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb new file mode 100644 index 00000000000..fd6485abdfd --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = "CD-HIT" +version = "4.8.1" + +homepage = 'http://weizhong-lab.ucsd.edu/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] + +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +list_of_executables = ["cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd-hit-div", "cd-hit-454"] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(list_of_executables, "bin"), (["*.pl"], 'bin'), "README", "doc", "license.txt"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' From 02f03bf09000af03b2c95bc92316b7cd5233d15e Mon Sep 17 00:00:00 2001 From: jdemeul Date: Thu, 28 Mar 2019 15:53:22 +0000 Subject: [PATCH 1015/5331] add missing Perl dependency --- easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb index fd6485abdfd..71c1e46e109 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb @@ -14,9 +14,10 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] - checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] +dependencies = [('Perl', '5.28.0')] + # make sure compilation flags are passed down (e.g. to enable OpenMP) buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' From 8016adac71e58a9e6e9b8bd9aacc51277ed3afeb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Mar 2019 17:05:50 +0100 Subject: [PATCH 1016/5331] adding easyconfigs: cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb --- .../cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..e51ff98eca1 --- /dev/null +++ b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'cdsapi' +version = '0.1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/wheel' +description = """A built-package format for Python.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f25c5df8ab0ab4e571a7022cb7714f6b91452bc0923bee0d8d0069abae1ffa1b'] + +dependencies = [('Python', '3.6.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From c0d9b7ab678a29d90fba373c378aac466bd35bbf Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 28 Mar 2019 11:40:06 -0500 Subject: [PATCH 1017/5331] Added XZ dependency --- .../p/Pysam/Pysam-0.12.0.1-intel-2017a-Python-2.7.13.eb | 1 + .../p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-2.7.14.eb | 1 + .../p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-3.6.3.eb | 1 + .../easyconfigs/p/Pysam/Pysam-0.13-intel-2017b-Python-2.7.14.eb | 1 + .../easyconfigs/p/Pysam/Pysam-0.13.0-intel-2017b-Python-3.6.3.eb | 1 + .../easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-2.7.14.eb | 1 + .../easyconfigs/p/Pysam/Pysam-0.14-intel-2018a-Python-3.6.4.eb | 1 + .../easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb | 1 + .../p/Pysam/Pysam-0.14.1-intel-2018a-Python-2.7.14.eb | 1 + .../easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-3.6.4.eb | 1 + 10 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017a-Python-2.7.13.eb index 433416ba21a..e4f241d7e5c 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017a-Python-2.7.13.eb @@ -26,6 +26,7 @@ dependencies = [ ('Python', '2.7.13'), ('ncurses', '6.0'), ('cURL', '7.54.0'), + ('XZ', '5.2.3'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-2.7.14.eb index cad440271c8..9edbd85fcd0 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-2.7.14.eb @@ -26,6 +26,7 @@ dependencies = [ ('Python', '2.7.14'), ('ncurses', '6.0'), ('cURL', '7.56.0'), + ('XZ', '5.2.3'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-3.6.3.eb index 68213728783..bc70913824d 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-3.6.3.eb @@ -26,6 +26,7 @@ dependencies = [ ('Python', '3.6.3'), ('ncurses', '6.0'), ('cURL', '7.56.0'), + ('XZ', '5.2.3'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.13-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.13-intel-2017b-Python-2.7.14.eb index f522572e4c9..08e13a8bdb3 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.13-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.13-intel-2017b-Python-2.7.14.eb @@ -25,6 +25,7 @@ dependencies = [ ('Python', '2.7.14'), ('ncurses', '6.0'), ('cURL', '7.56.1'), + ('XZ', '5.2.3'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.13.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.13.0-intel-2017b-Python-3.6.3.eb index c21f75f3808..8faf2620ade 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.13.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.13.0-intel-2017b-Python-3.6.3.eb @@ -26,6 +26,7 @@ dependencies = [ ('Python', '3.6.3'), ('ncurses', '6.0'), ('cURL', '7.56.0'), + ('XZ', '5.2.3'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-2.7.14.eb index dbc764021dc..c0c6842ed44 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-2.7.14.eb @@ -26,6 +26,7 @@ dependencies = [ ('Python', '2.7.14'), ('ncurses', '6.0'), ('cURL', '7.56.1'), + ('XZ', '5.2.3'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2018a-Python-3.6.4.eb index 8175bce01ff..6f5b0a7e6ab 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2018a-Python-3.6.4.eb @@ -26,6 +26,7 @@ dependencies = [ ('Python', '3.6.4'), ('ncurses', '6.0'), ('cURL', '7.58.0'), + ('XZ', '5.2.3'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb index 9962089f15d..d5aaef6c2d0 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb @@ -28,6 +28,7 @@ dependencies = [ ('Python', '3.6.4'), ('ncurses', '6.0'), ('cURL', '7.58.0'), + ('XZ', '5.2.3'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-2.7.14.eb index 8cc42956400..947304ce871 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-2.7.14.eb @@ -28,6 +28,7 @@ dependencies = [ ('Python', '2.7.14'), ('ncurses', '6.0'), ('cURL', '7.58.0'), + ('XZ', '5.2.3'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-3.6.4.eb index fa328ae32fd..d0acd598dc5 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-3.6.4.eb @@ -28,6 +28,7 @@ dependencies = [ ('Python', '3.6.4'), ('ncurses', '6.0'), ('cURL', '7.58.0'), + ('XZ', '5.2.3'), ] sanity_check_paths = { From 69c336b933a829e30ac71a1bcbcfc4c817297d6d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 28 Mar 2019 18:36:06 +0100 Subject: [PATCH 1018/5331] adding easyconfigs: NCL-6.6.2-intel-2018b.eb, g2lib-3.1.0-intel-2018b.eb, g2clib-1.6.0-intel-2018b.eb, HDF-4.2.14-GCCcore-7.3.0.eb, makedepend-1.0.6-GCCcore-7.3.0.eb and patches: g2lib-3.1.0_makefile.patch --- .../g/g2clib/g2clib-1.6.0-intel-2018b.eb | 25 +++++++++++ .../g/g2lib/g2lib-3.1.0-intel-2018b.eb | 31 +++++++++++++ .../g/g2lib/g2lib-3.1.0_makefile.patch | 21 +++++++++ .../h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb | 43 +++++++++++++++++++ .../makedepend-1.0.6-GCCcore-7.3.0.eb | 26 +++++++++++ .../n/NCL/NCL-6.6.2-intel-2018b.eb | 40 +++++++++++++++++ 6 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2018b.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-intel-2018b.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.1.0_makefile.patch create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2018b.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2018b.eb new file mode 100644 index 00000000000..7fcb9949a1c --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.0-intel-2018b.eb @@ -0,0 +1,25 @@ +name = 'g2clib' +version = '1.6.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = ['g2clib-%(version)s-with-JasPer-2.x.patch'] +checksums = [ + 'afec1ea29979b84369d0f46f305ed12f73f1450ec2db737664ec7f75c1163add', # g2clib-1.6.0.tar + '2e62502d7823be5407ea023029dd206930a1034421d141dd346b468e177a7fce', # g2clib-1.6.0-with-JasPer-2.x.patch +] + +dependencies = [ + ('JasPer', '2.0.14'), + ('libpng', '1.6.34'), +] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-intel-2018b.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-intel-2018b.eb new file mode 100644 index 00000000000..45366550623 --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0-intel-2018b.eb @@ -0,0 +1,31 @@ +name = 'g2lib' +version = '3.1.0' + +homepage = 'http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = [ + 'g2lib-3.1.0_makefile.patch', + 'g2lib-1.4.0-with-JasPer-2.x.patch', +] +checksums = [ + '8a2de259de82094c5867f8d7945359f211592a4a503f9ed65dc60469337414e7', # g2lib-3.1.0.tar + '702f76c77638fb36b662caf96890a69f19c507778c92aa1e163898b150cc8282', # g2lib-3.1.0_makefile.patch + 'cd4c668dab76ef3b61fa902c2eed24747517d4cbc3ec0aaffab37e6b80946170', # g2lib-1.4.0-with-JasPer-2.x.patch +] + +dependencies = [ + ('JasPer', '2.0.14'), + ('libpng', '1.6.34'), +] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FFLAGS="$FFLAGS -fpp -I." FC=$FC CC=$CC' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0_makefile.patch b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0_makefile.patch new file mode 100644 index 00000000000..59a1c2ea49d --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.1.0_makefile.patch @@ -0,0 +1,21 @@ +fix order of compilation in makefile +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ur g2lib-3.1.0.orig/makefile g2lib-3.1.0/makefile +--- g2lib-3.1.0.orig/makefile 2017-06-12 21:39:43.000000000 +0200 ++++ g2lib-3.1.0/makefile 2019-03-28 14:50:24.070862781 +0100 +@@ -134,6 +134,7 @@ + .SUFFIXES: .a .f .F .c + + $(LIB): $(LIB)(gridtemplates.o) \ ++ $(LIB)(intmath.o) \ + $(LIB)(pdstemplates.o) \ + $(LIB)(drstemplates.o) \ + $(LIB)(gribmod.o) \ +@@ -196,7 +197,6 @@ + $(LIB)(params.o) \ + $(LIB)(params_ecmwf.o) \ + $(LIB)(getidx.o) \ +- $(LIB)(intmath.o) \ + $(LIB)(gdt2gds.o) + + .F.f: diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..c1c65eb305c --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.14' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' + +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] + +builddependencies = [ + ('binutils', '2.30'), + ('Bison', '3.0.4'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '2.0.0'), + ('Szip', '2.1.1'), + ('zlib', '1.2.11'), +] + +configopts = '' +configopts += '--with-szlib=$EBROOTSZIP ' +configopts += '--includedir=%(installdir)s/include/%(namelower)s ' + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-7.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..d7faeb5aa14 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-7.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.6' + +homepage = "http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html" +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['845f6708fc850bf53f5b1d0fb4352c4feab3949f140b26f71b22faba354c3365'] + +builddependencies = [ + ('binutils', '2.30'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb new file mode 100644 index 00000000000..9e0124e0ac4 --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-intel-2018b.eb @@ -0,0 +1,40 @@ +name = 'NCL' +version = '6.6.2' + +homepage = 'http://www.ncl.ucar.edu' +description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'cstd': 'c99', 'openmp': True, 'pic': True} + +source_urls = ['https://github.com/NCAR/ncl/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['NCL-6.4.0_fix-types.patch'] +checksums = [ + 'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e', # 6.6.2.tar.gz + 'f6dfaf95e5de9045745e122cb44f9c035f81fab92f5892991ddfe93945891c8f', # NCL-6.4.0_fix-types.patch +] + +dependencies = [ + ('cURL', '7.60.0'), + ('JasPer', '2.0.14'), + ('g2lib', '3.1.0'), + ('g2clib', '1.6.0'), + ('HDF', '4.2.14'), + ('HDF5', '1.10.2'), + ('netCDF', '4.6.1'), + ('netCDF-Fortran', '4.4.4'), + ('Szip', '2.1.1'), + ('freetype', '2.9.1'), + ('zlib', '1.2.11'), + ('GDAL', '2.2.3', '-Python-3.6.6'), + ('UDUNITS', '2.2.26'), + ('ESMF', '7.1.0r'), + ('bzip2', '1.0.6'), + ('cairo', '1.14.12'), + ('libiconv', '1.15'), + ('GSL', '2.5'), +] +builddependencies = [('makedepend', '1.0.6')] + +moduleclass = 'data' From e67f235420e649bb38d8a5004ea678638195beb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Mar 2019 18:49:16 +0100 Subject: [PATCH 1019/5331] {chem}[intel/2018b] RDKit v2018.09.3 w/ Python 3.6.6 (+ Boost.Python dep) --- ....Python-1.67.0-intel-2018b-Python-3.6.6.eb | 29 ++++++++++++ ...DKit-2018.09.3-intel-2018b-Python-3.6.6.eb | 45 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..c0591e8f152 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.67.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.sourceforge.net/boost/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.65.1_fix-Python3.patch'] +checksums = [ + '8aa4e330c870ef50a896634c931adf468b21f8a69b77007e45c444151229f665', # boost_1_67_0.tar.gz + '5585f98fb67425ec465dcbe2878af046ccd2729a8cdb802acf5d71cfa4022c26', # Boost-1.65.1_fix-Python3.patch +] + +dependencies = [ + ('Python', '3.6.6'), + ('Boost', version), +] + +only_python_bindings = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..84be9e4f58f --- /dev/null +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'RDKit' +version = '2018.09.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.rdkit.org' +description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python." + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/rdkit/rdkit/archive/'] +sources = ['Release_%s.tar.gz' % version.replace('.', '_')] +checksums = ['3be20bade43657c0d74617ab99ca30f872eaaedc314a87f690ac38e5ef590224'] + +builddependencies = [ + ('CMake', '3.12.1'), + ('Eigen', '3.3.7', '', True), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('Python', '3.6.6'), + ('matplotlib', '3.0.0', versionsuffix), + ('Pillow', '5.3.0', versionsuffix), + ('Boost.Python', '1.67.0', versionsuffix), + ('cairo', '1.14.12'), +] + +separate_build_dir = True + +configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_INTREE=ON -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " +configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " +configopts += "-DPYTHON_NUMPY_INCLUDE_PATH=$EBROOTPYTHON/lib/python*/site-packages/numpy-*/numpy/core/include" + +sanity_check_paths = { + 'files': ['lib/libRDKitFMCS.%s' % SHLIB_EXT, 'lib/libRDKitOptimizer.%s' % SHLIB_EXT, + 'lib/libRDKitSubgraphs.%s' % SHLIB_EXT, 'lib/libRDKitRDBoost.%s' % SHLIB_EXT], + 'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'], +} + +sanity_check_commands = ["python -c 'import rdkit'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From c6311ac5d7f683e51061a7d1c6832ca5587d30a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Mar 2019 10:31:49 +0100 Subject: [PATCH 1020/5331] add 'circular' extension to R 3.5.1 easyconfigs --- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 3 +++ easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index ecf472fe005..02a6c98cee2 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -2108,6 +2108,9 @@ exts_list = [ ('parsedate', '1.1.3', { 'checksums': ['020005634099a057207a614928ced57900acd4952f147bebe6718034ea82e755'], }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 9e93f03acd2..38041a1bb7e 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -2106,6 +2106,9 @@ exts_list = [ ('parsedate', '1.1.3', { 'checksums': ['020005634099a057207a614928ced57900acd4952f147bebe6718034ea82e755'], }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), ] moduleclass = 'lang' From a0405171cebd3bf4e666cdbaccacbfe7bb917837 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 29 Mar 2019 10:55:55 +0100 Subject: [PATCH 1021/5331] add xproto easyconfig --- .../x/xproto/xproto-7.0.31-GCCcore-7.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-7.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..b787dbc1e88 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-7.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.30'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' From d90418b4fd84d866a0b6127b1cfdb38753a4457f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Mar 2019 11:50:57 +0100 Subject: [PATCH 1022/5331] adding easyconfigs: YAPS-1.1.0-foss-2018b-R-3.5.1.eb --- .../y/YAPS/YAPS-1.1.0-foss-2018b-R-3.5.1.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/y/YAPS/YAPS-1.1.0-foss-2018b-R-3.5.1.eb diff --git a/easybuild/easyconfigs/y/YAPS/YAPS-1.1.0-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/y/YAPS/YAPS-1.1.0-foss-2018b-R-3.5.1.eb new file mode 100644 index 00000000000..cfa80d64dba --- /dev/null +++ b/easybuild/easyconfigs/y/YAPS/YAPS-1.1.0-foss-2018b-R-3.5.1.eb @@ -0,0 +1,25 @@ +easyblock = 'RPackage' + +name = 'YAPS' +version = '1.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/dviraran/xCell' +description = "xCell is a gene signatures-based method learned from thousands of pure cell types from various sources." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/baktoft/yaps/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['978206bf7f03b22b9d909d2304239913c888c9b91b7a34f1c1d081fc506a07e2'] + +dependencies = [('R', '3.5.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From 6229fc4921db899e11ec5d6b13262277ce0d45a9 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 29 Mar 2019 15:30:42 +0100 Subject: [PATCH 1023/5331] Create PETSc-3.11.0-foss-2018b-downloaded-deps.eb --- ...PETSc-3.11.0-foss-2018b-downloaded-deps.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.11.0-foss-2018b-downloaded-deps.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.11.0-foss-2018b-downloaded-deps.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.11.0-foss-2018b-downloaded-deps.eb new file mode 100644 index 00000000000..f142ee08461 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.11.0-foss-2018b-downloaded-deps.eb @@ -0,0 +1,38 @@ +name = 'PETSc' +version = '3.11.0' +versionsuffix = '-downloaded-deps' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b3bed2a9263193c84138052a1b92d47299c3490dd24d1d0bf79fb884e71e678a'] + +# (build) dependencies provided through EasyBuild +builddependencies = [ + ('CMake', '3.12.1'), + ('flex', '2.6.4'), + ('Bison', '3.0.5'), +] +dependencies = [ + ('HDF5', '1.10.2'), + ('Valgrind', '3.14.0'), +] + +# external packages that are downloaded with --download-=1 and --download--static=1 +download_deps_static = ['hypre', 'metis', 'ml', 'mumps', 'parmetis', 'prometheus', 'ptscotch', 'suitesparse', + 'superlu', 'superlu_dist'] + +# triangle cannot be downloaded with --download-triangle-static because it fails +download_deps = ['triangle'] + +configopts = "--with-hdf5=1 --with-hdf5-dir=$EBROOTHDF5 --with-debugging --with-cxx-dialect=C++11" + +shared_libs = True + +moduleclass = 'numlib' From 1556b4500ecddfaddb9d705c2cd26bcb8a5c234e Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 29 Mar 2019 16:04:44 +0100 Subject: [PATCH 1024/5331] Create SLEPc-3.11.0-foss-2018b.eb --- .../s/SLEPc/SLEPc-3.11.0-foss-2018b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SLEPc/SLEPc-3.11.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.11.0-foss-2018b.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.11.0-foss-2018b.eb new file mode 100644 index 00000000000..91c58dcb984 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.11.0-foss-2018b.eb @@ -0,0 +1,21 @@ +name = 'SLEPc' +version = '3.11.0' + +homepage = 'http://slepc.upv.es/' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://slepc.upv.es/download/distrib'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bf29043c311fe2c549a25e2b0835095723a3eebc1dff288a233b32913b5762a2'] + +dependencies = [('PETSc', '3.11.0', '-downloaded-deps')] + +petsc_arch = 'installed-arch-linux2-c-opt' + +moduleclass = 'numlib' From d2c3e3056b237ffd6734834a10c88058b3adb0e2 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 29 Mar 2019 16:14:57 +0100 Subject: [PATCH 1025/5331] Create gmsh-3.0.6-foss-2018b-Python-3.6.6.eb --- .../gmsh-3.0.6-foss-2018b-Python-3.6.6.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..c418370c84f --- /dev/null +++ b/easybuild/easyconfigs/g/gmsh/gmsh-3.0.6-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'gmsh' +version = '3.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://geuz.org/gmsh' +description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {"usempi": True} + +source_urls = ['http://gmsh.info/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] +checksums = ['9700bcc440d7a6b16a49cbfcdcdc31db33efe60e1f5113774316b6fa4186987b'] + +builddependencies = [ + ('CMake', '3.12.1'), + ('SWIG', '3.0.12', versionsuffix), +] + +dependencies = [ + ('Python', '3.6.6'), + ('PETSc', '3.11.0', '-downloaded-deps'), + ('SLEPc', '3.11.0'), +] + +separate_build_dir = True + +configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/gmsh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From 527b4b68aae19ec84a42066955766364534408ac Mon Sep 17 00:00:00 2001 From: wapoelma Date: Fri, 29 Mar 2019 16:30:01 +0100 Subject: [PATCH 1026/5331] adding easyconfigs: Trinity-2.8.4-foss-2018b.eb --- .../t/Trinity/Trinity-2.8.4-foss-2018b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb new file mode 100644 index 00000000000..655df5ae21a --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb @@ -0,0 +1,31 @@ +name = 'Trinity' +version = '2.8.4' + +homepage = 'http://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['e119bfc302f8fbdb66b1222e9f14f5d61f46a1fc5581a06b363bd31d5a1bcbd4'] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.12.1'), +] + +dependencies = [ + ('Java', '1.8', '', True), + ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('Bowtie', '1.2.2'), + ('Bowtie2', '2.3.4.2'), + ('ncurses', '6.1'), + ('zlib', '1.2.11'), + ('Perl', '5.28.0'), +] + +moduleclass = 'bio' From 2daf3dca517b7b70cf429ce957636d05e3e612d4 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 29 Mar 2019 09:24:13 -0700 Subject: [PATCH 1027/5331] parasail 2.4 update --- .../p/parasail/parasail-2.4-foss-2018b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb b/easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb new file mode 100644 index 00000000000..b99ab4959c6 --- /dev/null +++ b/easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'parasail' +version = '2.4' + +homepage = 'https://github.com/jeffdaily/parasail' +description = """parasail is a SIMD C (C99) library containing implementations + of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global + pairwise sequence alignment algorithms. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/jeffdaily/parasail/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.11.4')] + +sanity_check_paths = { + 'files': ['bin/parasail_aligner', 'bin/parasail_stats', + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h' + ], + 'dirs': [], +} + +moduleclass = 'bio' From c517fded07e248eb64e2fd27dd3ef32f193bfb6b Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 29 Mar 2019 11:26:38 -0500 Subject: [PATCH 1028/5331] Added use_pip and download_dep_fail --- .../p/Pysam/Pysam-0.12.0.1-intel-2017a-Python-2.7.13.eb | 3 +++ .../p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-2.7.14.eb | 3 +++ .../p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-3.6.3.eb | 3 +++ .../p/Pysam/Pysam-0.13-intel-2017b-Python-2.7.14.eb | 3 +++ .../p/Pysam/Pysam-0.13.0-intel-2017b-Python-3.6.3.eb | 4 ++++ .../p/Pysam/Pysam-0.14-intel-2017b-Python-2.7.14.eb | 3 +++ .../p/Pysam/Pysam-0.14-intel-2018a-Python-3.6.4.eb | 3 +++ .../p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb | 3 +++ .../p/Pysam/Pysam-0.14.1-intel-2018a-Python-2.7.14.eb | 3 +++ .../p/Pysam/Pysam-0.14.1-intel-2018a-Python-3.6.4.eb | 3 +++ 10 files changed, 31 insertions(+) diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017a-Python-2.7.13.eb index e4f241d7e5c..6b18be08066 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017a-Python-2.7.13.eb @@ -29,6 +29,9 @@ dependencies = [ ('XZ', '5.2.3'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-2.7.14.eb index 9edbd85fcd0..b0133fa3678 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-2.7.14.eb @@ -29,6 +29,9 @@ dependencies = [ ('XZ', '5.2.3'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-3.6.3.eb index bc70913824d..0f621c18ab7 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.12.0.1-intel-2017b-Python-3.6.3.eb @@ -29,6 +29,9 @@ dependencies = [ ('XZ', '5.2.3'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.13-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.13-intel-2017b-Python-2.7.14.eb index 08e13a8bdb3..eb8a406638a 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.13-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.13-intel-2017b-Python-2.7.14.eb @@ -28,6 +28,9 @@ dependencies = [ ('XZ', '5.2.3'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.13.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.13.0-intel-2017b-Python-3.6.3.eb index 8faf2620ade..904a146bb26 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.13.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.13.0-intel-2017b-Python-3.6.3.eb @@ -29,6 +29,10 @@ dependencies = [ ('XZ', '5.2.3'), ] + +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-2.7.14.eb index c0c6842ed44..8f9ecf79669 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2017b-Python-2.7.14.eb @@ -29,6 +29,9 @@ dependencies = [ ('XZ', '5.2.3'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2018a-Python-3.6.4.eb index 6f5b0a7e6ab..d8cff133f2e 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14-intel-2018a-Python-3.6.4.eb @@ -29,6 +29,9 @@ dependencies = [ ('XZ', '5.2.3'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb index d5aaef6c2d0..1b72d46d0cd 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-foss-2018a-Python-3.6.4.eb @@ -31,6 +31,9 @@ dependencies = [ ('XZ', '5.2.3'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-2.7.14.eb index 947304ce871..92fd7ba3ae5 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-2.7.14.eb @@ -31,6 +31,9 @@ dependencies = [ ('XZ', '5.2.3'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-3.6.4.eb index d0acd598dc5..8631c655d28 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.14.1-intel-2018a-Python-3.6.4.eb @@ -31,6 +31,9 @@ dependencies = [ ('XZ', '5.2.3'), ] +use_pip = True +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 1d0fd94e3c7b7439af3a6fa28a0ebae3d3519c25 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 29 Mar 2019 10:04:51 -0700 Subject: [PATCH 1029/5331] parasail 2.4 update --- easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb b/easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb index b99ab4959c6..9f9a6930671 100644 --- a/easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb +++ b/easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/jeffdaily/parasail/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['9eec7bfca011c2b311e652dbcba3475d43a7c094ca6983ffc51ee53b2cbb0343'] builddependencies = [('CMake', '3.11.4')] From f862589852b7e4670dd5a63ceb4a51c692665fa5 Mon Sep 17 00:00:00 2001 From: Andrey Maslennikov Date: Sun, 31 Mar 2019 13:01:47 +0300 Subject: [PATCH 1030/5331] Use official OMPI release --- .../h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb | 2 +- ....eb => OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb} | 15 ++++----------- 2 files changed, 5 insertions(+), 12 deletions(-) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb => OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb} (76%) diff --git a/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb index 03cca0222b8..9149ad33f79 100644 --- a/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/h/HPCX/HPCX-2.3.0-GCC-8.2.0-2.31.1.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} dependencies = [ ('UCX', '1.5.0rc1', '-hpcx'), - ('OpenMPI', '4.0.x', '-hpcx') + ('OpenMPI', '4.0.0', '-hpcx') ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb similarity index 76% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb index 5b2066cbb05..892e9959bb1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.x-GCC-8.2.0-2.31.1-hpcx.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' -version = '4.0.x' +version = '4.0.0' versionsuffix = '-hpcx' homepage = 'http://www.open-mpi.org/' @@ -9,15 +9,9 @@ description = """Mellanox flavored Open MPI Project is an open source MPI-3 impl toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -sources = [{ - 'filename': 'openmpi-4.0.x.tar.gz', - 'git_config': { - 'url': 'https://github.com/open-mpi', - 'repo_name': 'ompi', - 'commit': '03cf3e4', - }, -}] -checksums = ['ef53605823b01499e09844a610614a555724603c72a1bb9a5ca59b35389f67ec'] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['36f10daa3f1b1d37530f686bf7f70966b2a13c0bc6e2e05aebc7e85e3d21b10d'] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] @@ -27,7 +21,6 @@ dependencies = [ ('UCX', '1.5.0rc1', '-hpcx') ] -preconfigopts = "./autogen.pl && " configopts = '--with-libevent=internal --enable-mpi1-compatibility ' configopts = '--with-slurm --with-platform=contrib/platform/mellanox/optimized ' configopts += '--with-ucx=$EBROOTUCX ' From 6726428176a6f523772b27b3164ea9306e131719 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 1 Apr 2019 11:19:12 +0200 Subject: [PATCH 1031/5331] Create gmsh-4.2.2-foss-2018b-Python-3.6.6.eb --- .../gmsh-4.2.2-foss-2018b-Python-3.6.6.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..c2fa2c81188 --- /dev/null +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'gmsh' +version = '4.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://geuz.org/gmsh' +description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {"usempi": True} + +source_urls = ['http://gmsh.info/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] +checksums = ['e9ee9f5c606bbec5f2adbb8c3d6023c4e2577f487fa4e4ecfcfc94a241cc8dcc'] + +builddependencies = [ + ('CMake', '3.12.1'), + ('SWIG', '3.0.12', versionsuffix), +] + +dependencies = [ + ('Python', '3.6.6'), + ('PETSc', '3.11.0', '-downloaded-deps'), + ('SLEPc', '3.11.0'), +] + +separate_build_dir = True + +configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/gmsh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From bbd73fe11eff6c9ce452897f736cb92480e16651 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Apr 2019 13:42:59 +0200 Subject: [PATCH 1032/5331] adding easyconfigs: Stacks-2.3e-foss-2018b.eb --- .../s/Stacks/Stacks-2.3e-foss-2018b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-2.3e-foss-2018b.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.3e-foss-2018b.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.3e-foss-2018b.eb new file mode 100644 index 00000000000..249f9db000a --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.3e-foss-2018b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '2.3e' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1c6439a4cfa42d4cf8196d4bca869234fba8c48a30e3e6c1d9c5e36f11aecf10'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks', + 'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks', + 'bin/tsv2bam', 'bin/ustacks'], + 'dirs': [], +} + +moduleclass = 'bio' From 55734d4d6859a6d992be283bfdd701efe269f0d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Apr 2019 13:45:00 +0200 Subject: [PATCH 1033/5331] adding easyconfigs: Stacks-1.48-intel-2018b.eb, sparsehash-2.0.3-GCCcore-7.3.0.eb --- .../s/Stacks/Stacks-1.48-intel-2018b.eb | 33 +++++++++++++++++++ .../sparsehash-2.0.3-GCCcore-7.3.0.eb | 30 +++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.48-intel-2018b.eb create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.48-intel-2018b.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.48-intel-2018b.eb new file mode 100644 index 00000000000..82f4936ba33 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.48-intel-2018b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.48' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e9f6251f5f609f9dd0bb1de17a51f69ce1a9af531548c4d2456a89783b1dcd1e'] + +dependencies = [ + ('zlib', '1.2.11'), + ('SAMtools', '1.9'), + ('sparsehash', '2.0.3'), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % b for b in [ + 'clone_filter', 'cstacks', 'denovo_map.pl', 'exec_velvet.pl', 'export_sql.pl', 'genotypes', 'index_radtags.pl', + 'kmer_filter', 'load_radtags.pl', 'load_sequences.pl', 'populations', 'process_radtags', 'process_shortreads', + 'pstacks', 'ref_map.pl', 'sort_read_pairs.pl', 'sstacks', 'stacks_export_notify.pl', 'ustacks']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-7.3.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..04e6a420b60 --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.3-GCCcore-7.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.3' + +homepage = 'https://github.com/sparsehash/sparsehash' + +description = """ + An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! + The SparseHash library contains several hash-map implementations, including + implementations that optimize for space or speed. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/sparsehash/sparsehash/archive'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['05e986a5c7327796dad742182b2d10805a8d4f511ad090da0490f146c1ff7a8c'] + +builddependencies = [ + ('binutils', '2.30'), +] + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' From f8365c17a6ed89b9523c6bee22cc3b101470314d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Apr 2019 14:19:34 +0200 Subject: [PATCH 1034/5331] adding easyconfigs: TINKER-8.6.1-foss-2018b.eb --- .../t/TINKER/TINKER-8.6.1-foss-2018b.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/t/TINKER/TINKER-8.6.1-foss-2018b.eb diff --git a/easybuild/easyconfigs/t/TINKER/TINKER-8.6.1-foss-2018b.eb b/easybuild/easyconfigs/t/TINKER/TINKER-8.6.1-foss-2018b.eb new file mode 100644 index 00000000000..c94eb49785d --- /dev/null +++ b/easybuild/easyconfigs/t/TINKER/TINKER-8.6.1-foss-2018b.eb @@ -0,0 +1,16 @@ +name = 'TINKER' +version = '8.6.1' + +homepage = 'http://dasher.wustl.edu/tinker' +description = """The TINKER molecular modeling software is a complete and general package for molecular mechanics + and dynamics, with some special features for biopolymers.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://dasher.wustl.edu/tinker/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['395556fd1a4c4907ab3f3207487db536693df883db71986a896ba1415f15fb6b'] + +runtest = True + +moduleclass = 'chem' From 3819924f613eb313e6cc75ed011efd29630349c9 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 1 Apr 2019 15:57:02 +0200 Subject: [PATCH 1035/5331] Update gmsh-4.2.2-foss-2018b-Python-3.6.6.eb Update for changes in python interface of gmsh 4.2.2 --- .../g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb index c2fa2c81188..d098c94f5ee 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb @@ -29,11 +29,11 @@ separate_build_dir = True configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} +modextrapaths = {'PYTHONPATH': ['lib64']} sanity_check_paths = { - 'files': ['bin/gmsh'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], + 'files': ['bin/gmsh', 'lib64/gmsh.py' ], + 'dirs': [], } moduleclass = 'math' From 9db9f667534965f41278c450f8a71d4853209fbd Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 2 Apr 2019 09:59:11 +0200 Subject: [PATCH 1036/5331] removed disliked whitespce in gmsh 4.2.2 --- .../easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb index d098c94f5ee..9b05a009cb9 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.2.2-foss-2018b-Python-3.6.6.eb @@ -32,7 +32,7 @@ configopts = '-DENABLE_FLTK=0 -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' modextrapaths = {'PYTHONPATH': ['lib64']} sanity_check_paths = { - 'files': ['bin/gmsh', 'lib64/gmsh.py' ], + 'files': ['bin/gmsh', 'lib64/gmsh.py'], 'dirs': [], } From 08c3080fca1df83f102ccd44a191b1a3b5da7336 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Tue, 2 Apr 2019 10:11:09 +0100 Subject: [PATCH 1037/5331] adding easyconfigs: libjpeg-turbo-2.0.2-GCCcore-7.3.0.eb --- .../libjpeg-turbo-2.0.2-GCCcore-7.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.2-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.2-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..7c5dd9d7f16 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.2-GCCcore-7.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.0.2' + +homepage = 'http://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['acb8599fe5399af114287ee5907aea4456f8f2c1cc96d26c28aebfdf5ee82fed'] + +builddependencies = [ + ('CMake', '3.12.1'), + ('binutils', '2.30'), +] + +dependencies = [ + ('NASM', '2.13.03'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 7d7fb7646086940e16f2bdd215dd6bc00bfb74b8 Mon Sep 17 00:00:00 2001 From: jdemeul Date: Tue, 2 Apr 2019 11:36:02 +0000 Subject: [PATCH 1038/5331] {bio}[foss/2018b,Python/3.6.6] cutadapt v2.1 --- .../cutadapt-2.1-foss-2018b-Python-3.6.6.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..536fd24f538 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modufied by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS + +easyblock = 'PythonPackage' + +name = 'cutadapt' +version = '2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['09fd222a27cc1eeb571633f2bd54442ea9d4ff668ef1f475fd9d5253a7d315ef'] + +dependencies = [ + ('Python', '3.6.6'), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 29c7518dbaa4e990098964ee88a92019cef9e451 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 2 Apr 2019 13:44:15 +0200 Subject: [PATCH 1039/5331] adding easyconfigs: emcee-2.2.1-foss-2018b-Python-2.7.15.eb, emcee-2.2.1-intel-2018b-Python-2.7.15.eb, emcee-2.2.1-foss-2018b-Python-3.6.6.eb, emcee-2.2.1-intel-2018b-Python-3.6.6.eb --- .../emcee-2.2.1-foss-2018b-Python-2.7.15.eb | 32 +++++++++++++++++++ .../emcee-2.2.1-foss-2018b-Python-3.6.6.eb | 32 +++++++++++++++++++ .../emcee-2.2.1-intel-2018b-Python-2.7.15.eb | 32 +++++++++++++++++++ .../emcee-2.2.1-intel-2018b-Python-3.6.6.eb | 32 +++++++++++++++++++ 4 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..22551cfb059 --- /dev/null +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'emcee' +version = '2.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://dfm.io/emcee' +description = """Emcee is an extensible, pure-Python implementation of +Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. +It's designed for Bayesian parameter estimation and it's really sweet! """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'] + +dependencies = [ + ('Python', '2.7.15'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'], +} + +sanity_check_commands = [ + ('python -c "import emcee; emcee.test()"')] + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..241fc7a1bca --- /dev/null +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'emcee' +version = '2.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://dfm.io/emcee' +description = """Emcee is an extensible, pure-Python implementation of +Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. +It's designed for Bayesian parameter estimation and it's really sweet! """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'] + +dependencies = [ + ('Python', '3.6.6'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'], +} + +sanity_check_commands = [ + ('python -c "import emcee; emcee.test()"')] + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..4d83e7fbff0 --- /dev/null +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'emcee' +version = '2.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://dfm.io/emcee' +description = """Emcee is an extensible, pure-Python implementation of +Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. +It's designed for Bayesian parameter estimation and it's really sweet! """ + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'] + +dependencies = [ + ('Python', '2.7.15'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'], +} + +sanity_check_commands = [ + ('python -c "import emcee; emcee.test()"')] + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..4d32b18d8c9 --- /dev/null +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'emcee' +version = '2.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://dfm.io/emcee' +description = """Emcee is an extensible, pure-Python implementation of +Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. +It's designed for Bayesian parameter estimation and it's really sweet! """ + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b83551e342b37311897906b3b8acf32979f4c5542e0a25786ada862d26241172'] + +dependencies = [ + ('Python', '3.6.6'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'], +} + +sanity_check_commands = [ + ('python -c "import emcee; emcee.test()"')] + +moduleclass = 'astro' From 20563300860a9558646cd3fc2cc4816d1b5a3982 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 2 Apr 2019 14:00:14 +0200 Subject: [PATCH 1040/5331] emcee:code style --- .../e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb | 3 +-- .../easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb | 3 +-- .../e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb | 3 +-- .../e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb | 3 +-- 4 files changed, 4 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb index 22551cfb059..dc3b51af293 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb @@ -26,7 +26,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'], } -sanity_check_commands = [ - ('python -c "import emcee; emcee.test()"')] +sanity_check_commands = [('python -c "import emcee; emcee.test()"')] moduleclass = 'astro' diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb index 241fc7a1bca..4c68af0d06a 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb @@ -26,7 +26,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'], } -sanity_check_commands = [ - ('python -c "import emcee; emcee.test()"')] +sanity_check_commands = [('python -c "import emcee; emcee.test()"')] moduleclass = 'astro' diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb index 4d83e7fbff0..d4fd9e97104 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb @@ -26,7 +26,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'], } -sanity_check_commands = [ - ('python -c "import emcee; emcee.test()"')] +sanity_check_commands = [('python -c "import emcee; emcee.test()"')] moduleclass = 'astro' diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb index 4d32b18d8c9..ee1a28e7a0d 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb @@ -26,7 +26,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'], } -sanity_check_commands = [ - ('python -c "import emcee; emcee.test()"')] +sanity_check_commands = [('python -c "import emcee; emcee.test()"')] moduleclass = 'astro' From 4b00e745ea601e5d769a670123842d7a5452c04b Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 2 Apr 2019 15:21:49 +0200 Subject: [PATCH 1041/5331] adding easyconfigs: scikit-learn-0.20.0-foss-2018b-Python-2.7.15.eb, scikit-learn-0.20.0-intel-2018b-Python-2.7.15.eb --- ...t-learn-0.20.0-foss-2018b-Python-2.7.15.eb | 34 +++++++++++++++++++ ...-learn-0.20.0-intel-2018b-Python-2.7.15.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-2.7.15.eb create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-2.7.15.eb new file mode 100755 index 00000000000..3b8faa9e1b2 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.20.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18'] + +dependencies = [ + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-2.7.15.eb new file mode 100755 index 00000000000..11f5ae28a67 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.0-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.20.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18'] + +dependencies = [ + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' From ceab1e1384d627fca560462a3abe3530c7708e2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Apr 2019 16:14:26 +0200 Subject: [PATCH 1042/5331] add easyconfig for FastANI 1.1 built with intel/2018b + add clarification & author in FastANI patch file --- .../f/FastANI/FastANI-1.1-foss-2018b.eb | 2 +- .../f/FastANI/FastANI-1.1-intel-2018b.eb | 41 +++++++++++++++++++ .../f/FastANI/FastANI-1.1-memcpy.patch | 3 +- 3 files changed, 44 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.1-intel-2018b.eb diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb index ad53f8b43b5..d47a188b5ac 100644 --- a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-foss-2018b.eb @@ -21,7 +21,7 @@ sources = ['v%(version)s.zip'] patches = ['%(name)s-%(version)s-memcpy.patch'] checksums = [ 'ffb776ddfa2595bba5611b0b017aad5089f9a19ea020c7d708d09c628bb926b3', # v1.1.zip - 'c2d751b1003ef9501fa54596a23a0083908e7590b1065ddb544484467572be58', # FastANI-1.1-memcpy.patch + 'fada27c448b5a1cfabc9780b57093ee7b57ac84e3d2b9fd65efb4cbe38220190', # FastANI-1.1-memcpy.patch ] preconfigopts = 'autoconf && ' diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-intel-2018b.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-intel-2018b.eb new file mode 100644 index 00000000000..1fd567fd8bc --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-intel-2018b.eb @@ -0,0 +1,41 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org + +easyblock = 'ConfigureMake' + +name = 'FastANI' +version = '1.1' + +homepage = "http://www.iodbc.org/" +description = """FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean + nucleotide identity of orthologous gene pairs shared between two microbial + genomes. FastANI supports pairwise comparison of both complete and draft + genome assemblies.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] +sources = ['v%(version)s.zip'] +patches = ['%(name)s-%(version)s-memcpy.patch'] +checksums = [ + 'ffb776ddfa2595bba5611b0b017aad5089f9a19ea020c7d708d09c628bb926b3', # v1.1.zip + 'fada27c448b5a1cfabc9780b57093ee7b57ac84e3d2b9fd65efb4cbe38220190', # FastANI-1.1-memcpy.patch +] + +preconfigopts = 'autoconf && ' + +builddependencies = [('Autoconf', '2.69')] + +dependencies = [ + ('GSL', '2.5'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fastANI'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch index ca0b7d3b682..cc2b7561d47 100644 --- a/easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.1-memcpy.patch @@ -1,4 +1,5 @@ -remove memcpy wrapper +remove memcpy wrapper to fix hang +author: John Dey (Fred Hutch) diff -ruN FastANI-1.1.orig/Makefile.in FastANI-1.1/Makefile.in --- FastANI-1.1.orig/Makefile.in 2018-08-01 09:29:53.000000000 -0700 +++ FastANI-1.1/Makefile.in 2018-12-07 16:00:29.231658000 -0800 From 9622b69320acd262946045a072f424dbe0fb2c6d Mon Sep 17 00:00:00 2001 From: h_zimm01 Date: Tue, 2 Apr 2019 16:40:31 +0200 Subject: [PATCH 1043/5331] adding easyconfigs: Mono-5.18.1.0-foss-2018a.eb --- .../m/Mono/Mono-5.18.1.0-foss-2018a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mono/Mono-5.18.1.0-foss-2018a.eb diff --git a/easybuild/easyconfigs/m/Mono/Mono-5.18.1.0-foss-2018a.eb b/easybuild/easyconfigs/m/Mono/Mono-5.18.1.0-foss-2018a.eb new file mode 100644 index 00000000000..8e881674e7d --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-5.18.1.0-foss-2018a.eb @@ -0,0 +1,22 @@ +name = 'Mono' +version = '5.18.1.0' + +homepage = 'http://www.mono-project.com/' +description = """An open source, cross-platform, implementation of C# and the CLR that is + binary compatible with Microsoft.NET.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['a92a8fb54f8faa922cdb203cf0bee93bf418f08144f5bc018c5013948d03a4f0'] + +builddependencies = [ + ('Autotools', '20170619'), + ('CMake', '3.10.2'), + ('gettext', '0.19.8.1', '-libxml2-2.9.7'), +] + +configopts = "--with-large-heap=yes --without-x" + +moduleclass = 'lang' From 2f5a02d33a979a67eb0248e582f0774b5b1d9d2f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Tue, 2 Apr 2019 16:59:25 +0200 Subject: [PATCH 1044/5331] Fix OTF2, OPARI2, and Score-P download URLs --- .../__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb | 4 ++-- .../__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb | 4 ++-- .../__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb | 4 ++-- .../__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb | 4 ++-- .../s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb | 4 ++-- easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb | 4 ++-- easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb | 2 +- easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb | 4 ++-- easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb | 4 ++-- easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb | 4 ++-- easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb | 2 +- easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb | 4 ++-- easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb | 4 ++-- easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb | 2 +- easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb | 2 +- 19 files changed, 31 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb index 07e343af8a2..332eeb80775 100644 --- a/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb @@ -29,9 +29,9 @@ description = """The lightweight measurement module (LWM2) is a low overhead pro toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {"usempi": True} -# http://www.vi-hps.org/upload/projects/hopsa/lwm2-1.1.tar.gz +# http://www.vi-hps.org/cms/upload/projects/hopsa/lwm2-1.1.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/projects/hopsa/'] +source_urls = ['http://www.vi-hps.org/cms/upload/projects/hopsa/'] # compiler toolchain depencies dependencies = [ diff --git a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb index 6ba1cb4abdf..9295366d5a1 100644 --- a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb @@ -19,9 +19,9 @@ description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://www.vi-hps.org/upload/packages/opari2/opari2-1.0.7.tar.gz +# http://www.vi-hps.org/cms/upload/packages/opari2/opari2-1.0.7.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] sanity_check_paths = { 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], diff --git a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb index 14ec77b8ce0..4be3e38a7f4 100644 --- a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb @@ -19,9 +19,9 @@ description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.1.tar.gz +# http://www.vi-hps.org/cms/upload/packages/opari2/opari2-1.1.1.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] sanity_check_paths = { 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], diff --git a/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb index ec87a9a0a1f..216333c0c13 100644 --- a/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb @@ -18,9 +18,9 @@ description = """The Open Trace Format 2 is a highly scalable, memory efficient toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz +# http://www.vi-hps.org/cms/upload/packages/otf2/otf2-1.2.1.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] sanity_check_paths = { # note by Bernd Mohr: on some systems libraries end up in lib/ diff --git a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb index dbfcd3190c6..3d850188b25 100644 --- a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb @@ -20,9 +20,9 @@ description = """The Score-P measurement infrastructure is a highly scalable and toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} toolchainopts = {"usempi": True} -# http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.1.tar.gz +# http://www.vi-hps.org/cms/upload/packages/scorep/scorep-1.2.1.tar.gz sources = ["scorep-%(version)s.tar.gz"] -source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] # compiler toolchain depencies dependencies = [ diff --git a/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb index fa8505d85c1..a374e6c1b8f 100644 --- a/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb @@ -29,9 +29,9 @@ description = """The lightweight measurement module (LWM2) is a low overhead pro toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {"usempi": True} -# http://www.vi-hps.org/upload/projects/hopsa/lwm2-1.1.tar.gz +# http://www.vi-hps.org/cms/upload/projects/hopsa/lwm2-1.1.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/projects/hopsa/'] +source_urls = ['http://www.vi-hps.org/cms/upload/projects/hopsa/'] # compiler toolchain depencies dependencies = [ diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb index cbd3a839746..6b33eb65bdd 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb @@ -19,9 +19,9 @@ description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, toolchain = {'name': 'goolf', 'version': '1.5.14'} -# http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.1.tar.gz +# http://www.vi-hps.org/cms/upload/packages/opari2/opari2-1.1.1.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] sanity_check_paths = { 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb index c6cc202fedd..396221c0748 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb @@ -20,7 +20,7 @@ description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] checksums = [ '9a262c7ca05ff0ab5f7775ae96f3539e', # opari2-1.1.2.tar.gz diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb index c859d761df9..36bba061687 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -17,9 +17,9 @@ description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, toolchain = {'name': 'goolf', 'version': '1.5.14'} -# http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.1.tar.gz +# http://www.vi-hps.org/cms/upload/packages/opari2/opari2-1.1.1.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] sanity_check_paths = { 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb index 4c1cdfb9224..c2dae6a7d17 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb @@ -24,7 +24,7 @@ description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] checksums = [ '72350dbdb6139f2e68a5055a4f0ba16c', # opari2-2.0.tar.gz diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb index 6e577637597..524ddf1d8ae 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb @@ -19,9 +19,9 @@ description = """The Open Trace Format 2 is a highly scalable, memory efficient toolchain = {'name': 'goolf', 'version': '1.5.14'} -# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz +# http://www.vi-hps.org/cms/upload/packages/otf2/otf2-1.2.1.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] sanity_check_paths = { # note by Bernd Mohr: on some systems libraries end up in lib/ diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb index b3e56a69868..46aba80c9ac 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb @@ -18,9 +18,9 @@ description = """The Open Trace Format 2 is a highly scalable, memory efficient toolchain = {'name': 'ictce', 'version': '5.3.0'} -# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz +# http://www.vi-hps.org/cms/upload/packages/otf2/otf2-1.2.1.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] sanity_check_paths = { # note by Bernd Mohr: on some systems libraries end up in lib/ diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb index d76e3051fb8..f984d416ad0 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb @@ -19,7 +19,7 @@ description = """The Open Trace Format 2 is a highly scalable, memory efficient toolchain = {'name': 'foss', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ '16a9df46e0da78e374f5d12c8cdc1109', # otf2-1.5.1.tar.gz diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb index 2e24f54ef86..66f6f4e2922 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb @@ -22,7 +22,7 @@ description = """The Open Trace Format 2 is a highly scalable, memory efficient toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ '5b546188b25bc1c4e285e06dddf75dfc', # otf2-2.0.tar.gz diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb index 41a3d0f3c9f..996a5d96b2e 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb @@ -22,7 +22,7 @@ description = """The Open Trace Format 2 is a highly scalable, memory efficient toolchain = {'name': 'foss', 'version': '2017a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ '5b546188b25bc1c4e285e06dddf75dfc', # otf2-2.0.tar.gz diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb index 26a76a0f44b..c45a3234436 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb @@ -17,9 +17,9 @@ description = """The Score-P measurement infrastructure is a highly scalable and toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'usempi': True} -# http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.1.tar.gz +# http://www.vi-hps.org/cms/upload/packages/scorep/scorep-1.2.1.tar.gz sources = ['scorep-%(version)s.tar.gz'] -source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] # compiler toolchain depencies dependencies = [ diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb index 3f228919973..cf46c39d628 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb @@ -17,9 +17,9 @@ description = """The Score-P measurement infrastructure is a highly scalable and toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {"usempi": True} -# http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.1.tar.gz +# http://www.vi-hps.org/cms/upload/packages/scorep/scorep-1.2.1.tar.gz sources = ["scorep-%(version)s.tar.gz"] -source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] # compiler toolchain depencies dependencies = [ diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb index c70a882623e..7c941a5af17 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {"usempi": True} sources = ["scorep-%(version)s.tar.gz"] -source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] checksums = [ '17bd732cf54097d35157bf0d8284ad78', # scorep-1.4.tar.gz diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index 65fe9f43f32..ab82ae68a92 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -22,7 +22,7 @@ description = """The Score-P measurement infrastructure is a highly scalable and toolchain = {'name': 'foss', 'version': '2016a'} sources = ['scorep-%(version)s.tar.gz'] -source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] # Backported fix to prevent build-score/configure from picking up CFLAGS etc.; # included in Score-P 2.0.2 and above From 27f63d40f189fda8034ae20f1648c1003c309a84 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 2 Apr 2019 17:03:34 +0200 Subject: [PATCH 1045/5331] emcee: +'download_dep_fail = True' --- .../easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb | 1 + .../easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb | 1 + .../easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb | 1 + .../easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb index dc3b51af293..fc0663e9cbd 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-2.7.15.eb @@ -20,6 +20,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb index 4c68af0d06a..282aafc7937 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-foss-2018b-Python-3.6.6.eb @@ -20,6 +20,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb index d4fd9e97104..9e386cfc73b 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-2.7.15.eb @@ -20,6 +20,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb index ee1a28e7a0d..2b5fce09e27 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-2.2.1-intel-2018b-Python-3.6.6.eb @@ -20,6 +20,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_check_paths = { 'files': [], From e57e8e5b3093a3f962da19a70bb4fbbbcf3b171f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Apr 2019 17:42:53 +0200 Subject: [PATCH 1046/5331] {bio}[intel/2018b] GTDB-Tk v0.2.2, DendroPy v4.4.0 w/ Python 2.7.15 --- ...endroPy-4.4.0-intel-2018b-Python-2.7.15.eb | 37 ++++++++++++++++ ...GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb | 43 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..421f316402b --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'] + +download_dep_fail = True +use_pip = True + +dependencies = [('Python', '2.7.15')] + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..2f23e48dd30 --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'GTDB-Tk' +version = '0.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), + ('DendroPy', '4.4.0', versionsuffix), + ('matplotlib', '2.2.3', versionsuffix), + ('prodigal', '2.6.3'), + ('HMMER', '3.2.1'), + ('pplacer', '1.1.alpha19', '', True), + ('FastANI', '1.1'), + ('FastTree', '2.1.10'), +] + +#use_pip = True + +exts_list = [ + ('future', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future'], + 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gtdbtk'], + 'source_tmpl': 'gtdbtk-%(version)s.tar.gz', + 'checksums': ['23f6dd77e0102cfbc88d0e1c1cc4ba61a1df64ec71848a160ac4d9b5d2e81d1d'], + 'modulename': 'gtdbtk', + }), +] + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 4f9e8179c9b1a936e24c62fb46b4b9685c7713c7 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 2 Apr 2019 11:04:59 -0500 Subject: [PATCH 1047/5331] adding easyconfigs: RStan-2.18.2-foss-2017b-R-3.4.3.eb, RStan-2.18.2-intel-2017b-R-3.4.3.eb --- .../RStan/RStan-2.18.2-foss-2017b-R-3.4.3.eb | 62 +++++++++++++++++++ .../RStan/RStan-2.18.2-intel-2017b-R-3.4.3.eb | 62 +++++++++++++++++++ 2 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/r/RStan/RStan-2.18.2-foss-2017b-R-3.4.3.eb create mode 100644 easybuild/easyconfigs/r/RStan/RStan-2.18.2-intel-2017b-R-3.4.3.eb diff --git a/easybuild/easyconfigs/r/RStan/RStan-2.18.2-foss-2017b-R-3.4.3.eb b/easybuild/easyconfigs/r/RStan/RStan-2.18.2-foss-2017b-R-3.4.3.eb new file mode 100644 index 00000000000..84fa45f267e --- /dev/null +++ b/easybuild/easyconfigs/r/RStan/RStan-2.18.2-foss-2017b-R-3.4.3.eb @@ -0,0 +1,62 @@ +easyblock = 'Bundle' + +name = 'RStan' +version = '2.18.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/stan-dev/rstan' +description = """RStan is the R interface to Stan. Stan is a state-of-the-art + platform for statistical modeling and high-performance statistical computation.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [ + ('R', '3.4.3', '-X11-20171023') +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('BH', '1.66.0-1', { + 'checksums': ['17d9eb5512d74aa7dd02ec98953408422e728b01ce63493a6a473070b9596a92'], + }), + ('inline', '0.3.15', { + 'checksums': ['ff043fe13c1991a3b285bed256ff4a9c0ba10bee764225a34b285875b7d69c68'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('callr', '2.0.0', { + 'checksums': ['b89482fa11c02058e636a19e9286a30f4e2c299a7b1aa52d87cd839520b2a4bb'], + }), + ('pkgbuild', '1.0.0', { + 'checksums': ['a9691dd3e27cd053a5d4cc8df8b46baa9915c95d4ce03b8e4cb4c77a0a403f82'], + }), + ('loo', '2.1.0', { + 'checksums': ['1bf4a1ef85d151577ff96d4cf2a29c9ef24370b0b1eb08c70dcf45884350e87d'], + }), + ('StanHeaders', '2.18.1', { + 'checksums': ['ce0d609a7cd11725b1203bdeae92acc54da3a48b8266eb9dbdb9d95b14df9209'], + }), + ('rstan', version, { + 'checksums': ['4d75dad95610d5a1d1c89a4ddbaf4326462e4ffe0ad28aed2129f2d9292e70ff'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['rstan'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/RStan/RStan-2.18.2-intel-2017b-R-3.4.3.eb b/easybuild/easyconfigs/r/RStan/RStan-2.18.2-intel-2017b-R-3.4.3.eb new file mode 100644 index 00000000000..4f78a954229 --- /dev/null +++ b/easybuild/easyconfigs/r/RStan/RStan-2.18.2-intel-2017b-R-3.4.3.eb @@ -0,0 +1,62 @@ +easyblock = 'Bundle' + +name = 'RStan' +version = '2.18.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/stan-dev/rstan' +description = """RStan is the R interface to Stan. Stan is a state-of-the-art + platform for statistical modeling and high-performance statistical computation.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [ + ('R', '3.4.3', '-X11-20171023') +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('BH', '1.66.0-1', { + 'checksums': ['17d9eb5512d74aa7dd02ec98953408422e728b01ce63493a6a473070b9596a92'], + }), + ('inline', '0.3.15', { + 'checksums': ['ff043fe13c1991a3b285bed256ff4a9c0ba10bee764225a34b285875b7d69c68'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('callr', '2.0.0', { + 'checksums': ['b89482fa11c02058e636a19e9286a30f4e2c299a7b1aa52d87cd839520b2a4bb'], + }), + ('pkgbuild', '1.0.0', { + 'checksums': ['a9691dd3e27cd053a5d4cc8df8b46baa9915c95d4ce03b8e4cb4c77a0a403f82'], + }), + ('loo', '2.1.0', { + 'checksums': ['1bf4a1ef85d151577ff96d4cf2a29c9ef24370b0b1eb08c70dcf45884350e87d'], + }), + ('StanHeaders', '2.18.1', { + 'checksums': ['ce0d609a7cd11725b1203bdeae92acc54da3a48b8266eb9dbdb9d95b14df9209'], + }), + ('rstan', version, { + 'checksums': ['4d75dad95610d5a1d1c89a4ddbaf4326462e4ffe0ad28aed2129f2d9292e70ff'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['rstan'], +} + +moduleclass = 'data' From 62d4ca09310cb03c67e81ab68afff3eb04b5c3a9 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 2 Apr 2019 17:14:30 -0500 Subject: [PATCH 1048/5331] adding easyconfigs: Sphinx-1.8.1-foss-2017b-Python-2.7.14.eb, Sphinx-1.8.1-foss-2017b-Python-3.6.3.eb, Sphinx-1.8.1-intel-2017b-Python-2.7.14.eb, Sphinx-1.8.1-intel-2017b-Python-3.6.3.eb --- .../Sphinx-1.8.1-foss-2017b-Python-2.7.14.eb | 88 +++++++++++++++++++ .../Sphinx-1.8.1-foss-2017b-Python-3.6.3.eb | 88 +++++++++++++++++++ .../Sphinx-1.8.1-intel-2017b-Python-2.7.14.eb | 88 +++++++++++++++++++ .../Sphinx-1.8.1-intel-2017b-Python-3.6.3.eb | 88 +++++++++++++++++++ 4 files changed, 352 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..19cb7ea3777 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,88 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx' +version = '1.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sphinx.pocoo.org/' +description = """Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. + It was originally created for the new Python documentation, and it has excellent facilities for the + documentation of Python projects, but C/C++ is already supported as well, and it is planned to add + special support for other languages as well.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [('Python', '2.7.14')] + +use_pip = True + +exts_list = [ + ('packaging', '18.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], + }), + ('MarkupSafe', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], + }), + ('sphinxcontrib-websupport', '1.1.0', { + 'modulename': 'sphinxcontrib.websupport', + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], + 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], + # can't use pip here because it doesn't support namespaces + # cfr. https://github.com/pypa/pip/issues/1924 + 'use_pip': False, + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], + 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], + }), + ('imagesize', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], + }), + ('Docutils', '0.14', { + 'source_tmpl': 'docutils-%(version)s.tar.gz', + 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], + 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], + }), + ('Babel', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], + }), + ('alabaster', '0.7.12', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], + 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], + }), + ('sphinx_rtd_theme', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], + 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], + }), + ('numpydoc', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], + 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], + }), +] + +sanity_check_paths = { + 'files': ['bin/sphinx-%s' % x for x in ['apidoc', 'autogen', 'build', 'quickstart']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..e5ebc21dbed --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,88 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx' +version = '1.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sphinx.pocoo.org/' +description = """Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. + It was originally created for the new Python documentation, and it has excellent facilities for the + documentation of Python projects, but C/C++ is already supported as well, and it is planned to add + special support for other languages as well.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [('Python', '3.6.3')] + +use_pip = True + +exts_list = [ + ('packaging', '18.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], + }), + ('MarkupSafe', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], + }), + ('sphinxcontrib-websupport', '1.1.0', { + 'modulename': 'sphinxcontrib.websupport', + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], + 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], + # can't use pip here because it doesn't support namespaces + # cfr. https://github.com/pypa/pip/issues/1924 + 'use_pip': False, + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], + 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], + }), + ('imagesize', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], + }), + ('Docutils', '0.14', { + 'source_tmpl': 'docutils-%(version)s.tar.gz', + 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], + 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], + }), + ('Babel', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], + }), + ('alabaster', '0.7.12', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], + 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], + }), + ('sphinx_rtd_theme', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], + 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], + }), + ('numpydoc', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], + 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], + }), +] + +sanity_check_paths = { + 'files': ['bin/sphinx-%s' % x for x in ['apidoc', 'autogen', 'build', 'quickstart']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..c43976b768c --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,88 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx' +version = '1.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sphinx.pocoo.org/' +description = """Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. + It was originally created for the new Python documentation, and it has excellent facilities for the + documentation of Python projects, but C/C++ is already supported as well, and it is planned to add + special support for other languages as well.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [('Python', '2.7.14')] + +use_pip = True + +exts_list = [ + ('packaging', '18.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], + }), + ('MarkupSafe', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], + }), + ('sphinxcontrib-websupport', '1.1.0', { + 'modulename': 'sphinxcontrib.websupport', + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], + 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], + # can't use pip here because it doesn't support namespaces + # cfr. https://github.com/pypa/pip/issues/1924 + 'use_pip': False, + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], + 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], + }), + ('imagesize', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], + }), + ('Docutils', '0.14', { + 'source_tmpl': 'docutils-%(version)s.tar.gz', + 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], + 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], + }), + ('Babel', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], + }), + ('alabaster', '0.7.12', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], + 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], + }), + ('sphinx_rtd_theme', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], + 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], + }), + ('numpydoc', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], + 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], + }), +] + +sanity_check_paths = { + 'files': ['bin/sphinx-%s' % x for x in ['apidoc', 'autogen', 'build', 'quickstart']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..30615223fa9 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,88 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx' +version = '1.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sphinx.pocoo.org/' +description = """Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. + It was originally created for the new Python documentation, and it has excellent facilities for the + documentation of Python projects, but C/C++ is already supported as well, and it is planned to add + special support for other languages as well.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [('Python', '3.6.3')] + +use_pip = True + +exts_list = [ + ('packaging', '18.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], + }), + ('MarkupSafe', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], + }), + ('sphinxcontrib-websupport', '1.1.0', { + 'modulename': 'sphinxcontrib.websupport', + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], + 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], + # can't use pip here because it doesn't support namespaces + # cfr. https://github.com/pypa/pip/issues/1924 + 'use_pip': False, + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], + 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], + }), + ('imagesize', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], + }), + ('Docutils', '0.14', { + 'source_tmpl': 'docutils-%(version)s.tar.gz', + 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], + 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], + }), + ('Babel', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], + }), + ('alabaster', '0.7.12', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], + 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], + }), + ('sphinx_rtd_theme', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], + 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], + }), + ('numpydoc', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], + 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], + }), +] + +sanity_check_paths = { + 'files': ['bin/sphinx-%s' % x for x in ['apidoc', 'autogen', 'build', 'quickstart']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' From 98b2493a21e12f52feeb6a3ff70219d56ac478ba Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Apr 2019 09:00:35 +0200 Subject: [PATCH 1049/5331] Add SHA256 checksums --- .../__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb | 4 ++++ .../__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb | 4 ++++ .../__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb | 4 ++++ .../__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb | 4 ++++ .../s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb | 4 ++++ easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb | 4 ++++ easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb | 4 ++++ easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb | 2 +- easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb | 4 ++++ easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb | 4 ++++ easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb | 4 ++++ easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb | 2 +- easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb | 4 ++++ easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb | 4 ++++ easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb | 2 +- easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb | 4 ++-- 19 files changed, 56 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb index 332eeb80775..f682205c249 100644 --- a/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb @@ -33,6 +33,10 @@ toolchainopts = {"usempi": True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/projects/hopsa/'] +checksums = [ + 'f7708468db74ebf931e19a0d9b788dbedd0dbd1e24a8fb6de6c7c34b324cc4eb', # lwm2-1.1.tar.gz +] + # compiler toolchain depencies dependencies = [ ('PAPI', '5.2.0'), diff --git a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb index 9295366d5a1..c6d83ab6aa5 100644 --- a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb @@ -23,6 +23,10 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] +checksums = [ + '8d6fe152c740eaec9294e9d8c0938bf7bb25371e35486af7b95c16cf0159efc0', # opari2-1.0.7.tar.gz +] + sanity_check_paths = { 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], 'dirs': [], diff --git a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb index 4be3e38a7f4..0ca9cf5a9a7 100644 --- a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb @@ -23,6 +23,10 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] +checksums = [ + 'c5d067eedf34c197ffe06e986dddebba5e58eec5f39712b08034213b6fcbb59c', # opari2-1.1.1.tar.gz +] + sanity_check_paths = { 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], 'dirs': [], diff --git a/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb index 216333c0c13..1f06fb20fa1 100644 --- a/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb @@ -22,6 +22,10 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] +checksums = [ + '1db9fb0789de4a9c3c96042495e4212a22cb581f734a1593813adaf84f2288e4', # otf2-1.2.1.tar.gz +] + sanity_check_paths = { # note by Bernd Mohr: on some systems libraries end up in lib/ 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], diff --git a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb index 3d850188b25..3149e153794 100644 --- a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb @@ -24,6 +24,10 @@ toolchainopts = {"usempi": True} sources = ["scorep-%(version)s.tar.gz"] source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] +checksums = [ + '6cf6c433c0a7456549bb4447d32d6846442fdbc364735e8f70644d66fdafc950', # scorep-1.2.1.tar.gz +] + # compiler toolchain depencies dependencies = [ ('binutils', '2.22'), diff --git a/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb index a374e6c1b8f..02771726824 100644 --- a/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb @@ -33,6 +33,10 @@ toolchainopts = {"usempi": True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/projects/hopsa/'] +checksums = [ + 'f7708468db74ebf931e19a0d9b788dbedd0dbd1e24a8fb6de6c7c34b324cc4eb', # lwm2-1.1.tar.gz +] + # compiler toolchain depencies dependencies = [ ('PAPI', '5.2.0'), diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb index 6b33eb65bdd..f0f7712b49e 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb @@ -23,6 +23,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] +checksums = [ + 'c5d067eedf34c197ffe06e986dddebba5e58eec5f39712b08034213b6fcbb59c', # opari2-1.1.1.tar.gz +] + sanity_check_paths = { 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], 'dirs': [], diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb index 396221c0748..262f0768164 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb @@ -23,7 +23,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] checksums = [ - '9a262c7ca05ff0ab5f7775ae96f3539e', # opari2-1.1.2.tar.gz + '8405c2903730d94c828724b3a5f8889653553fb8567045a6c54ac0816237835d', # opari2-1.1.2.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb index 36bba061687..8a2a51f4043 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -21,6 +21,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] +checksums = [ + '8405c2903730d94c828724b3a5f8889653553fb8567045a6c54ac0816237835d', # opari2-1.1.2.tar.gz +] + sanity_check_paths = { 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], 'dirs': [], diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb index c2dae6a7d17..86f6a5b4cd5 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb @@ -27,7 +27,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] checksums = [ - '72350dbdb6139f2e68a5055a4f0ba16c', # opari2-2.0.tar.gz + '0c4e575be05627cd001d692204f10caef37b2f3d1ec825f98cbe1bfa4232b0b7', # opari2-2.0.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb index 524ddf1d8ae..ec102367d47 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb @@ -23,6 +23,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] +checksums = [ + '1db9fb0789de4a9c3c96042495e4212a22cb581f734a1593813adaf84f2288e4', # otf2-1.2.1.tar.gz +] + sanity_check_paths = { # note by Bernd Mohr: on some systems libraries end up in lib/ 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb index 46aba80c9ac..0040b6982b3 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb @@ -22,6 +22,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] +checksums = [ + '1db9fb0789de4a9c3c96042495e4212a22cb581f734a1593813adaf84f2288e4', # otf2-1.2.1.tar.gz +] + sanity_check_paths = { # note by Bernd Mohr: on some systems libraries end up in lib/ 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb index f984d416ad0..b75637ea32c 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb @@ -22,7 +22,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ - '16a9df46e0da78e374f5d12c8cdc1109', # otf2-1.5.1.tar.gz + 'a4dc9f6c99376030b43a4c7b1ee77cfb530b03928ea688c6d1a380b3f4e8e488', # otf2-1.5.1.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb index 66f6f4e2922..8f5efab449a 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb @@ -25,7 +25,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ - '5b546188b25bc1c4e285e06dddf75dfc', # otf2-2.0.tar.gz + 'bafe0ac08e0a13e71568e5774dc83bd305d907159b4ceeb53d2e9f6e29462754', # otf2-2.0.tar.gz ] builddependencies = [('SIONlib', '1.6.1', '-tools')] diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb index 996a5d96b2e..5e43710d573 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb @@ -25,7 +25,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ - '5b546188b25bc1c4e285e06dddf75dfc', # otf2-2.0.tar.gz + 'bafe0ac08e0a13e71568e5774dc83bd305d907159b4ceeb53d2e9f6e29462754', # otf2-2.0.tar.gz ] builddependencies = [('SIONlib', '1.7.1', '-tools')] diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb index c45a3234436..2f681f7b0ac 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb @@ -21,6 +21,10 @@ toolchainopts = {'usempi': True} sources = ['scorep-%(version)s.tar.gz'] source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] +checksums = [ + '6cf6c433c0a7456549bb4447d32d6846442fdbc364735e8f70644d66fdafc950', # scorep-1.2.1.tar.gz +] + # compiler toolchain depencies dependencies = [ ('Cube', '4.2'), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb index cf46c39d628..dde4eb01cf5 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb @@ -21,6 +21,10 @@ toolchainopts = {"usempi": True} sources = ["scorep-%(version)s.tar.gz"] source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] +checksums = [ + 'f3d705bec3d703c23f8ff2b831eab3bc6182710de20621aa761ecf6a6686751d', # scorep-1.2.3.tar.gz +] + # compiler toolchain depencies dependencies = [ ('binutils', '2.22'), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb index 7c941a5af17..5c40af34b02 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb @@ -24,7 +24,7 @@ sources = ["scorep-%(version)s.tar.gz"] source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] checksums = [ - '17bd732cf54097d35157bf0d8284ad78', # scorep-1.4.tar.gz + 'c4ac89c88648fb843a20172b2a3b163561e5be39b7be8036754b420a464b7e28', # scorep-1.4.tar.gz ] # compiler toolchain depencies diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index ab82ae68a92..98e525c427a 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -31,8 +31,8 @@ patches = [ ] checksums = [ - '031a82fa26e2c9412e55d964f92fc9e9', # scorep-2.0.1.tar.gz - '557b3a292591740271be7f336d5b7473', # Score-P-2.0.1_fix_score_configure.patch + 'e871cfdbcf51384e252037af2bf4d4e8c5200619263e85e3c8b7d211090911ef', # scorep-2.0.1.tar.gz + '0397fcb4a13e1fb3036beca25ba508801e30ab61c8ea4a737d80bc8c6072f18d', # Score-P-2.0.1_fix_score_configure.patch ] dependencies = [ From 8ba24e20aa5279b69702d35b3acaf2f7636ebab9 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 3 Apr 2019 09:10:48 +0200 Subject: [PATCH 1050/5331] Fix description of Leptonica --- .../easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb index cb338d1c679..abfd4950335 100644 --- a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.77.0-GCCcore-7.3.0.eb @@ -4,7 +4,7 @@ name = 'Leptonica' version = '1.77.0' homepage = 'http://www.leptonica.org' -description = """Leptonica is a pedagogically-oriented open source site containing software +description = """Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.""" toolchain = {'name': 'GCCcore', 'version': '7.3.0'} From d787fd17b8c5ccf1cdfb4e6a6ff411683edd37ab Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 3 Apr 2019 10:04:12 +0200 Subject: [PATCH 1051/5331] Style fixes --- .../__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb | 2 +- .../__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb | 2 +- .../__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb | 2 +- .../__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb | 2 +- .../s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb | 2 +- easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb | 2 +- easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb | 2 +- easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb | 2 +- easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb | 2 +- easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb | 4 ++-- 19 files changed, 20 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb index f682205c249..89182efc33d 100644 --- a/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb @@ -34,7 +34,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/projects/hopsa/'] checksums = [ - 'f7708468db74ebf931e19a0d9b788dbedd0dbd1e24a8fb6de6c7c34b324cc4eb', # lwm2-1.1.tar.gz + 'f7708468db74ebf931e19a0d9b788dbedd0dbd1e24a8fb6de6c7c34b324cc4eb', # lwm2-1.1.tar.gz ] # compiler toolchain depencies diff --git a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb index c6d83ab6aa5..3b401552933 100644 --- a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.0.7-gompi-1.4.12-no-OFED.eb @@ -24,7 +24,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] checksums = [ - '8d6fe152c740eaec9294e9d8c0938bf7bb25371e35486af7b95c16cf0159efc0', # opari2-1.0.7.tar.gz + '8d6fe152c740eaec9294e9d8c0938bf7bb25371e35486af7b95c16cf0159efc0', # opari2-1.0.7.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb index 0ca9cf5a9a7..4ab8a3c40e3 100644 --- a/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OPARI2/OPARI2-1.1.1-gompi-1.4.12-no-OFED.eb @@ -24,7 +24,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] checksums = [ - 'c5d067eedf34c197ffe06e986dddebba5e58eec5f39712b08034213b6fcbb59c', # opari2-1.1.1.tar.gz + 'c5d067eedf34c197ffe06e986dddebba5e58eec5f39712b08034213b6fcbb59c', # opari2-1.1.1.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb index 1f06fb20fa1..e48e211bcc5 100644 --- a/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/o/OTF2/OTF2-1.2.1-gompi-1.4.12-no-OFED.eb @@ -23,7 +23,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ - '1db9fb0789de4a9c3c96042495e4212a22cb581f734a1593813adaf84f2288e4', # otf2-1.2.1.tar.gz + '1db9fb0789de4a9c3c96042495e4212a22cb581f734a1593813adaf84f2288e4', # otf2-1.2.1.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb index 3149e153794..60ff58a3ea8 100644 --- a/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/s/Score-P/Score-P-1.2.1-gompi-1.4.12-no-OFED.eb @@ -25,7 +25,7 @@ sources = ["scorep-%(version)s.tar.gz"] source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] checksums = [ - '6cf6c433c0a7456549bb4447d32d6846442fdbc364735e8f70644d66fdafc950', # scorep-1.2.1.tar.gz + '6cf6c433c0a7456549bb4447d32d6846442fdbc364735e8f70644d66fdafc950', # scorep-1.2.1.tar.gz ] # compiler toolchain depencies diff --git a/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb index 02771726824..43cf04dcdf1 100644 --- a/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/LWM2/LWM2-1.1-ictce-5.3.0.eb @@ -34,7 +34,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/projects/hopsa/'] checksums = [ - 'f7708468db74ebf931e19a0d9b788dbedd0dbd1e24a8fb6de6c7c34b324cc4eb', # lwm2-1.1.tar.gz + 'f7708468db74ebf931e19a0d9b788dbedd0dbd1e24a8fb6de6c7c34b324cc4eb', # lwm2-1.1.tar.gz ] # compiler toolchain depencies diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb index f0f7712b49e..9444ab5ab76 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.1-goolf-1.5.14.eb @@ -24,7 +24,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] checksums = [ - 'c5d067eedf34c197ffe06e986dddebba5e58eec5f39712b08034213b6fcbb59c', # opari2-1.1.1.tar.gz + 'c5d067eedf34c197ffe06e986dddebba5e58eec5f39712b08034213b6fcbb59c', # opari2-1.1.1.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb index 262f0768164..eccd246655c 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb @@ -23,7 +23,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] checksums = [ - '8405c2903730d94c828724b3a5f8889653553fb8567045a6c54ac0816237835d', # opari2-1.1.2.tar.gz + '8405c2903730d94c828724b3a5f8889653553fb8567045a6c54ac0816237835d', # opari2-1.1.2.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb index 8a2a51f4043..31dab125a57 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -22,7 +22,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] checksums = [ - '8405c2903730d94c828724b3a5f8889653553fb8567045a6c54ac0816237835d', # opari2-1.1.2.tar.gz + '8405c2903730d94c828724b3a5f8889653553fb8567045a6c54ac0816237835d', # opari2-1.1.2.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb index 86f6a5b4cd5..beb366bbdf0 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0-foss-2016a.eb @@ -27,7 +27,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] checksums = [ - '0c4e575be05627cd001d692204f10caef37b2f3d1ec825f98cbe1bfa4232b0b7', # opari2-2.0.tar.gz + '0c4e575be05627cd001d692204f10caef37b2f3d1ec825f98cbe1bfa4232b0b7', # opari2-2.0.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb index ec102367d47..c1d21dab651 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb @@ -24,7 +24,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ - '1db9fb0789de4a9c3c96042495e4212a22cb581f734a1593813adaf84f2288e4', # otf2-1.2.1.tar.gz + '1db9fb0789de4a9c3c96042495e4212a22cb581f734a1593813adaf84f2288e4', # otf2-1.2.1.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb index 0040b6982b3..0b5f7725488 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-ictce-5.3.0.eb @@ -23,7 +23,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ - '1db9fb0789de4a9c3c96042495e4212a22cb581f734a1593813adaf84f2288e4', # otf2-1.2.1.tar.gz + '1db9fb0789de4a9c3c96042495e4212a22cb581f734a1593813adaf84f2288e4', # otf2-1.2.1.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb index b75637ea32c..d1299cf7c39 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb @@ -22,7 +22,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ - 'a4dc9f6c99376030b43a4c7b1ee77cfb530b03928ea688c6d1a380b3f4e8e488', # otf2-1.5.1.tar.gz + 'a4dc9f6c99376030b43a4c7b1ee77cfb530b03928ea688c6d1a380b3f4e8e488', # otf2-1.5.1.tar.gz ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb index 8f5efab449a..42aca20511e 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2016a.eb @@ -25,7 +25,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ - 'bafe0ac08e0a13e71568e5774dc83bd305d907159b4ceeb53d2e9f6e29462754', # otf2-2.0.tar.gz + 'bafe0ac08e0a13e71568e5774dc83bd305d907159b4ceeb53d2e9f6e29462754', # otf2-2.0.tar.gz ] builddependencies = [('SIONlib', '1.6.1', '-tools')] diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb index 5e43710d573..eeca405dee9 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.0-foss-2017a.eb @@ -25,7 +25,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] checksums = [ - 'bafe0ac08e0a13e71568e5774dc83bd305d907159b4ceeb53d2e9f6e29462754', # otf2-2.0.tar.gz + 'bafe0ac08e0a13e71568e5774dc83bd305d907159b4ceeb53d2e9f6e29462754', # otf2-2.0.tar.gz ] builddependencies = [('SIONlib', '1.7.1', '-tools')] diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb index 2f681f7b0ac..793f7e52b31 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.1-goolf-1.5.14.eb @@ -22,7 +22,7 @@ sources = ['scorep-%(version)s.tar.gz'] source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] checksums = [ - '6cf6c433c0a7456549bb4447d32d6846442fdbc364735e8f70644d66fdafc950', # scorep-1.2.1.tar.gz + '6cf6c433c0a7456549bb4447d32d6846442fdbc364735e8f70644d66fdafc950', # scorep-1.2.1.tar.gz ] # compiler toolchain depencies diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb index dde4eb01cf5..497f70b12d0 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb @@ -22,7 +22,7 @@ sources = ["scorep-%(version)s.tar.gz"] source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] checksums = [ - 'f3d705bec3d703c23f8ff2b831eab3bc6182710de20621aa761ecf6a6686751d', # scorep-1.2.3.tar.gz + 'f3d705bec3d703c23f8ff2b831eab3bc6182710de20621aa761ecf6a6686751d', # scorep-1.2.3.tar.gz ] # compiler toolchain depencies diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb index 5c40af34b02..a0d6b3442b4 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb @@ -24,7 +24,7 @@ sources = ["scorep-%(version)s.tar.gz"] source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] checksums = [ - 'c4ac89c88648fb843a20172b2a3b163561e5be39b7be8036754b420a464b7e28', # scorep-1.4.tar.gz + 'c4ac89c88648fb843a20172b2a3b163561e5be39b7be8036754b420a464b7e28', # scorep-1.4.tar.gz ] # compiler toolchain depencies diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb index 98e525c427a..cd65e74d88e 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-2.0.1-foss-2016a.eb @@ -31,8 +31,8 @@ patches = [ ] checksums = [ - 'e871cfdbcf51384e252037af2bf4d4e8c5200619263e85e3c8b7d211090911ef', # scorep-2.0.1.tar.gz - '0397fcb4a13e1fb3036beca25ba508801e30ab61c8ea4a737d80bc8c6072f18d', # Score-P-2.0.1_fix_score_configure.patch + 'e871cfdbcf51384e252037af2bf4d4e8c5200619263e85e3c8b7d211090911ef', # scorep-2.0.1.tar.gz + '0397fcb4a13e1fb3036beca25ba508801e30ab61c8ea4a737d80bc8c6072f18d', # Score-P-2.0.1_fix_score_configure.patch ] dependencies = [ From 3398955e6efb7d97e96297fa4608f8d6c6344edd Mon Sep 17 00:00:00 2001 From: jose_d Date: Wed, 3 Apr 2019 10:55:14 +0200 Subject: [PATCH 1052/5331] expat: code style --- .../easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb index 347dc48e678..a89464d7fc6 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.2.6-GCCcore-8.2.0.eb @@ -18,13 +18,13 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_BZ2] checksums = ['17b43c2716d521369f82fc2dc70f359860e90fa440bea65b3b85f0b246ea81f2'] -# since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf -# docbook2X needs XML-Parser and XML-Parser needs expat -# so circular dependency. "--without-docbook" breaks this circle. -configopts = ['--without-docbook'] - builddependencies = [ ('binutils', '2.31.1'), ] +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + moduleclass = 'tools' From 77c7affdf5b79d43027b0d2b732a9a5de7b83f1a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Apr 2019 16:20:52 +0200 Subject: [PATCH 1053/5331] adding easyconfigs: GATE-8.2-foss-2018b-Python-2.7.15.eb --- .../GATE/GATE-8.2-foss-2018b-Python-2.7.15.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATE/GATE-8.2-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/g/GATE/GATE-8.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GATE/GATE-8.2-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..7e85664f0e4 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-8.2-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,30 @@ +name = 'GATE' +version = '8.2' +versionsuffix = '-Python-2.7.15' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://www.opengatecollaboration.org/sites/default/files/'] +sources = ['Gate-%(version)s.tar.gz'] +patches = ['GATE-7.0_Makefile-prefix.patch'] +checksums = [ + 'edd8b1017310442bb6819a2815d61b63b1da1aef613fea2678aede134cbad741', # Gate-8.2.tar.gz + 'e72c230df1cdd05c07ac405b22bf26931abdcd3e5f7b942e9c88251ac24cc6af', # GATE-7.0_Makefile-prefix.patch +] + +builddependencies = [('CMake', '3.12.1')] +dependencies = [ + ('Geant4', '10.5'), + ('CLHEP', '2.4.1.0'), + ('ROOT', '6.14.06', versionsuffix), +] + +# enable extra capabilities (Davis requires Geant4 10.04 or newer) +configopts = "-DGATE_USE_OPTICAL=1 -DGATE_USE_DAVIS=1" + +moduleclass = 'cae' From 1be42a31ce7f9e948a62c2092d53d40b790c5f05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Apr 2019 16:34:21 +0200 Subject: [PATCH 1054/5331] add missing configopts in GATE 8.1 easyconfig to enable Davis feature --- .../g/GATE/GATE-8.1.p01-foss-2018b-Python-2.7.15.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/GATE/GATE-8.1.p01-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GATE/GATE-8.1.p01-foss-2018b-Python-2.7.15.eb index fed239034fa..4954e2293c6 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-8.1.p01-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-8.1.p01-foss-2018b-Python-2.7.15.eb @@ -28,4 +28,7 @@ dependencies = [ ('ROOT', '6.14.06', versionsuffix), ] +# enable extra capabilities (Davis requires Geant4 10.04 or newer) +configopts = "-DGATE_USE_OPTICAL=1 -DGATE_USE_DAVIS=1" + moduleclass = 'cae' From 8085a83fc88436cd060198fd79e98bc827a90162 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 3 Apr 2019 10:32:31 -0500 Subject: [PATCH 1055/5331] adding easyconfigs: PANDAseq-2.11-intel-2017b.eb, PANDAseq-2.11-foss-2017b.eb --- .../p/PANDAseq/PANDAseq-2.11-foss-2017b.eb | 34 +++++++++++++++++++ .../p/PANDAseq/PANDAseq-2.11-intel-2017b.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/p/PANDAseq/PANDAseq-2.11-foss-2017b.eb create mode 100644 easybuild/easyconfigs/p/PANDAseq/PANDAseq-2.11-intel-2017b.eb diff --git a/easybuild/easyconfigs/p/PANDAseq/PANDAseq-2.11-foss-2017b.eb b/easybuild/easyconfigs/p/PANDAseq/PANDAseq-2.11-foss-2017b.eb new file mode 100644 index 00000000000..71a41647ce9 --- /dev/null +++ b/easybuild/easyconfigs/p/PANDAseq/PANDAseq-2.11-foss-2017b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'PANDAseq' +version = '2.11' + +homepage = 'https://github.com/neufeld/pandaseq' +description = """PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded + in the sequence, and reconstruct an overlapping sequence.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/neufeld/%(namelower)s/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6e3e35d88c95f57d612d559e093656404c1d48c341a8baa6bef7bb0f09fc8f82'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +builddependencies = [ + ('Autotools', '20170619'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "./autogen.sh &&" + +sanity_check_paths = { + 'files': ['bin/pandaseq', 'bin/pandaseq-checkid', 'bin/pandaseq-hang', 'bin/pandaxs', 'bin/pandaseq-diff', + 'lib/libpandaseq.%s' % SHLIB_EXT, 'lib/libpandaseq.a', 'lib/pkgconfig/pandaseq-%(version_major)s.pc'], + 'dirs': ['include/pandaseq-%(version_major)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PANDAseq/PANDAseq-2.11-intel-2017b.eb b/easybuild/easyconfigs/p/PANDAseq/PANDAseq-2.11-intel-2017b.eb new file mode 100644 index 00000000000..9bd312a6bad --- /dev/null +++ b/easybuild/easyconfigs/p/PANDAseq/PANDAseq-2.11-intel-2017b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'PANDAseq' +version = '2.11' + +homepage = 'https://github.com/neufeld/pandaseq' +description = """PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded + in the sequence, and reconstruct an overlapping sequence.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://github.com/neufeld/%(namelower)s/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6e3e35d88c95f57d612d559e093656404c1d48c341a8baa6bef7bb0f09fc8f82'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +builddependencies = [ + ('Autotools', '20170619'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "./autogen.sh &&" + +sanity_check_paths = { + 'files': ['bin/pandaseq', 'bin/pandaseq-checkid', 'bin/pandaseq-hang', 'bin/pandaxs', 'bin/pandaseq-diff', + 'lib/libpandaseq.%s' % SHLIB_EXT, 'lib/libpandaseq.a', 'lib/pkgconfig/pandaseq-%(version_major)s.pc'], + 'dirs': ['include/pandaseq-%(version_major)s'], +} + +moduleclass = 'bio' From 1e69f8bd68b08a4cb8c8b2e4648bee2c0fcf8afc Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 3 Apr 2019 11:29:36 -0500 Subject: [PATCH 1056/5331] adding easyconfigs: Grace-5.1.25-foss-2017b-5build1.eb, Grace-5.1.25-intel-2017b-5build1.eb --- .../Grace/Grace-5.1.25-foss-2017b-5build1.eb | 37 +++++++++++++++++++ .../Grace/Grace-5.1.25-intel-2017b-5build1.eb | 37 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb create mode 100644 easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb new file mode 100644 index 00000000000..e5386963e73 --- /dev/null +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Grace' +version = '5.1.25' +versionsuffix = '-5build1' + +homepage = 'http://plasma-gate.weizmann.ac.il/Grace/' +description = """Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s%(versionsuffix)s.patch'] +checksums = [ + '751ab9917ed0f6232073c193aba74046037e185d73b77bab0f5af3e3ff1da2ac', # grace-5.1.25.tar.gz + '485fe80ef992e2068f5aa4bc94c0968b5bbef5491ff7c60c56152b61dcacbd46', # Grace-5.1.25-5build1.patch +] + +dependencies = [ + ('X11', '20171023'), + ('motif', '2.3.8'), + ('libpng', '1.6.32'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '1.5.2'), + ('FFTW', '3.3.6'), + ('netCDF', '4.5.0'), +] + +postinstallcmds = ['mv %(installdir)s/grace/* %(installdir)s && rmdir %(installdir)s/grace'] + +sanity_check_paths = { + 'files': ['lib/libgrace_np.a', 'bin/convcal', 'bin/fdf2fit', 'bin/grconvert', 'bin/xmgrace'], + 'dirs': ['include', 'fonts', 'templates'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb new file mode 100644 index 00000000000..29fc9ea0cf3 --- /dev/null +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Grace' +version = '5.1.25' +versionsuffix = '-5build1' + +homepage = 'http://plasma-gate.weizmann.ac.il/Grace/' +description = """Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s%(versionsuffix)s.patch'] +checksums = [ + '751ab9917ed0f6232073c193aba74046037e185d73b77bab0f5af3e3ff1da2ac', # grace-5.1.25.tar.gz + '485fe80ef992e2068f5aa4bc94c0968b5bbef5491ff7c60c56152b61dcacbd46', # Grace-5.1.25-5build1.patch +] + +dependencies = [ + ('X11', '20171023'), + ('motif', '2.3.8'), + ('libpng', '1.6.32'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '1.5.2'), + ('FFTW', '3.3.6'), + ('netCDF', '4.5.0'), +] + +postinstallcmds = ['mv %(installdir)s/grace/* %(installdir)s && rmdir %(installdir)s/grace'] + +sanity_check_paths = { + 'files': ['lib/libgrace_np.a', 'bin/convcal', 'bin/fdf2fit', 'bin/grconvert', 'bin/xmgrace'], + 'dirs': ['include', 'fonts', 'templates'], +} + +moduleclass = 'vis' From d9c6c74d22bf4799b9a7faa54e044f9ca3fb127d Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 3 Apr 2019 12:02:51 -0500 Subject: [PATCH 1057/5331] adding easyconfigs: PAML-4.9i-GCC-6.4.0-2.28.eb, PAML-4.9i-iccifort-2017.4.196-GCC-6.4.0-2.28.eb --- .../p/PAML/PAML-4.9i-GCC-6.4.0-2.28.eb | 27 +++++++++++++++++++ ...4.9i-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAML/PAML-4.9i-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/p/PAML/PAML-4.9i-iccifort-2017.4.196-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9i-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9i-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..9c7a9db52bf --- /dev/null +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9i-GCC-6.4.0-2.28.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'PAML' +version = '4.9i' + +homepage = 'http://abacus.gene.ucl.ac.uk/software/paml.html' +description = """PAML is a package of programs for phylogenetic + analyses of DNA or protein sequences using maximum likelihood.""" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} +toolchainopts = {'optarch': False} + +source_urls = ['http://abacus.gene.ucl.ac.uk/software'] +sources = ['%(namelower)s%(version)s.tgz'] +checksums = ['bbd28eec2971ef80a8751042cbfff0ee0b6e8b0ca3cfbb7d635c29dd23a934fb'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +start_dir = 'src' +files_to_copy = [(["baseml", "basemlg", "codeml", "pamp", "evolver", "yn00", "chi2"], 'bin')] + +sanity_check_paths = { + 'files': ['bin/baseml'], + 'dirs': ['bin'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9i-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9i-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..d37159ef9ce --- /dev/null +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9i-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'PAML' +version = '4.9i' + +homepage = 'http://abacus.gene.ucl.ac.uk/software/paml.html' +description = """PAML is a package of programs for phylogenetic + analyses of DNA or protein sequences using maximum likelihood.""" + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} +toolchainopts = {'optarch': False} + +source_urls = ['http://abacus.gene.ucl.ac.uk/software'] +sources = ['%(namelower)s%(version)s.tgz'] +checksums = ['bbd28eec2971ef80a8751042cbfff0ee0b6e8b0ca3cfbb7d635c29dd23a934fb'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +start_dir = 'src' +files_to_copy = [(["baseml", "basemlg", "codeml", "pamp", "evolver", "yn00", "chi2"], 'bin')] + +sanity_check_paths = { + 'files': ['bin/baseml'], + 'dirs': ['bin'] +} + +moduleclass = 'bio' From d4c9d0cea191804df08408458f335f82e01fbe7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Apr 2019 09:13:11 +0200 Subject: [PATCH 1058/5331] also consider archived easyconfigs in test_changed_files_pull_request --- test/easyconfigs/easyconfigs.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 57e7a9fb266..1a7b8eacc3b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -461,7 +461,17 @@ def test_changed_files_pull_request(self): if match: changed_ecs.append(match) else: - self.assertTrue(False, "Failed to find parsed easyconfig for %s" % ec_fn) + # if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR... + # so as a last resort, try to find the easyconfig file in __archive__ + easyconfigs_path = get_paths_for("easyconfigs")[0] + specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn)) + if len(specs) == 1: + ec = process_easyconfig(specs[0])[0] + changed_ecs.append(ec['ec']) + else: + error_msg = "Failed to find parsed easyconfig for %s" % ec_fn + error_msg += " (and could not isolate it in easyconfigs archive either)" + self.assertTrue(False, error_msg) # run checks on changed easyconfigs self.check_sha256_checksums(changed_ecs) From a6bd8fbcdd1bfdd5aa24e2db09d220a246f7a8d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Apr 2019 10:18:25 +0200 Subject: [PATCH 1059/5331] enable use_pip in GTDB-Tk easyconfig --- .../g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb index 2f23e48dd30..f3f78a99363 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb @@ -20,7 +20,7 @@ dependencies = [ ('FastTree', '2.1.10'), ] -#use_pip = True +use_pip = True exts_list = [ ('future', '0.17.1', { From 3e9532b6b2a096dc4c6d76eee423f1e21a9d697c Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 4 Apr 2019 10:47:51 +0200 Subject: [PATCH 1060/5331] Rename arrow to Arrow --- .../Arrow-0.7.1-intel-2017b-Python-3.6.3.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/{arrow/arrow-0.7.1-intel-2017b-Python-3.6.3.eb => Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb} (98%) diff --git a/easybuild/easyconfigs/a/arrow/arrow-0.7.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb similarity index 98% rename from easybuild/easyconfigs/a/arrow/arrow-0.7.1-intel-2017b-Python-3.6.3.eb rename to easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb index 23c5fa9a989..3c43fc0ef5a 100644 --- a/easybuild/easyconfigs/a/arrow/arrow-0.7.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb @@ -1,6 +1,6 @@ easyblock = 'CMakeMake' -name = 'arrow' +name = 'Arrow' version = '0.7.1' versionsuffix = '-Python-%(pyver)s' From 8b65ac2e5b81babb2e66508dcef75204802f49eb Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 4 Apr 2019 10:52:43 +0200 Subject: [PATCH 1061/5331] Fix bat to use Arrow --- .../easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb index 0d6e665e2f3..14e32e948ee 100644 --- a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb @@ -14,7 +14,7 @@ dependencies = [ ('Python', '3.6.3'), ('PyYAML', '3.12', versionsuffix), ('scikit-learn', '0.19.1', versionsuffix), - ('arrow', '0.7.1', versionsuffix), + ('Arrow', '0.7.1', versionsuffix), ('Spark', '2.2.0', '-Hadoop-2.6-Java-1.8.0_152%(versionsuffix)s'), ] From b3c35d845a90a5acd49a7ead529bc491ee3a60a4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 4 Apr 2019 12:04:33 +0200 Subject: [PATCH 1062/5331] Use PythonBundle --- .../a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb | 4 ++++ .../easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb | 5 +++-- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb index 3c43fc0ef5a..c34f5094b3b 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb @@ -28,6 +28,10 @@ start_dir = 'cpp' separate_build_dir = True exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} exts_list = [ ('pyarrow', version, { # The python bindings of Arrow diff --git a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb index 14e32e948ee..b8e438ba56f 100644 --- a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'bat' version = '0.3.3' @@ -18,7 +18,8 @@ dependencies = [ ('Spark', '2.2.0', '-Hadoop-2.6-Java-1.8.0_152%(versionsuffix)s'), ] -exts_defaultclass = 'PythonPackage' +use_pip = True +download_dep_fail = True exts_list = [ ('requests', '2.18.4', { From bb81aa2ebc40a950499edeb38947b9ea00ccfbc1 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 4 Apr 2019 12:34:59 +0200 Subject: [PATCH 1063/5331] Fix tests --- .../easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb index b8e438ba56f..49f5784e439 100644 --- a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb @@ -19,7 +19,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True exts_list = [ ('requests', '2.18.4', { From fdf9c1d3b74cbf35a842a5115b94aae70d5596f8 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 4 Apr 2019 13:11:34 +0200 Subject: [PATCH 1064/5331] Fix remarks --- .../b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb index 49f5784e439..7e3c3e59cb8 100644 --- a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb @@ -42,11 +42,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'] -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'data' From dcab125b5134298a4126922f86a8d4ba33aff49b Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 4 Apr 2019 13:55:51 +0200 Subject: [PATCH 1065/5331] Don't use pip for Arrow --- .../easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb index c34f5094b3b..75ad9458c57 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb @@ -30,7 +30,6 @@ separate_build_dir = True exts_defaultclass = 'PythonPackage' exts_default_options = { 'download_dep_fail': True, - 'use_pip': True, } exts_list = [ From 885d7484dbac979516d28f078909bed485e7ca3a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 4 Apr 2019 14:21:56 +0200 Subject: [PATCH 1066/5331] Add urllib3 dep to bat --- .../easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb index 7e3c3e59cb8..c09d1241dbb 100644 --- a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb @@ -21,6 +21,10 @@ dependencies = [ use_pip = True exts_list = [ + ('urllib3', '1.22', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], + }), ('requests', '2.18.4', { 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], From 746c2c8f2f7e31f0090edf894f34d664c92883d6 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Thu, 4 Apr 2019 14:34:14 +0100 Subject: [PATCH 1067/5331] adding easyconfigs: VirtualGL-2.6.1-foss-2018b.eb --- .../v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb new file mode 100644 index 00000000000..84f60047fda --- /dev/null +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb @@ -0,0 +1,47 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'VirtualGL' +version = '2.6.1' + +homepage = 'https://virtualgl.org/' +description = """VirtualGL is an open source toolkit that gives any Linux or +Unix remote display software the ability to run OpenGL applications with full +hardware acceleration. Some remote display software cannot be used with OpenGL +applications at all. Other remote display software forces OpenGL applications +to use a slow, software-only renderer, to the detriment of performance as well +as compatibility. The traditional method of displaying OpenGL applications to +an X server on a different machine (indirect rendering) supports hardware +acceleration, but this approach requires that all of the OpenGL commands and +3D data be sent over the network to be rendered. That is not a tenable +proposition unless the 3D data is relatively small and static, unless the +network is very fast, and unless the OpenGL application is specifically tuned +for a remote X-Windows environment.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('libjpeg-turbo', '2.0.0'), + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), +] +builddependencies = [('CMake', '3.12.1')] + +binaries = [ + 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', + 'vglclient', 'vglconfig', 'vglconnect', 'vglgenkey', 'vgllogin', 'vglrun', + 'vglserver_config' +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binaries], + 'dirs': ['lib64', 'share', 'include'], +} + +moduleclass = 'vis' From 5f23cb888ccaf656ab9442d7dc60d266fb34f3d0 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Thu, 4 Apr 2019 14:45:20 +0100 Subject: [PATCH 1068/5331] Checksum added --- easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb index 84f60047fda..07324de9678 100644 --- a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb @@ -24,6 +24,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['38d1d32efe97adaea6754f4559520454d4f0d2400964ebc59f8ac01f0146e23f'] dependencies = [ ('libjpeg-turbo', '2.0.0'), From 5e4456c88cd494210c4929c3c04238292c70da56 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Thu, 4 Apr 2019 17:14:25 +0200 Subject: [PATCH 1069/5331] IPython: v5.8.0 with foss2018b Python2 --- .../IPython-5.8.0-foss-2018b-Python-2.7.15.eb | 244 ++++++++++++++++++ 1 file changed, 244 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..dab61d49acd --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,244 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '5.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), + ('ZeroMQ', '4.2.5'), + ('matplotlib', '2.2.3', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('Pygments', '2.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'checksums': ['5ffada19f6203563680669ee7f53b64dabbeb100eb51b61996085e99c03b284a'], + }), + ('ipython_genutils', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('certifi', '2018.11.29', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + }), + ('pexpect', '4.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('futures', '3.2.0', { + 'modulename': 'concurrent.futures', + 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], + 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), + ('ptyprocess', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('scandir', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], + }), + ('pathlib2', '2.3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], + }), + ('pickleshare', '0.7.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('traitlets', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], + }), + ('parso', '0.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], + 'checksums': ['68406ebd7eafe17f8e40e15a84b56848eccbf27d7c1feb89e93d8fca395706db'], + }), + ('jedi', '0.13.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], + 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], + }), + ('configparser', '3.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], + 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], + }), + ('testpath', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], + 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('wcwidth', '0.1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + }), + ('prompt_toolkit', '1.0.15', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], + 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], + }), + ('MarkupSafe', '1.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('ipywidgets', '7.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + 'checksums': ['a3e224f430163f767047ab9a042fc55adbcab0c24bbe6cf9f306c4f89fdf0ba3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/j/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('Send2Trash', '1.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], + 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], + }), + ('webencodings', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], + 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], + }), + ('bleach', '3.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], + 'checksums': ['3fdf7f77adcf649c9911387df51254b813185e32b2c6619f690b593a617e19fa'], + }), + ('pyrsistent', '0.14.11', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyrsistent/'], + 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], + }), + ('attrs', '19.1.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], + }), + ('vcversioner', '2.16.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/v/vcversioner/'], + 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], + }), + ('jsonschema', '3.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], + }), + ('pandocfilters', '1.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], + }), + ('pyzmq', '18.0.0', { + 'modulename': 'zmq', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], + 'checksums': ['b30c339eb58355f51f4f54dd61d785f1ff58c86bca1c3a5916977631d121867b'], + }), + ('entrypoints', '0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('jupyter_core', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], + }), + ('nbformat', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], + }), + ('mistune', '0.8.4', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('defusedxml', '0.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], + 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], + }), + ('nbconvert', '5.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], + }), + ('terminado', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], + }), + ('tornado', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], + }), + ('jupyter_client', '5.2.4', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + 'checksums': ['b5f9cb06105c1d2d30719db5ffb3ea67da60919fb68deaefa583deccd8813551'], + }), + ('backcall', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], + 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], + }), + ('ipykernel', '4.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + 'checksums': ['699103c8e64886e3ec7053f2a6aa83bb90426063526f63a818732ff385202bad'], + }), + ('prometheus_client', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prometheus_client/'], + 'checksums': ['1b38b958750f66f208bcd9ab92a633c0c994d8859c831f7abc1f46724fcee490'], + }), + ('notebook', '5.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + 'checksums': ['d908673a4010787625c8952e91a22adf737db031f2aa0793ad92f6558918a74a'], + }), + ('widgetsnbextension', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + 'checksums': ['fa618be8435447a017fd1bf2c7ae922d0428056cfc7449f7a8641edf76b48265'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "iptest", +] + +moduleclass = 'tools' From 3fcf073357788a84ceef823561f428e9660ffff3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Apr 2019 17:31:11 +0200 Subject: [PATCH 1070/5331] {bio}[intel/2018b] RNAIndel v0.3.0, Pysam v0.15.1 w/ Python 3.6.6 --- .../Pysam-0.15.1-intel-2018b-Python-3.6.6.eb | 42 +++++++++++++++++++ ...RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb | 31 ++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..df802ef6580 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Erich Birngruber +# Gregor Mendel Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.15.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['12221285af17e32b8f3fed033f90c6177a798afe41420eb5c3352d4e18ee12ed'] + +dependencies = [ + ('Python', '3.6.6'), + ('ncurses', '6.1'), + ('cURL', '7.60.0'), + ('XZ', '5.2.4'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..8b2eeb87e55 --- /dev/null +++ b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'RNAIndel' +version = '0.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/stjude/RNAIndel' +description = """RNAIndel calls coding indels and classifies them into somatic, germline, + and artifact from tumor RNA-Seq data.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8f93e9cf53adfb2aa17a6d4c968d2d7ce8d73f8fcffc8934b76dd03876b195be'] + +dependencies = [ + ('Python', '3.6.6'), + ('Pysam', '0.15.1', versionsuffix), + ('scikit-learn', '0.20.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 05bc6b20f9393e0a05febd7059257f8f70f62455 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 4 Apr 2019 09:02:18 -0700 Subject: [PATCH 1071/5331] add binutils fix checksums, line length --- .../e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb | 20 +++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb index f518fe65d32..33f744ee8f9 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb @@ -2,7 +2,8 @@ # George Tsouloupas # Fotis Georgatos # -# This work implements a part of the HPCBIOS project and is a component of the policy: +# This work implements a part of the HPCBIOS project and is a component +# of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html # foss-2016b modified by: # Adam Huffman @@ -13,9 +14,9 @@ name = 'EMBOSS' version = '6.6.0' homepage = 'http://emboss.sourceforge.net/' -description = """EMBOSS is 'The European Molecular Biology Open Software Suite'. - EMBOSS is a free Open Source software analysis package specially developed for - the needs of the molecular biology (e.g. EMBnet) user community.""" +description = """EMBOSS is 'The European Molecular Biology Open Software Suite' +. EMBOSS is a free Open Source software analysis package specially developed + for the needs of the molecular biology (e.g. EMBnet) user community.""" toolchain = {'name': 'foss', 'version': '2018b'} @@ -24,10 +25,15 @@ source_urls = [ 'ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0', ] sources = [SOURCE_TAR_GZ] -patches = ['EMBOSS-6.6.0_disable-embossupdate.patch'] +patches = ['%(name)s-%(version)s_disable-embossupdate.patch'] checksums = [ '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', # EMBOSS-6.6.0.tar.gz - 'b9beee4340a05289f938b4cf6b041459209cdf922c6295aa01cff1998bfb6d9c', # EMBOSS-6.6.0_disable-embossupdate.patch + 'c72977f710b3146d5880b4aff91c0565f4ab5fd8f695c77ac53a5c0b08216b25', # EMBOSS-6.6.0_disable-embossupdate.patch +] + +builddependencies = [ + ('binutils', '2.30'), + ('CMake', '3.11.4') ] dependencies = [ @@ -40,3 +46,5 @@ configopts = " --with-hpdf=$EBROOTLIBHARU " # jemboss.jar does not build in a parallel build parallel = 1 + +moduleclass = 'bio' From 04a5d8a39b0c0210f87bbfba48fab0c15da24c5c Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 4 Apr 2019 09:31:19 -0700 Subject: [PATCH 1072/5331] add binutils fix checksums, line length --- .../l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb index f42cd8ef545..88911a2c9a1 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb @@ -1,11 +1,13 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# EasyBuild easyconfig # # Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA -# Authors:: George Tsouloupas , Fotis Georgatos +# Authors:: George Tsouloupas , +# Fotis Georgatos # License:: MIT/GPL # $Id$ # -# This work implements a part of the HPCBIOS project and is a component of the policy: +# This work implements a part of the HPCBIOS project and is a component of the +# policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## # Modified for foss-2016b by: @@ -18,7 +20,8 @@ name = 'libharu' version = '2.3.0' homepage = 'http://libharu.org/' -description = """libHaru is a free, cross platform, open source library for generating PDF files.""" +description = """libHaru is a free, cross platform, open source library for + generating PDF files.""" toolchain = {'name': 'GCCcore', 'version': '7.3.0'} @@ -28,7 +31,10 @@ checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] dependencies = [('libpng', '1.6.34')] -builddependencies = [('CMake', '3.11.4')] +builddependencies = [ + ('binutils', '2.30'), + ('CMake', '3.11.4') +] parallel = 1 From 1730a9b8c4179055ba79049db9622dcf2121cbc2 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 4 Apr 2019 10:08:57 -0700 Subject: [PATCH 1073/5331] add binutils fix checksums, line length --- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb index 33f744ee8f9..784aee829bf 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb @@ -31,10 +31,7 @@ checksums = [ 'c72977f710b3146d5880b4aff91c0565f4ab5fd8f695c77ac53a5c0b08216b25', # EMBOSS-6.6.0_disable-embossupdate.patch ] -builddependencies = [ - ('binutils', '2.30'), - ('CMake', '3.11.4') -] +builddependencies = [('CMake', '3.11.4')] dependencies = [ ('X11', '20180604'), From 82825d65d8f70ff1a7efd59f385d715857b0a261 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Apr 2019 20:10:31 +0200 Subject: [PATCH 1074/5331] add missing Java dependency for RNAIndel + enhance sanity check --- .../r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb index 8b2eeb87e55..7cc11725a88 100644 --- a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb @@ -18,14 +18,17 @@ dependencies = [ ('Python', '3.6.6'), ('Pysam', '0.15.1', versionsuffix), ('scikit-learn', '0.20.0', versionsuffix), + ('Java', '1.8', '', True), ] download_dep_fail = True use_pip = True sanity_check_paths = { - 'files': [], + 'files': ['bin/rnaindel'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["rnaindel --help"] + moduleclass = 'bio' From 30a1e03718f9109f9c81da25c6a8265119eee8da Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 4 Apr 2019 13:20:27 -0500 Subject: [PATCH 1075/5331] adding easyconfigs: MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb, MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb --- ....4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb | 41 +++++++++++++++++++ ...0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb | 41 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb new file mode 100644 index 00000000000..a9e9745531f --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.0.4' +versionsuffix = '-Perl-%(perlver)s-Python-%(pyver)s' + +homepage = 'http://meme-suite.org' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = [ + 'b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4', # meme-5.0.4.tar.gz +] + +dependencies = [ + ('libxml2', '2.9.7'), + ('libxslt', '1.1.32'), + ('zlib', '1.2.11'), + ('Perl', '5.26.0'), + ('Python', '2.7.14') +] + +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python' + +# Remove Python3 script +postinstallcmds = ['rm %(installdir)s/bin/dreme-py3'] + +sanity_check_paths = { + 'files': ["bin/meme", "bin/dreme", "bin/meme-chip"], + 'dirs': ["lib"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb new file mode 100644 index 00000000000..02987e87fa1 --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.0.4' +versionsuffix = '-Perl-%(perlver)s-Python-%(pyver)s' + +homepage = 'http://meme-suite.org' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = [ + 'b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4', # meme-5.0.4.tar.gz +] + +dependencies = [ + ('libxml2', '2.9.7'), + ('libxslt', '1.1.32'), + ('zlib', '1.2.11'), + ('Perl', '5.26.0'), + ('Python', '3.6.3') +] + +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' + +# Remove Python2 script +postinstallcmds = ['rm %(installdir)s/bin/dreme'] + +sanity_check_paths = { + 'files': ["bin/meme", "bin/dreme-py3", "bin/meme-chip"], + 'dirs': ["lib"], +} + +moduleclass = 'bio' From f216b39441128e54c71a541fb02757c1a69156c4 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Thu, 4 Apr 2019 20:26:53 +0200 Subject: [PATCH 1076/5331] Fix bat --- .../b/bat/bat-0.3.3-fix-pyspark.patch | 13 +++++++++++++ .../bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb | 19 ++++++++++++++++--- 2 files changed, 29 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/b/bat/bat-0.3.3-fix-pyspark.patch diff --git a/easybuild/easyconfigs/b/bat/bat-0.3.3-fix-pyspark.patch b/easybuild/easyconfigs/b/bat/bat-0.3.3-fix-pyspark.patch new file mode 100644 index 00000000000..60977bdfe7d --- /dev/null +++ b/easybuild/easyconfigs/b/bat/bat-0.3.3-fix-pyspark.patch @@ -0,0 +1,13 @@ +Fix typo: spark -> pyspark (both exist) +diff -ur bat-0.3.3.orig/setup.py bat-0.3.3/setup.py +--- bat-0.3.3.orig/setup.py 2017-10-19 00:40:21.000000000 +0200 ++++ bat-0.3.3/setup.py 2019-04-04 20:18:38.006386077 +0200 +@@ -39,7 +39,7 @@ + 'scipy', + 'pandas', + 'scikit-learn', +- 'spark', ++ 'pyspark', + 'pyarrow' + ], + extras_require={ diff --git a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb index c09d1241dbb..c687edfaa09 100644 --- a/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/b/bat/bat-0.3.3-intel-2017b-Python-3.6.3.eb @@ -21,6 +21,14 @@ dependencies = [ use_pip = True exts_list = [ + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('certifi', '2018.1.18', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['edbc3f203427eef571f79a7692bb160a2b0f7ccaa31953e99bd17e307cf63f7d'], + }), ('urllib3', '1.22', { 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], @@ -31,18 +39,23 @@ exts_list = [ }), ('pathtools', '0.1.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pathtools'], - 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], # pathtools-0.1.2.tar.gz + 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], }), ('argh', '0.26.2', { 'source_urls': ['https://pypi.python.org/packages/source/a/argh'], - 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], # argh-0.26.2.tar.gz + 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], }), ('watchdog', '0.8.3', { 'source_urls': ['https://pypi.python.org/packages/source/w/watchdog'], - 'checksums': ['7e65882adb7746039b6f3876ee174952f8eaaa34491ba34333ddf1fe35de4162'], # watchdog-0.8.3.tar.gz + 'checksums': ['7e65882adb7746039b6f3876ee174952f8eaaa34491ba34333ddf1fe35de4162'], }), (name, version, { + 'patches': ['bat-0.3.3-fix-pyspark.patch'], 'source_urls': ['https://pypi.python.org/packages/source/b/bat'], + 'checksums': [ + 'ebc012826c23b25a890d88eb355467940c77ac50ef85fbd891a6e8ddb2620d44', # bat-0.3.3.tar.gz + '5ed4fdea82733ad8a47707867803b9522100307d1bcd0c1fd8f624c778020256', # bat-0.3.3-fix-pyspark.patch + ], }), ] From ef61382a3b0804dc012c7d8116c175f801267a12 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 4 Apr 2019 13:29:49 -0500 Subject: [PATCH 1077/5331] Removed obsolete EC files --- .../m/MEME/MEME-5.0.4-foss-2017b.eb | 31 ------------------- .../m/MEME/MEME-5.0.4-intel-2017b.eb | 31 ------------------- 2 files changed, 62 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb delete mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb deleted file mode 100644 index e3999060dff..00000000000 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MEME' -version = '5.0.4' - -homepage = 'http://meme-suite.org' -description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or - GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using - MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate - motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment - using SpaMo or CentriMo.""" - - -toolchain = {'name': 'foss', 'version': '2017b'} - -source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] -checksums = ['b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4'] - -dependencies = [ - ('libxml2', '2.9.7'), - ('libxslt', '1.1.32'), - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ["bin/meme"], - 'dirs': ["lib"], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb deleted file mode 100644 index 0e826f73806..00000000000 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'MEME' -version = '5.0.4' - -homepage = 'http://meme-suite.org' -description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or - GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using - MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate - motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment - using SpaMo or CentriMo.""" - - -toolchain = {'name': 'intel', 'version': '2017b'} - -source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] -checksums = ['b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4'] - -dependencies = [ - ('libxml2', '2.9.7'), - ('libxslt', '1.1.32'), - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ["bin/meme"], - 'dirs': ["lib"], -} - -moduleclass = 'bio' From 445a4631da97f4086f178445ce26e08eda9a77c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Apr 2019 20:35:56 +0200 Subject: [PATCH 1078/5331] {lib}[intel/2018b] POT v0.5.1 w/ Python 3.6.6 --- .../POT/POT-0.5.1-intel-2018b-Python-3.6.6.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/POT/POT-0.5.1-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/POT/POT-0.5.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/POT/POT-0.5.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..8fa9aca152f --- /dev/null +++ b/easybuild/easyconfigs/p/POT/POT-0.5.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'POT' +version = '0.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/rflamary/POT' +description = """POT (Python Optimal Transport) is a Python library provide several solvers for optimization problems + related to Optimal Transport for signal, image processing and machine learning.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3f8584b153e9850a83267b1b3f88e43ae0e5f68ae57ee79da9390bc19a93f836'] + +dependencies = [ + ('Python', '3.6.6'), + ('matplotlib', '3.0.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'ot'} + +moduleclass = 'lib' From d772e298f771f3d719e8e24832ab02a13b547ad8 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 4 Apr 2019 13:39:40 -0500 Subject: [PATCH 1079/5331] Add intel EC files --- ...4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb | 40 ++++++++++++++++++ ....4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb | 41 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb new file mode 100644 index 00000000000..056d3f58155 --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.0.4' +versionsuffix = '-Perl-%(perlver)s-Python-%(pyver)s' + +homepage = 'http://meme-suite.org' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = [ + 'b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4', # meme-5.0.4.tar.gz +] + +dependencies = [ + ('libxml2', '2.9.7'), + ('libxslt', '1.1.32'), + ('zlib', '1.2.11'), + ('Perl', '5.26.0'), + ('Python', '2.7.14') +] + +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python' + +# Remove Python3 script +postinstallcmds = ['rm %(installdir)s/bin/dreme-py3'] + +sanity_check_paths = { + 'files': ["bin/meme", "bin/dreme", "bin/meme-chip"], + 'dirs': ["lib"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb new file mode 100644 index 00000000000..11405742ef1 --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.0.4' +versionsuffix = '-Perl-%(perlver)s-Python-%(pyver)s' + +homepage = 'http://meme-suite.org' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = [ + 'b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4', # meme-5.0.4.tar.gz +] + +dependencies = [ + ('libxml2', '2.9.7'), + ('libxslt', '1.1.32'), + ('zlib', '1.2.11'), + ('Perl', '5.26.0'), + ('Python', '3.6.3') +] + +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' + +# Remove Python2 script +postinstallcmds = ['rm %(installdir)s/bin/dreme'] + +sanity_check_paths = { + 'files': ["bin/meme", "bin/dreme-py3", "bin/meme-chip"], + 'dirs': ["lib"], +} + +moduleclass = 'bio' From 8a615bb5e96f266c34696a988a1d86cad92c3f46 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 4 Apr 2019 13:42:48 -0500 Subject: [PATCH 1080/5331] Fix style --- .../MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb | 5 +---- .../m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb | 5 +---- .../MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb | 4 +--- .../MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb | 5 +---- 4 files changed, 4 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb index a9e9745531f..b3c0c3c833f 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb @@ -11,14 +11,11 @@ description = """The MEME Suite allows you to: * discover motifs using MEME, DRE motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.""" - toolchain = {'name': 'foss', 'version': '2017b'} source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] sources = ['%(namelower)s-%(version)s.tar.gz'] -checksums = [ - 'b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4', # meme-5.0.4.tar.gz -] +checksums = ['b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4'] dependencies = [ ('libxml2', '2.9.7'), diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb index 02987e87fa1..431ab54df3f 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb @@ -11,14 +11,11 @@ description = """The MEME Suite allows you to: * discover motifs using MEME, DRE motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.""" - toolchain = {'name': 'foss', 'version': '2017b'} source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] sources = ['%(namelower)s-%(version)s.tar.gz'] -checksums = [ - 'b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4', # meme-5.0.4.tar.gz -] +checksums = ['b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4'] dependencies = [ ('libxml2', '2.9.7'), diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb index 056d3f58155..69b1bb86188 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb @@ -15,9 +15,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] sources = ['%(namelower)s-%(version)s.tar.gz'] -checksums = [ - 'b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4', # meme-5.0.4.tar.gz -] +checksums = ['b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4'] dependencies = [ ('libxml2', '2.9.7'), diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb index 11405742ef1..6d5725edbd0 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb @@ -11,14 +11,11 @@ description = """The MEME Suite allows you to: * discover motifs using MEME, DRE motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.""" - toolchain = {'name': 'intel', 'version': '2017b'} source_urls = ['http://meme-suite.org/meme-software/%(version)s/'] sources = ['%(namelower)s-%(version)s.tar.gz'] -checksums = [ - 'b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4', # meme-5.0.4.tar.gz -] +checksums = ['b5e067c8b9d9fe4a2a35d4f4d053714beb380c0c06b54ed94737dd31d93c4cf4'] dependencies = [ ('libxml2', '2.9.7'), From 9e264cdc064807535f3b0e0910018fa70f68ed50 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 4 Apr 2019 14:24:22 -0500 Subject: [PATCH 1081/5331] change the sanity_check_paths --- easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb | 2 +- .../snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb index 54a9fb3994a..e495f15dba4 100644 --- a/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb @@ -32,7 +32,7 @@ files_to_copy = [ sanity_check_paths = { 'files': ["bin/snap", "bin/forge", "bin/zoe-loop"], - 'dirs': [""], + 'dirs': [], } modextravars = {'ZOE': '%(installdir)s/Zoe'} diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index dff22109e19..7e8e4eadd97 100644 --- a/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -32,7 +32,7 @@ files_to_copy = [ sanity_check_paths = { 'files': ["bin/snap", "bin/forge", "bin/zoe-loop"], - 'dirs': [""], + 'dirs': [], } modextravars = {'ZOE': '%(installdir)s/Zoe'} From a66d09ea77a55351084f812f24703027714d9d8f Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 4 Apr 2019 14:27:44 -0500 Subject: [PATCH 1082/5331] rename the patch file name, add the version number --- .../easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb | 4 ++-- .../snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 4 ++-- ...ection.patch => snap_2013-11-29_makefile_correction.patch} | 0 3 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/s/snap/{snap_makefile_correction.patch => snap_2013-11-29_makefile_correction.patch} (100%) diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb index e495f15dba4..6d68356f0ae 100644 --- a/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb @@ -16,10 +16,10 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = ['http://korflab.ucdavis.edu/Software'] sources = [SOURCE_TAR_GZ] -patches = ['snap_makefile_correction.patch'] +patches = ['%(name)s_%(version)s_makefile_correction.patch'] checksums = [ 'e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a', # snap-2013-11-29.tar.gz - '02ea6dc6006ca5a5173dd2fc6a01b679a0910a68e0b51d00b7b9f732e4f79dcc', # snap_makefile_correction.patch + '02ea6dc6006ca5a5173dd2fc6a01b679a0910a68e0b51d00b7b9f732e4f79dcc', # snap_2013-11-29_makefile_correction.patch ] files_to_copy = [ diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 7e8e4eadd97..8f16265ffc2 100644 --- a/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -16,10 +16,10 @@ toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} source_urls = ['http://korflab.ucdavis.edu/Software'] sources = [SOURCE_TAR_GZ] -patches = ['snap_makefile_correction.patch'] +patches = ['%(name)s_%(version)s_makefile_correction.patch'] checksums = [ 'e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a', # snap-2013-11-29.tar.gz - '02ea6dc6006ca5a5173dd2fc6a01b679a0910a68e0b51d00b7b9f732e4f79dcc', # snap_makefile_correction.patch + '02ea6dc6006ca5a5173dd2fc6a01b679a0910a68e0b51d00b7b9f732e4f79dcc', # snap_2013-11-29_makefile_correction.patch ] files_to_copy = [ diff --git a/easybuild/easyconfigs/s/snap/snap_makefile_correction.patch b/easybuild/easyconfigs/s/snap/snap_2013-11-29_makefile_correction.patch similarity index 100% rename from easybuild/easyconfigs/s/snap/snap_makefile_correction.patch rename to easybuild/easyconfigs/s/snap/snap_2013-11-29_makefile_correction.patch From 8371a5c08874d29bfba03588f7216bc16096f65f Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Thu, 4 Apr 2019 14:37:31 -0500 Subject: [PATCH 1083/5331] add the Zoe folder to sanity_check_paths --- easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb | 2 +- .../snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb index 6d68356f0ae..0ee58e0b052 100644 --- a/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb @@ -32,7 +32,7 @@ files_to_copy = [ sanity_check_paths = { 'files': ["bin/snap", "bin/forge", "bin/zoe-loop"], - 'dirs': [], + 'dirs': ["Zoe"], } modextravars = {'ZOE': '%(installdir)s/Zoe'} diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 8f16265ffc2..ffc5f1222ad 100644 --- a/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -32,7 +32,7 @@ files_to_copy = [ sanity_check_paths = { 'files': ["bin/snap", "bin/forge", "bin/zoe-loop"], - 'dirs': [], + 'dirs': ["Zoe"], } modextravars = {'ZOE': '%(installdir)s/Zoe'} From dca0c8106177253ffc662900011fabcdb20146f1 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 4 Apr 2019 15:50:25 -0500 Subject: [PATCH 1084/5331] Do not fail if script does not exists --- .../m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb | 2 +- .../m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb | 2 +- .../m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb | 2 +- .../m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb index b3c0c3c833f..925eb8e2cfa 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-2.7.14.eb @@ -28,7 +28,7 @@ dependencies = [ configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python' # Remove Python3 script -postinstallcmds = ['rm %(installdir)s/bin/dreme-py3'] +postinstallcmds = ['rm -f %(installdir)s/bin/dreme-py3'] sanity_check_paths = { 'files': ["bin/meme", "bin/dreme", "bin/meme-chip"], diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb index 431ab54df3f..6e4591bd5b3 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-foss-2017b-Perl-5.26.0-Python-3.6.3.eb @@ -28,7 +28,7 @@ dependencies = [ configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' # Remove Python2 script -postinstallcmds = ['rm %(installdir)s/bin/dreme'] +postinstallcmds = ['rm -f %(installdir)s/bin/dreme'] sanity_check_paths = { 'files': ["bin/meme", "bin/dreme-py3", "bin/meme-chip"], diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb index 69b1bb86188..554c028a3d8 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-2.7.14.eb @@ -28,7 +28,7 @@ dependencies = [ configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python' # Remove Python3 script -postinstallcmds = ['rm %(installdir)s/bin/dreme-py3'] +postinstallcmds = ['rm -f %(installdir)s/bin/dreme-py3'] sanity_check_paths = { 'files': ["bin/meme", "bin/dreme", "bin/meme-chip"], diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb index 6d5725edbd0..00f9a477f08 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.0.4-intel-2017b-Perl-5.26.0-Python-3.6.3.eb @@ -28,7 +28,7 @@ dependencies = [ configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' # Remove Python2 script -postinstallcmds = ['rm %(installdir)s/bin/dreme'] +postinstallcmds = ['rm -f %(installdir)s/bin/dreme'] sanity_check_paths = { 'files': ["bin/meme", "bin/dreme-py3", "bin/meme-chip"], From 95f4d7cc8356e00e5a86dfabab054f3b3f9ea5b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Apr 2019 10:17:10 +0200 Subject: [PATCH 1085/5331] use https:// in homepage & source_urls for recent OpenMPI 2.x, 3.x & 4.x easyconfigs --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb | 6 +++--- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb | 6 +++--- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb | 6 +++--- .../OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 6 +++--- .../o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb | 7 +++---- .../OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 6 +++--- .../easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb | 7 +++---- .../easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017.02.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017b.eb | 4 ++-- .../OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 6 ++---- .../easyconfigs/o/OpenMPI/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-2.1.2-gcccuda-2018a.eb | 2 +- .../OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 4 +--- .../OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb | 4 +--- .../easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb | 4 ++-- .../OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb | 4 ++-- .../o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb | 4 ++-- .../o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb | 4 ++-- .../OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 4 ++-- .../o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb | 4 ++-- .../o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb | 4 ++-- .../easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb | 4 ++-- 28 files changed, 61 insertions(+), 71 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb index e3bfbb19387..fd242bdb887 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.0.0' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '5.2.0'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['6603d39a68d14bc7c44bba3e439289a86ddabd5ab1e8b570916d68a140484c00'] dependencies = [('hwloc', '1.11.3')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb index bf0ea1fac7f..2e78f0b5776 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-GCC-6.2.0-2.27.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.0.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['5c576eafb2ff10c338c67549ba1cf299a704bd052f648f4b7854115e4d07fabd'] dependencies = [('hwloc', '1.11.4')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb index 8932952ef8c..caf6050e22e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-gcccuda-2016.10.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.0.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'gcccuda', 'version': '2016.10'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['5c576eafb2ff10c338c67549ba1cf299a704bd052f648f4b7854115e4d07fabd'] dependencies = [('hwloc', '1.11.4')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index e5da8ab4028..35384ba54f6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.1-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.0.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-5.4.0-2.26'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['5c576eafb2ff10c338c67549ba1cf299a704bd052f648f4b7854115e4d07fabd'] dependencies = [('hwloc', '1.11.4')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb index fa054e97d75..4a63cacafdf 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27-opa.eb @@ -4,15 +4,14 @@ name = 'OpenMPI' version = '2.0.2' versionsuffix = '-opa' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -checksums = ['886698becc5bea8c151c0af2074b8392'] +checksums = ['32914cc64780d3980066f3be3920b028cd381c94d1262a55415fc1d002bae0a5'] dependencies = [('hwloc', '1.11.5')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb index 8a9cb98af56..b2e8a0edf31 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-GCC-6.3.0-2.27.eb @@ -3,15 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.0.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -checksums = ['886698becc5bea8c151c0af2074b8392'] +checksums = ['32914cc64780d3980066f3be3920b028cd381c94d1262a55415fc1d002bae0a5'] dependencies = [('hwloc', '1.11.5')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb index aaab9634c1c..48aabf2b2c8 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-gcccuda-2017.01.eb @@ -3,15 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.0.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'gcccuda', 'version': '2017.01'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -checksums = ['886698becc5bea8c151c0af2074b8392'] +checksums = ['32914cc64780d3980066f3be3920b028cd381c94d1262a55415fc1d002bae0a5'] dependencies = [('hwloc', '1.11.5')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 784ae60b96a..0301ba91e33 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.0.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['886698becc5bea8c151c0af2074b8392'] +checksums = ['32914cc64780d3980066f3be3920b028cd381c94d1262a55415fc1d002bae0a5'] dependencies = [('hwloc', '1.11.5')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb index 35b681fcd94..3364e4a6a5c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb @@ -3,15 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.1.0' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -checksums = ['c058052b53d209c7521079e3d2da613b'] +checksums = ['265a9c64a468cce464edd069ed8612e1865c5f112f84f4a7a855fb2a0d15e74b'] dependencies = [('hwloc', '1.11.6')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb index cce042183bf..a458923dae0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.1.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017.02.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017.02.eb index 64cb58454b2..f892b0298f0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017.02.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017.02.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.1.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'gcccuda', 'version': '2017.02'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017b.eb index 360b16db41d..03f221313d0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.1.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'gcccuda', 'version': '2017b'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 876eab1d596..c5a9eca5c49 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -3,14 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.1.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} -sources = [SOURCELOWER_TAR_GZ] - -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb index 10713f1a54d..e2a34f73f91 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.1.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-gcccuda-2018a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-gcccuda-2018a.eb index b6cab3939f0..08dc0dfea8b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-gcccuda-2018a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-gcccuda-2018a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.1.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'gcccuda', 'version': '2018a'} diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 7791a41dc99..8a367e7662d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -3,13 +3,11 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.1.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} -sources = [SOURCELOWER_TAR_GZ] - source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['e5bf7b2d7517f5cb7c9e1fed15d2df2da501669072477b21a513e892a22663bc'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb index 87565f3890e..98d18f520cb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb @@ -3,13 +3,11 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '2.1.3' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2018.2.199-GCC-6.4.0-2.28'} -sources = [SOURCELOWER_TAR_GZ] - source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['3e2f7b349b7d28a85c88d65f71327fcc2300a56c1fb6cd9ff0647d806523435e'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb index 340404559fb..c1e81c2933e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '3.0.0' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'GCC', 'version': '7.2.0-2.29'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] checksums = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb index 10415797bc5..1785f380bd8 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.0-GCC-7.3.0-2.30.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '3.1.0' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-3.1_fix-ib-query.patch', diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb index fa65134b4c8..d700eed7109 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '3.1.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-3.1_fix-ib-query.patch', diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb index cc9bcaec6e8..33acb8eeb3f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '3.1.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'gcccuda', 'version': '2018b'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-3.1_fix-ib-query.patch', diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb index 472edc30183..12be3518598 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '3.1.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-3.1_fix-ib-query.patch', diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb index a33e4910590..b07343812d9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.2-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '3.1.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-3.1_fix-ib-query.patch', diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb index 745d6879c13..c16abf89d07 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '3.1.3' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] patches = [ '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 59f429004da..9665ef23d72 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '3.1.3' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] patches = [ '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb index 892e9959bb1..5963d943442 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1-hpcx.eb @@ -4,12 +4,12 @@ name = 'OpenMPI' version = '4.0.0' versionsuffix = '-hpcx' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """Mellanox flavored Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['36f10daa3f1b1d37530f686bf7f70966b2a13c0bc6e2e05aebc7e85e3d21b10d'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb index 588e497d2e8..97406ce2781 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '4.0.0' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['36f10daa3f1b1d37530f686bf7f70966b2a13c0bc6e2e05aebc7e85e3d21b10d'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb index dc19fcb2d8b..94ba27cd30f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.1-GCC-8.3.0-2.32.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '4.0.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'GCC', 'version': '8.3.0-2.32'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['e55e213fe09a214ab9f2c722acfd8bf7b39bbc1800e4b7a464d38df15e707f59'] From 4e216e170a87ee7b864f6a2ad027e07ca7597e49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Apr 2019 10:27:42 +0200 Subject: [PATCH 1086/5331] use https:// in homepage & source_urls for recent hwloc 1.11.x easyconfigs --- .../easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-GCC-4.9.3.eb | 5 +++-- .../hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 5 +++-- .../easyconfigs/h/hwloc/hwloc-1.11.10-GCCcore-7.3.0.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.11.11-GCCcore-8.2.0.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb | 5 +++-- .../easyconfigs/h/hwloc/hwloc-1.11.2-GNU-4.9.3-2.25.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb | 5 +++-- .../easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb | 5 +++-- .../easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb | 4 ++-- .../easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb | 5 +++-- .../h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb | 5 +++-- .../h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb | 5 +++-- .../easyconfigs/h/hwloc/hwloc-1.11.3-gcccuda-2016.08.eb | 5 +++-- .../hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 5 +++-- .../hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb | 5 +++-- .../easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb | 5 +++-- .../h/hwloc/hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb | 7 +++---- .../easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb | 5 +++-- .../hwloc-1.11.4-iccifort-2017.1.132-GCC-5.4.0-2.26.eb | 7 +++---- .../easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb | 5 +++-- .../easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb | 5 +++-- .../hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb | 7 +++---- .../easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb | 5 +++-- .../easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-5.4.0.eb | 4 ++-- .../easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-6.4.0.eb | 4 ++-- .../easyconfigs/h/hwloc/hwloc-1.11.8-GCCcore-6.4.0.eb | 2 +- .../easyconfigs/h/hwloc/hwloc-1.11.8-GCCcore-7.2.0.eb | 2 +- easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-intel-2017a.eb | 4 ++-- 31 files changed, 81 insertions(+), 64 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb index 5b67b5f4908..1a32f79bd72 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.0' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -17,7 +17,8 @@ dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['c6e6b2b5958a3670acf727b2aed43f16a68ece6cf87eb6de489e90e12a3da4a6'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-GCC-4.9.3.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-GCC-4.9.3.eb index 4d49031a3a4..2331b04cf01 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-GCC-4.9.3.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.1' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '4.9.3'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['b41f877d79b6026640943d57ef25311299378450f2995d507a5e633da711be61'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index d803930b96c..677b44492b8 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.1' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -17,7 +17,8 @@ dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['b41f877d79b6026640943d57ef25311299378450f2995d507a5e633da711be61'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.10-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.10-GCCcore-7.3.0.eb index 108f7dd2b3e..631e4ab510d 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.10-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.10-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.10' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """ The Portable Hardware Locality (hwloc) software package provides a portable diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.11-GCCcore-8.2.0.eb index 47bccca7f98..2554dc5714d 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.11-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.11-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.11' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """ The Portable Hardware Locality (hwloc) software package provides a portable diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb index 0af84a15f7c..3e13a1b0995 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.2' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['d11f091ed54c56c325ffca1083113a405fcd8a25d5888af64f5cd6cf587b7b0a'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GNU-4.9.3-2.25.eb index 41a09546a09..1e3b8cfcc40 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.2-GNU-4.9.3-2.25.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.2' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -17,7 +17,8 @@ dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['d11f091ed54c56c325ffca1083113a405fcd8a25d5888af64f5cd6cf587b7b0a'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb index ef0b1e1c2c9..862e37f486e 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.3' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ information about modern computing hardware so as to exploit it accordingly and toolchain = {'name': 'GCC', 'version': '5.2.0'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb index 5a122dc9232..984a779ad86 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.3.0-2.26.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.3' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb index 12e87742fa0..6e151472fd3 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.3' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,7 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0'] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb index 659a1fdf270..ac9425c4b68 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-6.1.0-2.27.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.3' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '6.1.0-2.27'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb index 7ea9401fcdd..dcf601bad7a 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.3-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.3' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0'] dependencies = [ ('numactl', '2.0.11', '', ('GCCcore', '4.9.3')), diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb index e7bd276c18f..879d56d6941 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-PGI-16.4-GCC-5.3.0-2.26.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.3' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'PGI', 'version': '16.4-GCC-5.3.0-2.26'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0'] dependencies = [ ('numactl', '2.0.11', '', ('GCCcore', '5.3.0')), diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-gcccuda-2016.08.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-gcccuda-2016.08.eb index 4a821b0537f..184bf3e0b96 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-gcccuda-2016.08.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-gcccuda-2016.08.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = "1.11.3" -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'gcccuda', 'version': '2016.08'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index d786ed3e2f8..08fdd8e999b 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.3' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -17,7 +17,8 @@ dependencies = [('numactl', '2.0.11')] configopts = "--enable-libnuma=$EBROOTNUMACTL" -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index b656f492fea..270c23616c4 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.3' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -17,7 +17,8 @@ dependencies = [('numactl', '2.0.11')] configopts = "--enable-libnuma=$EBROOTNUMACTL" -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb index aad28dd23b6..2b7ec280852 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.3' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'intel', 'version': '2016a'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb index 651e1648ba8..6ca58dae8da 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.3' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'intel', 'version': '2016b'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['03a1cc63f23fed7e17e4d4369a75dc77d5c145111b8578b70e0964a12712dea0'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb index 071326cd0d5..f751c322bbe 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-GCC-6.2.0-2.27.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.4' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ information about modern computing hardware so as to exploit it accordingly and toolchain = {'name': 'GCC', 'version': '6.2.0-2.27'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['1b6a58049c31ce36aff162cf4332998fd468486bd08fdfe0249a47437311512d'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb index 6138766fd96..9c561663fc8 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-PGI-16.7-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.4' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,10 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'PGI', 'version': '16.7-GCC-5.4.0-2.26'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] - -checksums = ['b6f23eb59074fd09fdd84905d50b103d'] +checksums = ['1b6a58049c31ce36aff162cf4332998fd468486bd08fdfe0249a47437311512d'] dependencies = [ ('numactl', '2.0.11', '', ('GCCcore', '5.4.0')), diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb index ed51d673262..d1b3f90af80 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-gcccuda-2016.10.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.4' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ information about modern computing hardware so as to exploit it accordingly and toolchain = {'name': 'gcccuda', 'version': '2016.10'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['1b6a58049c31ce36aff162cf4332998fd468486bd08fdfe0249a47437311512d'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-iccifort-2017.1.132-GCC-5.4.0-2.26.eb index a68a5876d6c..6e802ef5830 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.4' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,10 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-5.4.0-2.26'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] - -checksums = ['b6f23eb59074fd09fdd84905d50b103d'] +checksums = ['1b6a58049c31ce36aff162cf4332998fd468486bd08fdfe0249a47437311512d'] dependencies = [ ('numactl', '2.0.11', '', ('GCCcore', '5.4.0')), diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb index 547c202aa95..80d8f9dc2ed 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-5.4.0-2.26.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.5' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ information about modern computing hardware so as to exploit it accordingly and toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['da2c780fce9b5440a1a7d1caf78f637feff9181a9d1ca090278cae4bea71b3df'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb index 1aeec6a1167..840abff9151 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-GCC-6.3.0-2.27.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.5' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ information about modern computing hardware so as to exploit it accordingly and toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['da2c780fce9b5440a1a7d1caf78f637feff9181a9d1ca090278cae4bea71b3df'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb index 51bcdefbaf0..6268190b97a 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.5-iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.5' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,10 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'iccifort', 'version': '2017.1.132-GCC-6.3.0-2.27'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] - -checksums = ['8f5fe6a9be2eb478409ad5e640b2d3ba'] +checksums = ['da2c780fce9b5440a1a7d1caf78f637feff9181a9d1ca090278cae4bea71b3df'] dependencies = [ ('numactl', '2.0.11'), diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb index 93ceada29dd..548870a7699 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.6-GCC-6.3.0-2.28.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.6' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ information about modern computing hardware so as to exploit it accordingly and toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['67963f15197e6b551539c4ed95a4f8882be9a16cf336300902004361cf89bdee'] dependencies = [('numactl', '2.0.11')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-5.4.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-5.4.0.eb index 44e3d6a6e75..d5663e5d0bf 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-5.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.7' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """ The Portable Hardware Locality (hwloc) software package provides a portable @@ -18,7 +18,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['ac16bed9cdd3c63bca1fe1ac3de522a1376b1487c4fc85b7b19592e28fd98e26'] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-6.4.0.eb index fe87c4d6ed3..0ad7e79f6df 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.7-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.7' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """ The Portable Hardware Locality (hwloc) software package provides a portable @@ -18,7 +18,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['ac16bed9cdd3c63bca1fe1ac3de522a1376b1487c4fc85b7b19592e28fd98e26'] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-GCCcore-6.4.0.eb index 1286b29e6d9..af6caec6124 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.8' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """ The Portable Hardware Locality (hwloc) software package provides a portable diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-GCCcore-7.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-GCCcore-7.2.0.eb index 772feab7dee..262e2ba0496 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-GCCcore-7.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.8' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """ The Portable Hardware Locality (hwloc) software package provides a portable diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-intel-2017a.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-intel-2017a.eb index 0b22a250c25..506a70b4d69 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-intel-2017a.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.8-intel-2017a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.11.8' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """ The Portable Hardware Locality (hwloc) software package provides a portable @@ -18,7 +18,7 @@ description = """ toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['8af89b1164a330e36d18210360ea9bb305e19f9773d1c882855d261a13054ea8'] From a2c6e53d6628918ec93082deef0ae8b94a50306c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Apr 2019 10:32:34 +0200 Subject: [PATCH 1087/5331] use https:// in homepage & source_urls for old hwloc 1.x easyconfigs --- easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.9.2.eb | 5 +++-- .../h/hwloc/hwloc-1.10.0-iccifort-2015.1.133-GCC-4.9.2.eb | 5 +++-- .../h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-GCC-4.6.3.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-ictce-5.3.0.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.6-ictce-5.3.0.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.6.4.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.7.2.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-GCC-4.8.2.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb | 5 +++-- .../h/hwloc/hwloc-1.8.1-iccifort-2013_sp1.2.144.eb | 5 +++-- easybuild/easyconfigs/h/hwloc/hwloc-1.9-GCC-4.8.3.eb | 5 +++-- .../easyconfigs/h/hwloc/hwloc-1.9-iccifort-2013_sp1.4.211.eb | 5 +++-- 19 files changed, 57 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.9.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.9.2.eb index 24816732939..c3bf4244e67 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-GCC-4.9.2.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.10.0' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -17,7 +17,8 @@ dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['1134b0ede4ee2280b4beb95e51a2b0080df4e59b98976e79d49bc4b7337cd461'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.1.133-GCC-4.9.2.eb index 3ecf13cb7d2..6f0d705aae5 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.1.133-GCC-4.9.2.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.10.0' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'iccifort', 'version': '2015.1.133-GCC-4.9.2'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['1134b0ede4ee2280b4beb95e51a2b0080df4e59b98976e79d49bc4b7337cd461'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb index c0454d96329..c9dde59dc1b 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.0-iccifort-2015.2.164-GCC-4.9.2.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.10.0' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'iccifort', 'version': '2015.2.164-GCC-4.9.2'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['1134b0ede4ee2280b4beb95e51a2b0080df4e59b98976e79d49bc4b7337cd461'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb index ec221125479..e379563df89 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GCC-4.8.4.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = "1.10.1" -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,8 +13,9 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '4.8.4'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['ef7cc854a26a9bdef2bc5f14c8d627b7c4a34e3a2fd06aeb3dec2b3b0cc364fc'] dependencies = [('numactl', '2.0.10')] diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb index afa499ff97a..8261ef13c38 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.10.1' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -17,7 +17,8 @@ dependencies = [('numactl', '2.0.10')] configopts = "--enable-libnuma=$EBROOTNUMACTL" -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['ef7cc854a26a9bdef2bc5f14c8d627b7c4a34e3a2fd06aeb3dec2b3b0cc364fc'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-GCC-4.6.3.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-GCC-4.6.3.eb index 83008d4b9ba..a7d52c37cc6 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-GCC-4.6.3.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.5.1' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '4.6.3'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['0729f9d32ca2d4cefc234ff697b4511d25038aa249a8302b2cbd5d1c49e97847'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-ictce-5.3.0.eb index 12046c63a25..d215be5db36 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.5.1-ictce-5.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.5.1' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['0729f9d32ca2d4cefc234ff697b4511d25038aa249a8302b2cbd5d1c49e97847'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.6-ictce-5.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.6-ictce-5.3.0.eb index 11db3431f1f..6db27261ee8 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.6-ictce-5.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.6' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['1e25be3f8bb52296d9334b9d0720ac1d551a5274e579211fc116e5b39a27ae4d'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.6.4.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.6.4.eb index ca74b09ce12..c79a784fbb0 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.6.4.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.6.2' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '4.6.4'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['f3e567323c40445994b04dc3f6c8e4fd3a0d97fbfb76717439771ea0ba9b2a39'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.7.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.7.2.eb index 58f69d8db5b..c3ca5c9524b 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-GCC-4.7.2.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.6.2' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '4.7.2'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['f3e567323c40445994b04dc3f6c8e4fd3a0d97fbfb76717439771ea0ba9b2a39'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb index 4a1f0300da7..1d60815675b 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.6.2-ictce-5.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.6.2' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['f3e567323c40445994b04dc3f6c8e4fd3a0d97fbfb76717439771ea0ba9b2a39'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-GCC-4.8.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-GCC-4.8.2.eb index 13051e6d815..0e3655c36dd 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-GCC-4.8.2.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = "1.7.2" -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '4.8.2'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['966e62fe85109b921bad46c33dc8abbf36507d168a91e8ab3cda1346d6b4cc6f'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb index 459fa88c69e..fdb750a7f23 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = "1.7.2" -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['966e62fe85109b921bad46c33dc8abbf36507d168a91e8ab3cda1346d6b4cc6f'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb index 1f891126fda..29707099c67 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = "1.7.2" -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['966e62fe85109b921bad46c33dc8abbf36507d168a91e8ab3cda1346d6b4cc6f'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb index ea7fbe41ddd..f5f77d8140d 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.2.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = "1.8.1" -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '4.8.2'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['20ce758a2f88dcb4b33251c0127e0c33adeaa5f1ff3b5ccfa6774670382af759'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb index 82f551b2472..6fe056207a8 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-GCC-4.8.3.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = "1.8.1" -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'GCC', 'version': '4.8.3'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['20ce758a2f88dcb4b33251c0127e0c33adeaa5f1ff3b5ccfa6774670382af759'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-iccifort-2013_sp1.2.144.eb index a67b8a8766a..ca024bd2498 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.8.1-iccifort-2013_sp1.2.144.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.8.1' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'iccifort', 'version': '2013_sp1.2.144'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['20ce758a2f88dcb4b33251c0127e0c33adeaa5f1ff3b5ccfa6774670382af759'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.9-GCC-4.8.3.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.9-GCC-4.8.3.eb index 5353d4e58c4..c14365dce17 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.9-GCC-4.8.3.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = "1.9" -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -17,7 +17,8 @@ dependencies = [('numactl', '2.0.9')] configopts = "--enable-libnuma=$EBROOTNUMACTL" -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['9fb572daef35a1c8608d1a6232a4a9f56846bab2854c50562dfb9a7be294f4e8'] moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.9-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.9-iccifort-2013_sp1.4.211.eb index c4ebd968ce5..16f04ebb85b 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.9-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.9-iccifort-2013_sp1.4.211.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '1.9' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various @@ -13,7 +13,8 @@ description = """The Portable Hardware Locality (hwloc) software package provide toolchain = {'name': 'iccifort', 'version': '2013_sp1.4.211'} -source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] +checksums = ['9fb572daef35a1c8608d1a6232a4a9f56846bab2854c50562dfb9a7be294f4e8'] moduleclass = 'system' From 5a40c4ce21447649cc96198b2ebf9692a551788a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Apr 2019 10:33:12 +0200 Subject: [PATCH 1088/5331] also fix homepage to use https:// in hwloc 2.x easyconfigs --- easybuild/easyconfigs/h/hwloc/hwloc-2.0.2-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.0.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.0.2-GCCcore-8.2.0.eb index 30d364092d8..72e874914ce 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.0.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.0.2-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '2.0.2' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """ The Portable Hardware Locality (hwloc) software package provides a portable diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb index daac466bc8f..78cc42f4ed7 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'hwloc' version = '2.0.3' -homepage = 'http://www.open-mpi.org/projects/hwloc/' +homepage = 'https://www.open-mpi.org/projects/hwloc/' description = """ The Portable Hardware Locality (hwloc) software package provides a portable From 28396fecc6522845121145f2473d18d0d5aaef83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Apr 2019 10:43:17 +0200 Subject: [PATCH 1089/5331] use https:// in homepage & source_urls for old OpenMPI 1.x easyconfigs --- .../o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb | 5 +++-- .../o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb | 5 +++-- .../o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb | 5 +++-- .../o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb | 6 +++--- .../o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb | 5 +++-- .../o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb | 5 +++-- .../o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb | 4 ++-- .../o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb | 6 +++--- .../o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb | 5 +++-- .../OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb | 6 +++--- .../o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb | 7 +++---- .../OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb | 6 +++--- .../o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb | 9 ++++++--- .../easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb | 5 +++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb | 5 +++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb | 5 +++-- .../o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb | 5 +++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb | 5 +++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb | 5 +++-- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb | 9 ++++++--- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb | 9 ++++++--- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb | 9 ++++++--- .../o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb | 9 ++++++--- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb | 9 ++++++--- .../easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb | 9 ++++++--- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb | 5 +++-- .../OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb | 5 +++-- .../o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb | 5 +++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb | 9 ++++++--- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb | 5 +++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb | 5 +++-- .../OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb | 6 +++--- .../o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb | 5 +++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb | 5 +++-- .../easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb | 5 +++-- .../OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb | 6 +++--- .../OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb | 6 +++--- .../o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb | 5 +++-- .../o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb | 5 +++-- .../o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb | 5 +++-- .../OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb | 6 +++--- 41 files changed, 146 insertions(+), 100 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb index 8c3ec42a915..a3ecb9ae568 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.1-GCC-4.9.3-2.25.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.10.1' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['90eda119e8dcae8d904e44f5fc38a5051a4fb94134f56dc24b9051baff8bb29e'] dependencies = [('hwloc', '1.11.2')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb index 88a19baaae6..9c0744dec39 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-4.9.3-2.25.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.10.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['01db467676cb5d974166591d403a8ffe38dfac4becb67071f59971e86bef0f63'] dependencies = [('hwloc', '1.11.2')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb index 30a39663a88..5aecc9dced2 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-5.3.0-2.26.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.10.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '5.3.0-2.26'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['01db467676cb5d974166591d403a8ffe38dfac4becb67071f59971e86bef0f63'] dependencies = [('hwloc', '1.11.3')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb index b5be2c3eb75..5e8a6489d3a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-GCC-6.1.0-2.27.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.10.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '6.1.0-2.27'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['01db467676cb5d974166591d403a8ffe38dfac4becb67071f59971e86bef0f63'] dependencies = [('hwloc', '1.11.3')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb index c2a1d59acd4..25f36912624 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.3-GCC-4.9.3-2.25.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.10.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'PGI', 'version': '16.3-GCC-4.9.3-2.25'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['01db467676cb5d974166591d403a8ffe38dfac4becb67071f59971e86bef0f63'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb index f9950da0ecb..5dec7f2fb48 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.2-PGI-16.4-GCC-5.3.0-2.26.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.10.2' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'PGI', 'version': '16.4-GCC-5.3.0-2.26'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['01db467676cb5d974166591d403a8ffe38dfac4becb67071f59971e86bef0f63'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb index 5941db03163..ab2f196232d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.10.3' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['681c2ed1c96d187a3c84f30811a2b143d26de74884a740e5d02ec265ef70ab00'] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb index bd82528708b..f16595e6072 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-6.1.0-2.27.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.10.3' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '6.1.0-2.27'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] - -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['681c2ed1c96d187a3c84f30811a2b143d26de74884a740e5d02ec265ef70ab00'] dependencies = [('hwloc', '1.11.3')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb index bac6321f61f..349cfd86882 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-gcccuda-2016.08.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = "1.10.3" -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'gcccuda', 'version': '2016.08'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['681c2ed1c96d187a3c84f30811a2b143d26de74884a740e5d02ec265ef70ab00'] dependencies = [('hwloc', '1.11.3')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb index e24fff664a2..f18a3cea49b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.10.3' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - +checksums = ['681c2ed1c96d187a3c84f30811a2b143d26de74884a740e5d02ec265ef70ab00'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb index 1fab3dab1af..89b4afe6c6a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb @@ -3,15 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.10.4' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'PGI', 'version': '16.7-GCC-5.4.0-2.26'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - -checksums = ['fb2fdb6a5b65c80d7dfa4bc9a0caf665'] +checksums = ['492332cd77d8af8ce37ab9d82964dae7ddfc1c2c60c0b417973ff7a70cd89991'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb index fc54280f16e..5c394192ef6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.10.4' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2016.3.210-GCC-4.9.3-2.25'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - +checksums = ['492332cd77d8af8ce37ab9d82964dae7ddfc1c2c60c0b417973ff7a70cd89991'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb index e2dcab157e9..1401145faf3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb @@ -4,15 +4,18 @@ name = 'OpenMPI' version = '1.4.5' versionsuffix = "-no-OFED" -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.6.3'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - patches = ['pax_disable.patch'] +checksums = [ + 'a1306bb4d44d0cf3a89680c4c6723bb665126c9d5523022f187b944b9d4ea6a5', # openmpi-1.4.5.tar.gz + '7bd7c339aee9ee731d2c6a8641901886e52faf0913bfb7191d0edc449e2c0a81', # pax_disable.patch +] configopts = '--with-threads=posix --enable-shared --enable-mpi-threads --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb index 71d41c1e0fd..443f5d77a32 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.4.5' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.6.3'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['a1306bb4d44d0cf3a89680c4c6723bb665126c9d5523022f187b944b9d4ea6a5'] configopts = '--with-threads=posix --enable-shared --enable-mpi-threads --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb index 18c61b4abff..e8c23e02fd6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = "1.4.5" -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['a1306bb4d44d0cf3a89680c4c6723bb665126c9d5523022f187b944b9d4ea6a5'] builddependencies = [ ('Automake', '1.14'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index e0fdbd9b1d8..adab043e84a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.6.4' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.6.4'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['d8b507309dcbd463b76c1ae504998a8c6221292e6bf10533880ea264be604dc4'] dependencies = [('hwloc', '1.6.2')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 4310e30ba03..912f0b72baa 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -4,13 +4,14 @@ name = 'OpenMPI' version = '1.6.4' versionsuffix = '-no-OFED' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = "The Open MPI Project is an open source MPI-2 implementation." toolchain = {'name': 'GCC', 'version': '4.7.2'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['d8b507309dcbd463b76c1ae504998a8c6221292e6bf10533880ea264be604dc4'] dependencies = [('hwloc', '1.6.2')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 46d2a4a2336..0448f42b20a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.6.4' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['d8b507309dcbd463b76c1ae504998a8c6221292e6bf10533880ea264be604dc4'] dependencies = [('hwloc', '1.6.2')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 1af8bec01f1..a209872e344 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.6.5' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.7.2'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['ac308dc38e77c622aedea5f3fd368c800b6636d0500f2124c36a505a65806559'] dependencies = [ ('hwloc', '1.6.2'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 417cf55b81c..6758ace63c0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -4,17 +4,20 @@ name = 'OpenMPI' version = '1.6.5' versionsuffix = "-no-OFED" -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.7.3'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] +checksums = [ + 'ac308dc38e77c622aedea5f3fd368c800b6636d0500f2124c36a505a65806559', # openmpi-1.6.5.tar.gz + '7de06818f3e83e64ca004458acac679e95ba1c658f051e6a91db2b726c53f9bc', # OpenMPI-1.6.5-vt_cupti_events.patch +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index 9701c637eda..37e3e10827a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -4,17 +4,20 @@ name = 'OpenMPI' version = '1.6.5' versionsuffix = "-no-OFED" -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.8.1'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] +checksums = [ + 'ac308dc38e77c622aedea5f3fd368c800b6636d0500f2124c36a505a65806559', # openmpi-1.6.5.tar.gz + '7de06818f3e83e64ca004458acac679e95ba1c658f051e6a91db2b726c53f9bc', # OpenMPI-1.6.5-vt_cupti_events.patch +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 9c74aa620d5..76513a1069e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -3,17 +3,20 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.6.5' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.8.1'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] +checksums = [ + 'ac308dc38e77c622aedea5f3fd368c800b6636d0500f2124c36a505a65806559', # openmpi-1.6.5.tar.gz + '7de06818f3e83e64ca004458acac679e95ba1c658f051e6a91db2b726c53f9bc', # OpenMPI-1.6.5-vt_cupti_events.patch +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 9c4d7ed9f6a..da65f421b9b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -4,17 +4,20 @@ name = 'OpenMPI' version = '1.6.5' versionsuffix = '-no-OFED' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] +checksums = [ + 'ac308dc38e77c622aedea5f3fd368c800b6636d0500f2124c36a505a65806559', # openmpi-1.6.5.tar.gz + '7de06818f3e83e64ca004458acac679e95ba1c658f051e6a91db2b726c53f9bc', # OpenMPI-1.6.5-vt_cupti_events.patch +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 8985983b3f1..3c054b74501 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -3,17 +3,20 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.6.5' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] +checksums = [ + 'ac308dc38e77c622aedea5f3fd368c800b6636d0500f2124c36a505a65806559', # openmpi-1.6.5.tar.gz + '7de06818f3e83e64ca004458acac679e95ba1c658f051e6a91db2b726c53f9bc', # OpenMPI-1.6.5-vt_cupti_events.patch +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index 65455ee083f..ed990b6524e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -3,17 +3,20 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.6.5' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.8.3'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - patches = [ 'OpenMPI-1.6.5-vt_cupti_events.patch', ] +checksums = [ + 'ac308dc38e77c622aedea5f3fd368c800b6636d0500f2124c36a505a65806559', # openmpi-1.6.5.tar.gz + '7de06818f3e83e64ca004458acac679e95ba1c658f051e6a91db2b726c53f9bc', # OpenMPI-1.6.5-vt_cupti_events.patch +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 678e7e1afbe..f2d79ee4e27 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.6.5' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2013_sp1.2.144'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['ac308dc38e77c622aedea5f3fd368c800b6636d0500f2124c36a505a65806559'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 702e7940ba3..87ed1210027 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -4,13 +4,14 @@ name = 'OpenMPI' version = '1.6.5' versionsuffix = '-no-OFED' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2013_sp1.4.211'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['ac308dc38e77c622aedea5f3fd368c800b6636d0500f2124c36a505a65806559'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index dc145861ffa..e2a84b5fa43 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.6.5' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2013_sp1.4.211'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['ac308dc38e77c622aedea5f3fd368c800b6636d0500f2124c36a505a65806559'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb index 81d45b5e89a..e81b17c67f4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb @@ -3,15 +3,18 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = "1.7.3" -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.8.2'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - patches = ['OpenMPI-%(version)s-vt_cupti_events.patch'] +checksums = [ + 'bcddffc1e2bee64790205c95bd7dff62af43ea1276ac37987da44ed5ad815874', # openmpi-1.7.3.tar.gz + 'c155b47f44497658aecc56bb40fc93de8a2e3986be638679946e6e41cf047b3f', # OpenMPI-1.7.3-vt_cupti_events.patch +] dependencies = [('hwloc', '1.7.2')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb index 5503a3e1f60..306914b1a31 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = "1.8.1" -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.8.3'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['1ebeb5af9db47f1f0bb63d14265d34a7be0d99bb34a0b2a41c3e926f3d27fd50'] dependencies = [('hwloc', '1.9')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb index 8e54eb0f672..b38d1f410e1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = "1.8.3" -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['b7487ee77bde880308429a72f56612b840690cc3b927be4bf191677b9a2ef5a8'] dependencies = [('hwloc', '1.10.0')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index c0e27137e3b..ce97d627d4f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -4,14 +4,14 @@ name = 'OpenMPI' version = '1.8.3' versionsuffix = '-no-OFED' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2013_sp1.4.211'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - +checksums = ['b7487ee77bde880308429a72f56612b840690cc3b927be4bf191677b9a2ef5a8'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index f0ceedd49e6..09955e61a2a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.8.3' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2013_sp1.4.211'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['b7487ee77bde880308429a72f56612b840690cc3b927be4bf191677b9a2ef5a8'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index e841ac62557..0a21817e08e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = "1.8.4" -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.8.4'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['3c602955fa16d03806ec704e089e2a14fe092d7fe7d444972f4a99407f645661'] dependencies = [('hwloc', '1.10.1')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb index 825a80feb74..3655aea7a60 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.8.4' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['3c602955fa16d03806ec704e089e2a14fe092d7fe7d444972f4a99407f645661'] dependencies = [('hwloc', '1.10.0')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index 6731564586b..de48e1b108f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.8.4' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2015.1.133-GCC-4.9.2'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - +checksums = ['3c602955fa16d03806ec704e089e2a14fe092d7fe7d444972f4a99407f645661'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index d46d33479eb..c636d2c3e88 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.8.4' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2015.2.164-GCC-4.9.2'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - +checksums = ['3c602955fa16d03806ec704e089e2a14fe092d7fe7d444972f4a99407f645661'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb index 089abe6b34a..bfae88f68c9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.8.5' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['91de8828f7257b6c011a9015321c0fd027782ee04a269c74194f2e3c837e28c8'] dependencies = [('hwloc', '1.10.1')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb index b77284839a6..407a27162c4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.8.6' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['167bdc76b44b7961871ea5973ffc545035d44f577152c4a9ab8d2be795ce27d1'] dependencies = [('hwloc', '1.11.0')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb index d15e963eea0..3466298aeb9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb @@ -3,13 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.8.8' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +checksums = ['56764d8eea8fd1812be4e7e71314e3c60e300be9bb59eafe866348db1ac4e306'] dependencies = [('hwloc', '1.11.0')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb index a2ec79195bf..e46be7fa7cf 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '1.8.8' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-2 implementation.""" toolchain = {'name': 'iccifort', 'version': '2015.3.187-GNU-4.9.3-2.25'} +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - +checksums = ['56764d8eea8fd1812be4e7e71314e3c60e300be9bb59eafe866348db1ac4e306'] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path From a4270aef886456d282e5806d76f78777194f4911 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Fri, 5 Apr 2019 11:36:08 +0100 Subject: [PATCH 1090/5331] Some style cleaning --- .../v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb index 07324de9678..0425b7f385c 100644 --- a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb @@ -27,15 +27,15 @@ sources = ['%(version)s.tar.gz'] checksums = ['38d1d32efe97adaea6754f4559520454d4f0d2400964ebc59f8ac01f0146e23f'] dependencies = [ - ('libjpeg-turbo', '2.0.0'), - ('Mesa', '18.1.1'), - ('libGLU', '9.0.0'), + ('libjpeg-turbo', '2.0.0'), + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), ] builddependencies = [('CMake', '3.12.1')] binaries = [ - 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', - 'vglclient', 'vglconfig', 'vglconnect', 'vglgenkey', 'vgllogin', 'vglrun', + 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', + 'vglclient', 'vglconfig', 'vglconnect', 'vglgenkey', 'vgllogin', 'vglrun', 'vglserver_config' ] From aa3abeccd2edeef0f6f27f753c53ddb67d1532d2 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Fri, 5 Apr 2019 13:43:49 +0200 Subject: [PATCH 1091/5331] adding easyconfigs: pytest-4.4.0-foss-2018b-Python-2.7.15.eb, pytest-4.4.0-intel-2018b-Python-2.7.15.eb, pytest-4.4.0-foss-2018b-Python-3.6.6.eb, pytest-4.4.0-foss-2018b-Python-3.6.6.eb --- .../pytest-4.4.0-foss-2018b-Python-2.7.15.eb | 51 +++++++++++++++++++ .../pytest-4.4.0-foss-2018b-Python-3.6.6.eb | 51 +++++++++++++++++++ .../pytest-4.4.0-intel-2018b-Python-2.7.15.eb | 51 +++++++++++++++++++ 3 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..3c996624025 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '4.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [('Python', '2.7.15')] + +use_pip = True +download_dep_fail = True + +exts_list = [ + ('py', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + }), + ('attrs', '19.1.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + }), + ('pluggy', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + }), + ('atomicwrites', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + }), + ('more-itertools', '5.0.0', { + 'modulename': 'more_itertools', + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + }), + ('scandir', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + }), + ('pathlib2', '2.3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..429359b0c9f --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '4.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [('Python', '3.6.6')] + +use_pip = True +download_dep_fail = True + +exts_list = [ + ('py', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + }), + ('attrs', '19.1.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + }), + ('pluggy', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + }), + ('atomicwrites', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + }), + ('more-itertools', '5.0.0', { + 'modulename': 'more_itertools', + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + }), + ('scandir', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + }), + ('pathlib2', '2.3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..f2918bd2962 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '4.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [('Python', '2.7.15')] + +use_pip = True +download_dep_fail = True + +exts_list = [ + ('py', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + }), + ('attrs', '19.1.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + }), + ('pluggy', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + }), + ('atomicwrites', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + }), + ('more-itertools', '5.0.0', { + 'modulename': 'more_itertools', + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + }), + ('scandir', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + }), + ('pathlib2', '2.3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 548ae48428e2cc9299b06c7af34accc60ba64db9 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Fri, 5 Apr 2019 13:49:05 +0200 Subject: [PATCH 1092/5331] +pytest4.4.0-intel-2018b-Python-3.6.6 --- .../pytest-4.4.0-intel-2018b-Python-3.6.6.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..2c95634be3e --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '4.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [('Python', '3.6.6')] + +use_pip = True +download_dep_fail = True + +exts_list = [ + ('py', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + }), + ('attrs', '19.1.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + }), + ('pluggy', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + }), + ('atomicwrites', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + }), + ('more-itertools', '5.0.0', { + 'modulename': 'more_itertools', + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + }), + ('scandir', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + }), + ('pathlib2', '2.3.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From eb27720169a66a590198304e790f8c198cb019af Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Fri, 5 Apr 2019 14:25:40 +0200 Subject: [PATCH 1093/5331] pytest:remove download_dep_fail --- .../p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb | 1 - .../easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb | 1 - .../p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb | 1 - .../p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb | 1 - 4 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb index 3c996624025..58ba996f18d 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [('Python', '2.7.15')] use_pip = True -download_dep_fail = True exts_list = [ ('py', '1.8.0', { diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb index 429359b0c9f..be7a5f440d2 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [('Python', '3.6.6')] use_pip = True -download_dep_fail = True exts_list = [ ('py', '1.8.0', { diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb index f2918bd2962..64f8adb7723 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'intel', 'version': '2018b'} dependencies = [('Python', '2.7.15')] use_pip = True -download_dep_fail = True exts_list = [ ('py', '1.8.0', { diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb index 2c95634be3e..5a69c143e85 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'intel', 'version': '2018b'} dependencies = [('Python', '3.6.6')] use_pip = True -download_dep_fail = True exts_list = [ ('py', '1.8.0', { From c7f8f71b270db3d2df2b4dd1e3960f6d577309b2 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 5 Apr 2019 16:13:45 +0200 Subject: [PATCH 1094/5331] update version --- .../r/R/MCMCpack-1.4-4_intel_wd308.patch | 11 + .../easyconfigs/r/R/R-3.5.1-intel-2018b.eb | 2142 +++++++++++++++++ .../r/R/kohonen-3.0.6_intel-wd308.patch | 17 + .../r/R/liquidSVM-1.2.2_intel.patch | 35 + 4 files changed, 2205 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/MCMCpack-1.4-4_intel_wd308.patch create mode 100644 easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb create mode 100644 easybuild/easyconfigs/r/R/kohonen-3.0.6_intel-wd308.patch create mode 100644 easybuild/easyconfigs/r/R/liquidSVM-1.2.2_intel.patch diff --git a/easybuild/easyconfigs/r/R/MCMCpack-1.4-4_intel_wd308.patch b/easybuild/easyconfigs/r/R/MCMCpack-1.4-4_intel_wd308.patch new file mode 100644 index 00000000000..4c87221b05b --- /dev/null +++ b/easybuild/easyconfigs/r/R/MCMCpack-1.4-4_intel_wd308.patch @@ -0,0 +1,11 @@ +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ur MCMCpack.orig/src/Makevars.in MCMCpack/src/Makevars.in +--- MCMCpack.orig/src/Makevars.in 2018-09-14 04:12:54.000000000 +0200 ++++ MCMCpack/src/Makevars.in 2019-04-02 20:27:08.529883596 +0200 +@@ -1,2 +1,5 @@ + PKG_CPPFLAGS = -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC @MV_HAVE_IEEEFP_H@ @MV_HAVE_TRUNC@ ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 ++ + diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb new file mode 100644 index 00000000000..5681b50d007 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb @@ -0,0 +1,2142 @@ +name = 'R' +version = '3.5.1' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['0463bff5eea0f3d93fa071f79c18d0993878fd4f2e18ae6cf22c1639d11457ed'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('X11', '20180604'), + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.12'), + ('libreadline', '7.0'), + ('ncurses', '6.1'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.4'), + ('zlib', '1.2.11'), + ('SQLite', '3.24.0'), + ('PCRE', '8.41'), + ('libpng', '1.6.34'), # for plotting in R + ('libjpeg-turbo', '2.0.0'), # for plottting in R + ('LibTIFF', '4.0.9'), + ('Java', '1.8', '', True), + ('Tk', '8.6.8'), # for tcltk + ('cURL', '7.60.0'), # for RCurl + ('libxml2', '2.9.8'), # for XML + ('GDAL', '2.2.3', '-Python-3.6.6'), # for rgdal + ('PROJ', '5.0.0'), # for rgdal + ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.4.2'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '61.1'), # for rJava & gdsfmt + ('HDF5', '1.10.2'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.5'), # for RcppGSL + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on Aug 17, 2018 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-7', { + 'patches': ['Rmpi-0.6-5_impi5.patch'], + 'checksums': [ + '5c03989ba66db264670909b4ee307b243846bb9581e4781a6e0af7c08f7ec2ac', # Rmpi_0.6-7.tar.gz + 'f753f0b6434295be70fe29d36edb2047c091e465b7ff0cab56b93d55883c8dd3', # Rmpi-0.6-5_impi5.patch + ], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + 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('gridExtra', '2.3', { + 'checksums': ['81b60ce6f237ec308555471ae0119158b115463df696d2eca9b177ded8988e3b'], + }), + ('chron', '2.3-52', { + 'checksums': ['c47fcf4abb635babe6337604c876d4853d8a24639a98b71523746c56ce75b4a0'], + }), + ('viridis', '0.5.1', { + 'checksums': ['ddf267515838c6eb092938133035cee62ab6a78760413bfc28b8256165701918'], + }), + ('yaml', '2.2.0', { + 'checksums': ['55bcac87eca360ab5904914fcff473a6981a1f5e6d2215d2634344d0ac30c546'], + }), + ('jsonlite', '1.5', { + 'checksums': ['6490371082a387cb1834048ad8cdecacb8b6b6643751b50298c741490c798e02'], + }), + ('htmltools', '0.3.6', { + 'checksums': ['44affb82f9c2fd76c9e2b58f9229adb003217932b68c3fdbf1327c8d74c868a2'], + }), + ('htmlwidgets', '1.2', { + 'checksums': ['1a7d21c1f3306d53a36c05d6ea7873ddeffeda654cd9be689b6d78e62a688411'], + }), + ('knitr', '1.20', { + 'checksums': ['7b2409056af001970d1ed502a25fd84536aca4a21039479998507556446d0890'], + }), + ('rstudioapi', '0.7', { + 'checksums': ['a541bc76ef082d2c27e42fd683f8262cb195b1497af3509178d2642870397a8c'], + }), + ('htmlTable', '1.12', { + 'checksums': ['42f50b8d8704460388cc55708fd9159b576261ab8d3f5968cf24d6b3b619a1d8'], + }), + ('Hmisc', '4.1-1', { + 'checksums': ['991db21cdf73ffbf5b0239a4876b2e76fd243ea33528afd88dc968792f281498'], + }), + ('fastcluster', '1.1.25', { + 'checksums': ['f3661def975802f3dd3cec5b2a1379f3707eacff945cf448e33aec0da1ed4205'], + }), + ('registry', '0.5', { + 'checksums': ['5d8be59ba791987b2400e9e8eaaac614cd544c1aece785ec4782ea6d5ea00efb'], + }), + ('bibtex', '0.4.2', { + 'checksums': ['1f06ab3660c940405230ad16ff6e4ba38d4418a59cd9b16d78a4349f8b488372'], + }), + ('pkgmaker', '0.27', { + 'checksums': ['17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a'], + }), + ('rngtools', '1.3.1', { + 'checksums': ['763fc493cb821a4d3e514c0dc876d602a692c528e1d67f295dde70c77009e224'], + }), + ('doParallel', '1.0.11', { + 'checksums': ['4ccbd2eb46d3e4f5251b0c3de4d93d9168b02bb0be493656d6aea236667ff76a'], + }), + ('gridBase', '0.4-7', { + 'checksums': ['be8718d24cd10f6e323dce91b15fc40ed88bccaa26acf3192d5e38fe33e15f26'], + }), + ('NMF', '0.21.0', { + 'checksums': ['3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3'], + }), + ('irlba', '2.3.2', { + 'checksums': ['3fdf2d8fefa6ab14cd0992740de7958f9f501c71aca93229f5eb03c54558fc38'], + }), + ('igraph', '1.2.2', { + 'checksums': ['9da2dadf9c1ed495413b32464c6a32fae9d33636822754043e708d8dd6a9efad'], + }), + ('GeneNet', '1.2.13', { + 'checksums': ['3798caac3bef7dc87f97b3628eb29eb12365d571ce0837b5b6285b0be655a270'], + }), + ('ape', '5.1', { + 'checksums': ['b7d5dca66881638227a40aa59533904aa5efe0f4b867851b248e8f948a01a26e'], + }), + ('RJSONIO', '1.3-0', { + 'checksums': ['119334b7761c6c1c3cec52fa17dbc1b72eaebb520c53e68d873dea147cf48fb7'], + }), + ('caTools', '1.17.1.1', { + 'checksums': ['d53e2c5c77f1bd4744703d7196dbc9b4671a120bbb5b9b3edc45fc57c0650c06'], + }), + ('gplots', '3.0.1', { + 'checksums': ['343df84327ac3d03494992e79ee3afc78ba3bdc08af9a305ee3fb0a38745cb0a'], + }), + ('ROCR', '1.0-7', { + 'checksums': ['e7ef710f847e441a48b20fdc781dbc1377f5a060a5ee635234053f7a2a435ec9'], + }), + ('later', '0.7.3', { + 'checksums': ['5c57148c255ee5da61cb748550b73bad7094f4e045b99b362473be5e3dbc4212'], + }), + ('promises', '1.0.1', { + 'checksums': ['c2dbc7734adf009377a41e570dfe0d82afb91335c9d0ca1ef464b9bdcca65558'], + }), + ('httpuv', '1.4.5', { + 'checksums': ['f19113d45ba0617ff826abd7963224db61fa0a3dbfdde21f802419f7b362b7b5'], + }), + ('rjson', '0.2.20', { + 'checksums': ['3a287c1e5ee7c333ed8385913c0a307daf99335fbdf803e9dcca6e3d5adb3f6c'], + }), + ('sourcetools', '0.1.7', { + 'checksums': ['47984406efb3b3face133979ccbae9fefb7360b9a6ca1a1c11473681418ed2ca'], + }), + ('shiny', '1.1.0', { + 'checksums': ['70b564cd1b0ba89bae10bc94c6a3b50bd8ffb1a7d85f4aa41b2949e0ea245c89'], + }), + ('seqinr', '3.4-5', { + 'checksums': ['162a347495fd52cbb62e8187a4692e7c50b9fa62123c5ef98f2744c98a05fb9f'], + }), + ('LearnBayes', '2.15.1', { + 'checksums': ['9b110858456523ca0b2a63f22013c4e1fbda6674b9d84dc1f4de8bffc5260532'], + }), + ('deldir', '0.1-15', { + 'checksums': ['571011c208829f47ecd9f92a19fd94a8eb59de5a2645ab8c62e73926ade30710'], + }), + ('gmodels', '2.18.1', { + 'checksums': ['626140a34eb8c53dd0a06511a76c71bc61c48777fa76fcc5e6934c9c276a1369'], + }), + ('expm', '0.999-2', { + 'checksums': ['38f1e5bfa90f794486789695d0d9e49158c7eb9445dc171dd83dec3d8fa130d6'], + }), + ('spData', '0.2.9.3', { + 'checksums': ['fdcb3ff12e2fa1e1828a13589fd46f7a2e865ead82f81ffb31fb07199b022bc6'], + }), + ('spdep', '0.7-8', { + 'checksums': ['449e0936766dd1f77d93a03fac53aa5dc855b202db2777e5e86145b7d0540732'], + }), + ('vegan', '2.5-2', { + 'checksums': ['2ca4d1650dc23262478fcd9abdaa0132017c7602a19589e28a98987fe9c6fe8e'], + }), + ('adegenet', '2.1.1', { + 'checksums': ['3043fe5d731a38ff0e266f090dcda448640c3d0fd61934c76da32d082e5dce7a'], + }), + ('progress', '1.2.0', { + 'checksums': ['5bb9044d1376cf45e8231c94707ccb7f50996f37c52e40771e1f0cde16a81ce6'], + }), + ('rncl', '0.8.3', { + 'checksums': ['daaef6874438233c73a62b59a9ee10261e1e10d7ef18b7178d2d8b517fd4880d'], + }), + ('XML', '3.98-1.15', { + 'checksums': ['23d6ba04464ebfde56aa7eed45aaeac1739a49bd7ddaf27123b2ac4650d92632'], + }), + ('praise', '1.0.0', { + 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], + }), + ('testthat', '2.0.0', { + 'checksums': ['3bc047ad1c4522104023d4fbbfc9aceed14d316fdb16865a514f26b3e628b494'], + }), + ('rprojroot', '1.3-2', { + 'checksums': ['df5665834941d8b0e377a8810a04f98552201678300f168de5f58a587b73238b'], + }), + ('xfun', '0.3', { + 'checksums': ['897211d135a7fc5f955e4c810e0a0d8fa12b034b0a89dde47ab23e9b486b21e4'], + }), + ('tinytex', '0.6', { + 'checksums': ['6ea08758854b265fdc6b77ab4a6bcbac0178e93f57a43a5de85338a71a6dc99b'], + }), + ('rmarkdown', '1.10', { + 'checksums': ['39350e4d689d633089c1dc1e51dd04bef4497422818c98c17ff77094e6700256'], + }), + ('openssl', '1.0.2', { + 'checksums': ['2c17c6c555b0684b11bf02420dd8d3d83694d1fb4ee6325b44bdb309afbd4eb6'], + }), + ('httr', '1.3.1', { + 'checksums': ['22134d7426b2eba37f0cc34b99285499b8bac9fe75a7bc3222fbad179bf8f258'], + }), + ('reshape', '0.8.7', { + 'checksums': ['2fa6c87d1e89f182e51bc5a4fcda3d42d83b8fb4474ca525fa7a8db5081f3992'], + }), + ('xml2', '1.2.0', { + 'checksums': ['0a7a916fe9c5da9ac45aeb4c6b6b25d33c07652d422b9f2bb570f2e8f4ac9494'], + }), + ('triebeard', '0.3.0', { + 'checksums': ['bf1dd6209cea1aab24e21a85375ca473ad11c2eff400d65c6202c0fb4ef91ec3'], + }), + ('urltools', '1.7.1', { + 'checksums': ['4485f81ca14199e0c66ba477019253b0e7fe414e8ab6ada3f02cfe5a26770306'], + }), + ('httpcode', '0.2.0', { + 'checksums': ['fbc1853db742a2cc1df11285cf27ce2ea43bc0ba5f7d393ee96c7e0ee328681a'], + }), + ('crul', '0.6.0', { + 'checksums': ['004279f94ec5c2a3842c4d251c945aa4ecbb4891915c71d38a082a5c03c9d1ee'], + }), + ('bold', '0.5.0', { + 'checksums': ['f40963b847667cf8d69ba7ba3bd479bc117e1bc4df8bd1482a975dadff58b53d'], + }), + ('rredlist', '0.5.0', { + 'checksums': ['404db668f94aea7fe8c4da75085ea82b0bc9994f023ef4a52f4d75cf198db889'], + }), + ('rentrez', '1.2.1', { + 'checksums': ['74cf6dbe1b229518c25221534b20437b53cb663f1473cf9df5a59ca76b76ae84'], + }), + ('rotl', '3.0.4', { + 'checksums': ['1de6766f3ae08b1234c632b9c9cd9e579d5d426dfa6a0a8c2da6ddfe502084fd'], + }), + ('solrium', '1.0.0', { + 'checksums': ['0e362d4f3b700997bc417ea3ca21301ddbd7978ab3394affbe6861eb27308ee6'], + }), + ('ritis', '0.7.2', { + 'checksums': ['3a8c57fd498b6cbe7e4e2aa015b176d9d699b249f390735d0a5eb8f49eb3c7ae'], + }), + ('worrms', '0.2.8', { + 'checksums': ['6516b701c32443be86832fdbd5ab3e4161441d4b425fe4cd97f9c3b30ce945b8'], + }), + ('natserv', '0.1.4', { + 'checksums': ['07501608a2e79b20940cd0e22aca9db6150942eed5b6dad184ec957e153d8e63'], + }), + ('WikipediR', '1.5.0', { + 'checksums': ['f8d0e6f04fb65f7ad9c1c068852a6a8b699ffe8d39edf1f3fa07d32d087e8ff0'], + }), + ('WikidataR', '1.4.0', { + 'checksums': ['64b1d53d7023249b73a77a7146adc3a8957b7bf3d808ebd6734795e9f58f4b2a'], + }), + ('wikitaxa', '0.2.0', { + 'checksums': ['944523717b2571af02a6bf15a58100dfb69530f702ab919f1c5fd3d263588c19'], + }), + ('taxize', '0.9.4', { + 'checksums': ['559021f1a2393df36f0173aa865332ff129d5d1700333cbe9859183c12a3b9dc'], + }), + ('uuid', '0.1-2', { + 'checksums': ['dd71704dc336b0857981b92a75ed9877d4ca47780b1682def28839304cd3b1be'], + }), + ('RNeXML', '2.1.2', { + 'checksums': ['860dcdce074cd120a5d6cc1f253d4a409965f9d5326568310d3013e550ada52b'], + }), + ('phylobase', '0.8.4', { + 'checksums': ['d7c1a972c266ffe80345c7150608a85e6e2def4a3f079ac964ad9dbce2281002'], + }), + ('adephylo', '1.1-11', { + 'checksums': ['154bf2645eac4493b85877933b9445442524ca4891aefe4e80c294c398cff61a'], + }), + ('animation', '2.5', { + 'checksums': ['b232fef1b318c79710e5e1923d87baba4c85ffe2c77ddb188130e0911d8cb55f'], + }), + ('bigmemory.sri', '0.1.3', { + 'checksums': ['55403252d8bae9627476d1f553236ea5dc7aa6e54da6980526a6cdc66924e155'], + }), + ('bigmemory', '4.5.33', { + 'patches': ['bigmemory-4.5.19_icpc-wd308.patch'], + 'checksums': [ + '7237d9785d8ce3eab4e36ad3ce2c95cbae926326031661b4f237b7517f4b9479', # bigmemory_4.5.33.tar.gz + 'cf673010f63baff60bf5fe4521a3740aa6891bcfb64c1979a8f1e1aa21532549', # bigmemory-4.5.19_icpc-wd308.patch + ], + }), + ('calibrate', '1.7.2', { + 'checksums': ['78066a564f57f2110f1752d681d6b97915cf73135134330587fff8b46c581604'], + }), + ('clusterGeneration', '1.3.4', { + 'checksums': ['7c591ad95a8a9d7fb0e4d5d80dfd78f7d6a63cf7d11eb53dd3c98fdfb5b868aa'], + }), + ('raster', '2.6-7', { + 'checksums': ['fb91804fd465a4a6d9d9858e29fd05f41a99b8efdcc5cf4370ea253b68e42b01'], + }), + ('dismo', '1.1-4', { + 'checksums': ['f2110f716cd9e4cca5fd2b22130c6954658aaf61361d2fe688ba22bbfdfa97c8'], + }), + ('extrafontdb', '1.0', { + 'checksums': ['faa1bafee5d4fbc24d03ed237f29f1179964ebac6e3a46ac25b0eceda020b684'], + }), + ('Rttf2pt1', '1.3.7', { + 'checksums': ['4a4e50578b5c1dbfb90c289ee388c102de1f9c84f8b8ddb8d2294b58474e0e8a'], + }), + ('extrafont', '0.17', { + 'checksums': ['2f6d7d79a890424b56ddbdced361f8b9ddede5edd33e090b816b88a99315332d'], + }), + ('fields', '9.6', { + 'checksums': ['410424d74861ad0ba16f26e2b44bd63a9b590a190cc98c048dac55891422ffec'], + }), + ('shapefiles', '0.7', { + 'checksums': ['eeb18ea4165119519a978d4a2ba1ecbb47649deb96a7f617f5b3100d63b3f021'], + }), + ('fossil', '0.3.7', { + 'checksums': ['3feba6ceecaa6f2f68fdc1ceb0019395ccfadb0cf033e1709dddb690c7f210a1'], + }), + ('geiger', '2.0.6', { + 'checksums': ['e13b2c526378eaf9356b00bbe21b3c2c956327f8062fed638ccc1f49591c3eff'], + }), + ('glmnet', '2.0-16', { + 'checksums': ['a54ccd802fce6625f3b69d747b28efe62ed8cc23397a5f8df4777d177e2839af'], + }), + ('crosstalk', '1.0.0', { + 'checksums': ['b31eada24cac26f24c9763d9a8cbe0adfd87b264cf57f8725027fe0c7742ca51'], + }), + ('miniUI', '0.1.1.1', { + 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], + }), + ('ps', '1.1.0', { + 'checksums': ['5d5240d5bf1d48c721b3fdf47cfc9dbf878e388ea1f057b764db05bffdc4a9fe'], + }), + ('processx', '3.2.0', { + 'checksums': ['c4ba602fcbdc032ae9d94701b3e6b83a2dab1b53d0b4f9937b07a84eae22fddf'], + }), + ('webshot', '0.5.0', { + 'checksums': ['f0a1be8b0563d95550569a0620d546a9876d1e279a932e9293e4be57ff0f271f'], + }), + ('manipulateWidget', '0.10.0', { + 'checksums': ['3d61a3d0cedf5c8a850a3e62ed6af38c600dc3f25b44c4ff07a5093bf9ca4ffd'], + }), + ('rgl', '0.99.16', { + 'checksums': ['692a545ed2ff0f5e15289338736f0e3c092667574c43ac358d8004901d7a1a61'], + }), + ('labdsv', '1.8-0', { + 'checksums': ['dfaeb03a6e1bab6cfd384c00671235b22f2b4254cac1129b24a348cb353b6e65'], + }), + ('stabs', '0.6-3', { + 'checksums': ['e961ae21d45babc1162b6eeda874c4e3677fc286fd06f5427f071ad7a5064a9f'], + }), + ('modeltools', '0.2-22', { + 'checksums': ['256a088fc80b0d9182f984f9bd3d6207fb7c1e743f72e2ecb480e6c1d4ac34e9'], + }), + ('strucchange', '1.5-1', { + 'checksums': ['740e2e20477b9fceeef767ae1002adc5ec397cb0f7daba5289a2c23b0dddaf31'], + }), + ('TH.data', '1.0-9', { + 'checksums': ['d8318a172ce2b9f7f284dc297c8a8d5093de8eccbb566c8e7580e70938dfae0f'], + }), + ('multcomp', '1.4-8', { + 'checksums': ['a20876619312310e9523d67e9090af501383ce49dc6113c6b4ca30f9c943a73a'], + }), + ('coin', '1.2-2', { + 'checksums': ['d518065d3e1eb00121cb4e0200e1e4ae6b68eca6e249afc38bbffa35d24105bb'], + }), + ('party', '1.3-1', { + 'checksums': ['d16a2562efa42c083c6446bdef6596a0a913938551cae01aa1e98d91aa98088e'], + }), + ('libcoin', '1.0-1', { + 'checksums': ['181b7f01b6568361e36ee242a96e20f0204ccdac3eba07294bddea822fd868c4'], + }), + ('inum', '1.0-0', { + 'checksums': ['f532817a426b6a02d5ceffe01810d2103432a8defb68a0cae4318246a61a01ac'], + }), + ('partykit', '1.2-2', { + 'checksums': ['6f753f617a9672f0b90d50c40c69631162806a6b28a9cae20370960092cb1f85'], + }), + ('mboost', '2.9-0', { + 'checksums': ['c201c74df0fe81f1718ae9ca12676e4246b814a15f551b5be61c12396032dc41'], + }), + ('msm', '1.6.6', { + 'checksums': ['fd12512d3cdca5fab634bf6222d896482bd1876192939da475f251b3a873a71a'], + }), + ('nor1mix', '1.2-3', { + 'checksums': ['435e6519e832ef5229c51ccb2619640e6b50dfc7470f70f0c938d18a114273af'], + }), + ('np', '0.60-8', { + 'checksums': ['924c342feb2a862fa3871a45db5f8434dbbfb900cfc40c001a0872108a3a069e'], + }), + ('polynom', '1.3-9', { + 'checksums': ['d35a50925cc5552a6aac0816a91dbc03e9fd77da47e06d27572fde9dcbee9de8'], + }), + ('polspline', '1.1.13', { + 'checksums': ['937561842d754e40a48d2e6d0c49638739e3fdc9bb81e9d8d05adea828371f22'], + }), + ('rms', '5.1-2', { + 'checksums': ['f1cfeef466ac436105756679353a3468027d97a600e3be755b819aef30ed9207'], + }), + ('RWekajars', '3.9.2-1', { + 'checksums': ['0e6c00ea2a0798dec828a3a3eb61fbcf43da305f1664f62774fbdb8e473dd600'], + }), + ('RWeka', '0.4-38', { + 'checksums': ['aae1f24268f7c8183d0a516ef54eb2688472f34e4fa35bc90b0312d0c4df12b0'], + }), + ('slam', '0.1-43', { + 'checksums': ['b0c866cc529eb7b8c560ec3e945294e924cf934af6346a72ef4e3df6ecc7c443'], + }), + ('tm', '0.7-5', { + 'checksums': ['5d3150d2bf0964405be07c30aa6be3c415bf56e24e6041ac77ccb9de8c9ca317'], + }), + ('TraMineR', '2.0-8', { + 'checksums': ['394d4481707dfd8a4b0e28681097948ab36934dbe4084cf0917ae5f3e0bb9774'], + }), + ('chemometrics', '1.4.2', { + 'checksums': ['b705832fa167dc24b52b642f571ed1efd24c5f53ba60d02c7797986481b6186a'], + }), + ('FNN', '1.1.2.1', { + 'checksums': ['175fc43f45ad4d70092b46cae78abc588a0aa9c5a41f811c72114f555996c1d8'], + }), + ('ipred', '0.9-7', { + 'checksums': ['a4885c5c13c0e3a22da86956b5260cdb228a4eaeda55469ae60114433466a360'], + }), + ('statmod', '1.4.30', { + 'checksums': ['9d2c1722a85f53623a9ee9f73d835119ae22ae2b8ec7b50d675401e314ea641f'], + }), + ('miscTools', '0.6-22', { + 'checksums': ['d00bb2602d1d31e9e1e13c8868cfe69d432bbe15afa8d4bbb83b3c9e0b9dcfea'], + }), + ('maxLik', '1.3-4', { + 'checksums': ['181ab87721b1e6e3859c60d12eea2f67a7135bfa679db73c20a9ef76d82c4b4a'], + }), + ('mlogit', '0.3-0', { + 'checksums': ['c1d99d39fd411fb01d593f289325ff025bc714611818ed9310da7d1f167f2f3b'], + }), + ('getopt', '1.20.2', { + 'checksums': ['3d6c12d32d6cd4b2909be626e570e158b3ed960e4739510e3a251e7f172de38e'], + }), + ('gsalib', '2.1', { + 'checksums': ['e1b23b986c18b89a94c58d9db45e552d1bce484300461803740dacdf7c937fcc'], + }), + ('optparse', '1.6.0', { + 'checksums': ['10e816bb8f5b08d52cfd3a0028903a8c62ef9cf7bfd85f9dae8af442e82bfbb4'], + }), + ('labelled', '1.1.0', { + 'checksums': ['2a1eec22db648065ac06376d49d2973314619bcb0d308f79a31e4e2a38613f70'], + }), + ('classInt', '0.2-3', { + 'checksums': ['21f447330ce7eb6f069f48cacc4bca7d14521218463ecb74f1b3df5ddae0d1a9'], + }), + ('questionr', '0.6.3', { + 'checksums': ['6939d4b089aabfb9afedfaf263e89da65b26df50f0a087e00eacbd06294f53ed'], + }), + ('klaR', '0.6-14', { + 'checksums': ['51e9d9149ba77874ccecc816a2a75619e2f9615c091f6e8969da20615c2b29bd'], + }), + ('neuRosim', '0.2-12', { + 'checksums': ['f4f718c7bea2f4b61a914023015f4c71312f8a180124dcbc2327b71b7be256c3'], + }), + ('locfit', '1.5-9.1', { + 'checksums': ['f524148fdb29aac3a178618f88718d3d4ac91283014091aa11a01f1c70cd4e51'], + }), + ('GGally', '1.4.0', { + 'checksums': ['9a47cdf004c41f5e4024327b94227707f4dad3a0ac5556d8f1fba9bf0a6355fe'], + }), + ('beanplot', '1.2', { + 'checksums': ['49da299139a47171c5b4ccdea79ffbbc152894e05d552e676f135147c0c9b372'], + }), + ('clValid', '0.6-6', { + 'checksums': ['c13ef1b6258e34ba53615b78f39dbe4d8ba47b976b3c24a3eedaecf5ffba19ed'], + }), + ('matrixStats', '0.54.0', { + 'patches': ['matrixStats-0.53.1_O1.patch'], + 'checksums': [ + '8f0db4e181300a208b9aedbebfdf522a2626e6675d2662656efb8ba71b05a06f', # matrixStats_0.54.0.tar.gz + '96ef21a1d5ee4ccd1f4a6b74ef5aa2699a52c38b34613d8ff9f3c4af952aa8fd', # matrixStats-0.53.1_O1.patch + ], + }), + ('DiscriMiner', '0.1-29', { + 'checksums': ['5aab7671086ef9940e030324651976456f0e84dab35edb7048693ade885228c6'], + }), + ('ellipse', '0.4.1', { + 'checksums': ['1a9a9c52195b26c2b4d51ad159ab98aff7aa8ca25fdc6b2198818d1a0adb023d'], + }), + ('leaps', '3.0', { + 'checksums': ['55a879cdad5a4c9bc3b5697dd4d364b3a094a49d8facb6692f5ce6af82adf285'], + }), + ('pbkrtest', '0.4-7', { + 'checksums': ['5cbb03ad2b2468720a5a610a0ebda48ac08119a34fca77810a85f554225c23ea'], + }), + ('carData', '3.0-1', { + 'checksums': ['12e523d3507aa4ef6d7aa594f8f4ad0deff1e0e5334caecf4e613ec31f6f77a4'], + }), + ('maptools', '0.9-3', { + 'checksums': ['289f5051e6b562f7a5e88fdcf8db9fa01b0e4261f7c5c7330ef3a71a03d8ab43'], + }), + ('zip', '1.0.0', { + 'checksums': ['6fa9ec7b093b8c717c50f205d4335c31c43c2ecb51c0242c9a0337d8d84df965'], + }), + ('openxlsx', '4.1.0', { + 'checksums': ['ab7b127353061a0e1cd621783366ffdd7c858c6df31cbbdd39aaa353af10ffd8'], + }), + ('rematch', '1.0.1', { + 'checksums': ['a409dec978cd02914cdddfedc974d9b45bd2975a124d8870d52cfd7d37d47578'], + }), + ('cellranger', '1.1.0', { + 'checksums': ['5d38f288c752bbb9cea6ff830b8388bdd65a8571fd82d8d96064586bd588cf99'], + }), + ('readxl', '1.1.0', { + 'checksums': ['b63d21fc6510acb373e96deaec45e966a523ec75cbec75a089529297ed443116'], + }), + ('rio', '0.5.10', { + 'checksums': ['3dc2898ca3c5bbf62295b5b961a759a27a5739f7ce444eb51b933e20f7781d95'], + }), + ('car', '3.0-0', { + 'checksums': ['30a06984080a2e30c9296d2b0371bdfb8e29b5b7eb6e53f8877d51b4959242cf'], + }), + ('flashClust', '1.01-2', { + 'checksums': ['48a7849bb86530465ff3fbfac1c273f0df4b846e67d5eee87187d250c8bf9450'], + }), + ('FactoMineR', '1.41', { + 'checksums': ['a9889d69e298b8a01e8d0a5a54260730e742c95681e367d759829aad9a8740c0'], + }), + ('flexclust', '1.3-5', { + 'checksums': ['dbf49969c93a7b314d9dc3299a0764ed9a804ba7dcbdc08a1235f244f4b85059'], + }), + ('flexmix', '2.3-14', { + 'checksums': ['837c7f175a211b3c484b2c7b81ec9729889a614c5c6e7d70c95a2c1d60ff846a'], + }), + ('prabclus', '2.2-6', { + 'checksums': ['41792980e40ba18204fab92d85120dcd468860e2204e52fb42636c6f7aee5a62'], + }), + ('diptest', '0.75-7', { + 'checksums': ['462900100ca598ef21dbe566bf1ab2ce7c49cdeab6b7a600a50489b05f61b61b'], + }), + ('trimcluster', '0.1-2.1', { + 'checksums': ['b64a872a6c2ad677dfeecc776c9fe5aff3e8bab6bc6a8c86957b5683fd5d2300'], + }), + ('fpc', '2.1-11.1', { + 'checksums': ['ccfe4c5acb8b7c313b7c07076b994900b09f1d13459a0ca7815de337e12931ab'], + }), + ('BiasedUrn', '1.07', { + 'checksums': ['2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e'], + }), + ('TeachingDemos', '2.10', { + 'checksums': ['2ef4c2e36ba13e32f66000e84281a3616584c86b255bca8643ff3fe4f78ed704'], + }), + ('kohonen', '3.0.6', { + 'patches': ['kohonen-3.0.6_intel-wd308.patch'], + 'checksums': [ + '8bdddc9d51635580256c80e801bb7dc9981d637eeaf2cffcbd83ec64641a202c', # kohonen_3.0.6.tar.gz + '9c63b853cebd07417133a541375fc24ea30e1bc42bf99cdf67597ed1a6cdc8f1', # kohonen-3.0.6_intel-wd308.patch + ], + }), + ('base64', '2.0', { + 'checksums': ['8e259c2b12446197d1152b83a81bab84ccb5a5b77021a9b5645dd4c63c804bd1'], + }), + ('doRNG', '1.7.1', { + 'checksums': ['27533d54464889d1c21301594137fc0f536574e3a413d61d7df9463ab12a67e9'], + }), + ('nleqslv', '3.3.2', { + 'checksums': ['f54956cf67f9970bb3c6803684c84a27ac78165055745e444efc45cfecb63fed'], + }), + ('Deriv', '3.8.5', { + 'checksums': ['40d43da3a8e93068874415995fdeba9ca2ef109b55211b228b43d1fa85e62520'], + }), + ('RGCCA', '2.1.2', { + 'checksums': ['20f341fca8f616c556699790814debdf2ac7aa4dd9ace2071100c66af1549d7d'], + }), + ('pheatmap', '1.0.10', { + 'checksums': ['c7fde6bf25decec1945af18fbab2edcd6a129a3b31817bc50779fcc561d1fdcb'], + }), + ('pvclust', '2.0-0', { + 'checksums': ['1a4615214992307fd7c786cf4607a3ae2af5c0d4067f5053e1c195798a70d741'], + }), + ('RCircos', '1.2.0', { + 'checksums': ['7fd06e2efc33b5c30fc4ba3945b04021f255ba4ffcc394348df7488b9394444a'], + }), + ('lambda.r', '1.2.3', { + 'checksums': ['0cd8e37ba1a0960888016a85d492da51a57df54bd65ff920b08c79a3bfbe8631'], + }), + ('futile.options', '1.0.1', { + 'checksums': ['7a9cc974e09598077b242a1069f7fbf4fa7f85ffe25067f6c4c32314ef532570'], + }), + ('futile.logger', '1.4.3', { + 'checksums': ['5e8b32d65f77a86d17d90fd8690fc085aa0612df8018e4d6d6c1a60fa65776e4'], + }), + ('VennDiagram', '1.6.20', { + 'checksums': ['e51cb3fff23c6ec8191966490bf875a7415f8725d4054bae881a25febb9281c5'], + }), + ('xlsxjars', '0.6.1', { + 'checksums': ['37c1517f95f8bca6e3514429394d2457b9e62383305eba288416fb53ab2e6ae6'], + }), + ('xlsx', '0.6.1', { + 'checksums': ['a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4'], + }), + ('uroot', '2.0-9', { + 'patches': ['uroot-2.0-9_CUDA.patch'], + 'checksums': [ + '9b7616d64ed87b29ee45368bf7f08d15c0ec058e450c69171fbfecb44943ac5b', # uroot_2.0-9.tar.gz + '6be1eb433301f0078942da7268d927bfd25aba5087a86d671dd0a098e976117b', # uroot-2.0-9_CUDA.patch + ], + }), + ('forecast', '8.4', { + 'patches': ['forecast-6.1_icpc-wd308.patch'], + 'checksums': [ + '695cdf0376f1f519a236bec52722c41ea5896f2064f1403d0ad4914c5611188f', # forecast_8.4.tar.gz + '5100dce59858960fc2ade7c599ecda13f3473984fb2bd90f8fa6598653e7ddc2', # forecast-6.1_icpc-wd308.patch + ], + }), + ('fma', '2.3', { + 'checksums': ['f516eff79e14d4ffefcdc2db06d97ae57f998e37e871264457078f671384fafc'], + }), + ('expsmooth', '2.3', { + 'checksums': ['ac7da36347f983d6ec71715daefd2797fe2fc505c019f4965cff9f77ce79982a'], + }), + ('fpp', '0.5', { + 'checksums': ['9c87dd8591b8a87327cae7a03fd362a5492495a96609e5845ccbeefb96e916cb'], + }), + ('tensor', '1.5', { + 'checksums': ['e1dec23e3913a82e2c79e76313911db9050fb82711a0da227f94fc6df2d3aea6'], + }), + ('polyclip', '1.9-1', { + 'checksums': ['c5d578bf1b34fdc44c909a2cbd1e33ed842f09dd045005885669683b94fcb164'], + }), + ('goftest', '1.1-1', { + 'checksums': ['db6cb1ff6e18520b172e93fca5d7d953bd2d06f4af73bf90aa0a09df8cad71a0'], + }), + ('spatstat.utils', '1.9-0', { + 'checksums': ['3aef50d0bb48dbc57c95b1fb7af37c400499200e9f38cced1462027fcb1afd79'], + }), + ('spatstat.data', '1.3-1', { + 'checksums': ['c3ad35677c78aa04e6fb1927aa15abd21ff1fdac58a8b365ce54bc93034b8b8f'], + }), + ('spatstat', '1.56-1', { + 'checksums': ['8683dd4860311e70026f62e2590a9d7dda932484555d4c45f97cdb96c7cb7a60'], + }), + ('rgdal', '1.3-4', { + 'checksums': ['9dab55eca80e9df4982ee91bfcddde8195187b41120a824e27e0732c4c2575da'], + }), + ('gdalUtils', '2.0.1.14', { + 'checksums': ['890a502b2eb5f1b23655fab94caad5d32adca05b93f5db1d96d9dcde3f0e7737'], + }), + ('pracma', '2.1.4', { + 'checksums': ['0ccaef86c1446971ca244e6dbcc605222c2f652b23a5db921070e37a6240f5f9'], + }), + ('RCurl', '1.95-4.11', { + 'checksums': ['792a091cf5b80c460d98ed80fe1cad5d9406d0afc32e466e970ee4d2f68c97bf'], + }), + ('bio3d', '2.3-4', { + 'checksums': ['f9b39ab242cbedafcd98c1732cb1f5c0dd9ef66e28be39695e3420dd93e2bafe'], + }), + ('AUC', '0.3.0', { + 'checksums': ['e705f2c63d336249d19187f3401120d738d42d323fce905f3e157c2c56643766'], + }), + ('interpretR', '0.2.4', { + 'checksums': ['4c08a6dffd6fd5764f27812f3a085c53e6a21d59ae82d903c9c0da93fd1dd059'], + }), + ('cvAUC', '1.1.0', { + 'checksums': ['c4d8ed53b93869650aa2f666cf6d1076980cbfea7fa41f0b8227595be849738d'], + }), + ('SuperLearner', '2.0-24', { + 'checksums': ['adf658a2c885b125c570fb9b4fa9b84a6610cfa821f24c5a660d0d2327c4ef43'], + }), + ('lpSolve', '5.6.13', { + 'checksums': ['d5d41c53212dead4fd8e6425a9d3c5767cdc5feb19d768a4704116d791cf498d'], + }), + ('mediation', '4.4.6', { + 'checksums': ['b17784c001305d5f3b84573a673cef31475520d9baec972e42431be193bf305f'], + }), + ('ModelMetrics', '1.2.0', { + 'checksums': ['3021ae88733695a35d66e279e8e61861431f14c9916a341f0a562f675cf6ede9'], + }), + ('CVST', '0.2-2', { + 'checksums': ['854b8c983427ecf9f2f7798c4fd1c1d06762b5b0bcb1045502baadece6f78316'], + }), + ('DRR', '0.0.3', { + 'checksums': ['7493389c1fb9ddc4d4261e15bf2d4198603227275688b1d3e3994d47e976a1f9'], + }), + ('dimRed', '0.1.0', { + 'checksums': ['fb0cef7a21b8a5219c74e5227a282168599dd63e904130366f3d2fed8a625a39'], + }), + ('lubridate', '1.7.4', { + 'checksums': ['510ca87bd91631c395655ee5029b291e948b33df09e56f6be5839f43e3104891'], + }), + ('ddalpha', '1.3.4', { + 'checksums': ['41ba9952deb2e81713f2e308357d3b7adfe348135ba7e3c94c347db5e0029699'], + }), + ('gower', '0.1.2', { + 'checksums': ['eb91b2d2784d237c7055abcf3cfa4fc0b2226b855a0c29fc5a4e8eaa689079d5'], + }), + ('RcppRoll', '0.3.0', { + 'checksums': ['cbff2096443a8a38a6f1dabf8c90b9e14a43d2196b412b5bfe5390393f743f6b'], + }), + ('recipes', '0.1.3', { + 'checksums': ['be468f7b9b479e13785e90d239c4784679ad7648efd3d02cfc2a58a2fb1d10ef'], + }), + ('caret', '6.0-80', { + 'checksums': ['0705874a30bd5960a51616338534255734e792a4af3f28368e1040f7bf820d76'], + }), + ('adabag', '4.2', { + 'checksums': ['47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81'], + }), + ('parallelMap', '1.3', { + 'checksums': ['a52d93572c1b85281e41d8e3c2db97dda5fce96c222e04171b4489ec5000cd08'], + }), + ('ParamHelpers', '1.11', { + 'checksums': ['1614f4c0842cf822befc01228ab7263417f3423dd6a1dc24347b14f8491637a0'], + }), + ('ggvis', '0.4.3', { + 'checksums': ['34d517783016aaa1c4bef8972f4c06df5cd9ca0568035b647e60a8369043ecdc'], + }), + ('mlr', '2.12.1', { + 'checksums': ['9cbb98b82eb493b783fe8808a18d76f32881d941364466ef8829b852fabbc82c'], + }), + ('unbalanced', '2.0', { + 'checksums': ['9be32b1ce9d972f1abfff2fbe18f5bb5ba9c3f4fb1282063dc410b82ad4d1ea2'], + }), + ('RSNNS', '0.4-11', { + 'checksums': ['87943126e98ae47f366e3025d0f3dc2f5eb0aa2924508fd9ee9a0685d7cb477c'], + }), + ('abc.data', '1.0', { + 'checksums': ['b242f43c3d05de2e8962d25181c6b1bb6ca1852d4838868ae6241ca890b161af'], + }), + ('abc', '2.1', { + 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], + }), + ('lhs', '0.16', { + 'checksums': ['9cd199c3b5b2be1736d585ef0fd39a00e31fc015a053333a7a319668d0809425'], + }), + ('tensorA', '0.36.1', { + 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], + }), + ('EasyABC', '1.5', { + 'checksums': ['1dd7b1383a7c891cafb34d9cec65d92f1511a336cff1b219e63c0aa791371b9f'], + }), + ('shape', '1.4.4', { + 'checksums': ['f4cb1b7d7c84cf08d2fa97f712ea7eb53ed5fa16e5c7293b820bceabea984d41'], + }), + ('whisker', '0.3-2', { + 'checksums': ['484836510fcf123a66ddd13cdc8f32eb98e814cad82ed30c0294f55742b08c7c'], + }), + ('commonmark', '1.5', { + 'checksums': ['7fa81635bf0d26395fdd8dd830e16f9910a388faa949b2874aed7a505f2e9dcb'], + }), + ('desc', '1.2.0', { + 'checksums': ['e66fb5d4fc7974bc558abcdc107a1f258c9177a29dcfcf9164bc6b33dd08dae8'], + }), + ('callr', '2.0.4', { + 'checksums': ['0e3fa4e047f61f4e29ab2dee8f585861fb77a5f5ad6c81f125e98b6130c6a380'], + }), + ('pkgbuild', '1.0.0', { + 'checksums': ['a9691dd3e27cd053a5d4cc8df8b46baa9915c95d4ce03b8e4cb4c77a0a403f82'], + }), + ('pkgload', '1.0.0', { + 'checksums': ['fd8a20ccee59b3c8affaf287ac21c6f7c9adf4f2e5541227a1da256c931052e6'], + }), + ('roxygen2', '6.1.0', { + 'checksums': ['4af522cf79beebf96e591b8caf1465018e91310d12bb1a39a2cbed153499294a'], + }), + ('git2r', '0.23.0', { + 'checksums': ['3fd37340572ecc3ac8daf771b82a851635f8f7d416a4ab84f7d69522be044504'], + }), + ('rversions', '1.0.3', { + 'checksums': ['21d0809f46505de89a2be7be9449e39c39cff5bc77e584dec976ee6c0b884f44'], + }), + ('devtools', '1.13.6', { + 'checksums': ['b9749de8b095bd4983ef95a7700e53e4295a747fd20e9eae77dc372f5b2236b5'], + }), + ('Rook', '1.1-1', { + 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + }), + ('Cairo', '1.5-9', { + 'patches': ['Cairo-1.5-9.patch'], + 'checksums': [ + '2a867b6cae96671d6bc3acf9334d6615dc01f6ecf1953a27cde8a43c724a38f4', # Cairo_1.5-9.tar.gz + '3efa99888503949eefe586faf3f6f80566674c5a8cfb2c62b648b42f22466dfa', # Cairo-1.5-9.patch + ], + }), + ('RMTstat', '0.3', { + 'checksums': ['81eb4c5434d04cb66c749a434c33ceb1c07d92ba79765d4e9233c13a092ec2da'], + }), + ('Lmoments', '1.2-3', { + 'checksums': ['e974b65d6116d540bc2c934c40c5552f64d7781b77c259a5b7724b1338c9e08e'], + }), + ('distillery', '1.0-4', { + 'checksums': ['3d3a8445471b19a6b652761ca783994b2d2108b64ff539b0597a9db9697d17d4'], + }), + ('extRemes', '2.0-9', { + 'checksums': ['7543e0cb97f12d0dad5b60575b98e6b7e73dc6e87e622b8c39def734a562fb32'], + }), + ('pixmap', '0.4-11', { + 'checksums': ['6fa010749a59cdf56aad9f81271473b7d55697036203f2cd5d81372bcded7412'], + }), + ('tkrplot', '0.0-24', { + 'checksums': ['2873630a37d7ae1e09a5803d9a89ca0494edd83526c7b1860d9246543722f311'], + }), + ('misc3d', '0.8-4', { + 'checksums': ['75de3d2237f67f9e58a36e80a6bbf7e796d43eb46789f2dd1311270007bf5f62'], + }), + ('multicool', '0.1-10', { + 'patches': ['multicool-0.1-10_icpc-wd308.patch'], + 'checksums': [ + '5bb0cb0d9eb64420c862877247a79bb0afadacfe23262ec8c3fa26e5e34d6ff9', # multicool_0.1-10.tar.gz + '2afcb15d37d0e4adc43530e448325cb97bc46ebf4d1da9fe6c07cf0070fe0a0c', # multicool-0.1-10_icpc-wd308.patch + ], + }), + ('plot3D', '1.1.1', { + 'checksums': ['f6fe4a001387132626fc553ed1d5720d448b8064eb5a6917458a798e1d381632'], + }), + ('plot3Drgl', '1.0.1', { + 'checksums': ['466d428d25c066c9c96d892f24da930513d42b1bdf76d3b53628c3ba13c3e48a'], + }), + ('OceanView', '1.0.4', { + 'checksums': ['e67f6f376737e1e5cf22fdfe2769a8f674e90c886b0e43942e97d9a3e6924f1c'], + }), + ('ks', '1.11.3', { + 'checksums': ['0d69e85fb4dc97045fdc273b36cf44b185ab60a6d7b17e1eb0c6dddf074be47c'], + }), + ('logcondens', '2.1.5', { + 'checksums': ['72e61abc1f3eb28830266fbe5b0da0999eb5520586000a3024e7c26be93c02eb'], + }), + ('Iso', '0.0-17', { + 'checksums': ['c007d6eaf6335a15c1912b0804276ff39abce27b7a61539a91b8fda653629252'], + }), + ('penalized', '0.9-51', { + 'checksums': ['eaa80dca99981fb9eb576261f30046cfe492d014cc2bf286c447b03a92e299fd'], + }), + ('clusterRepro', '0.5-1.1', { + 'checksums': ['b7fcb9db0c762a2e6e22a0a0689affd73504c56f13c13b04272a946630334e6f'], + }), + ('randomForestSRC', '2.7.0', { + 'checksums': ['2bcb2734f7a3f6e372bd234b2db23fc9c896e9663032c5f04babb54a2093988b'], + }), + ('sm', '2.2-5.5', { + 'checksums': ['43e212a14c364b98b10018b56fe0a619ccffe4bde1294e6c45b3eafe7caf82e7'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-2', { + 'checksums': ['91d5aea1468394f9e2bda773ab51f8a16a198bfc1d8474c1c48bcaba87f9c0be'], + }), + ('matrixcalc', '1.0-3', { + 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], + }), + ('arm', '1.10-1', { + 'checksums': ['6f1158c9295e65bd649139224497d3356189b931ff143f9b374daae72548776f'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('visNetwork', '2.0.4', { + 'checksums': ['0503408b195a812bcf589f8d34f5c3f9a38e92e78b699c3c7d737f7054d5ed15'], + }), + ('rgexf', '0.15.3', { + 'checksums': ['2e8a7978d1fb977318e6310ba65b70a9c8890185c819a7951ac23425c6dc8147'], + }), + ('influenceR', '0.1.0', { + 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.0', { + 'checksums': ['2b186dae1b19018681b979e9444bf16559c42740d8382676fbaf3b0f8a44337e'], + }), + ('sem', '3.1-9', { + 'checksums': ['4a33780202506543da85877cd2813250114420d6ec5e75457bc67477cd332cb9'], + }), + ('jpeg', '0.1-8', { + 'checksums': ['d032befeb3a414cefdbf70ba29a6c01541c54387cc0a1a98a4022d86cbe60a16'], + }), + ('network', '1.13.0.1', { + 'checksums': ['60b71983b638c7812ccd986ead438ed7bb2bd8080c01c85d8ea70587275e73ad'], + }), + ('statnet.common', '4.1.4', { + 'checksums': ['2cea993a52f27d8a5a5e91d3a5dcffcc86523001f6f646cd26ec37c2486dbe91'], + }), + ('sna', '2.4', { + 'checksums': ['2292b3190e8d879e494527ae9d9d1174c31cb4183749ecb455aedd8d534048cf'], + }), + ('glasso', '1.10', { + 'checksums': ['e6fa74139a2b5f475f134cc0d6b4000ed870beb5865294e9f1d68b4d42bf505b'], + }), + ('huge', '1.2.7', { + 'checksums': ['042b771c334cf4d1a92c5c546ca025238919f772a50457594b7e0bd243498d8c'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('ggm', '2.3', { + 'checksums': ['832ffe81ff87c6f1a6644e689ebbfb172924b4c4584ac8108d1244d153219ed8'], + }), + ('BDgraph', '2.51', { + 'checksums': ['1d63eb0d492be3d547ec2f0af07c7158a24201c11e97d765a97dde78964a8c21'], + }), + ('pbapply', '1.3-4', { + 'checksums': ['cdfdaf9b8aecbe48daac858aecaf65a766b74a363d1eb7cd6ebf27c0549f6552'], + }), + ('qgraph', '1.5', { + 'checksums': ['05addcd3f03736bd863c81181055e9ba6db55088cbfe6e5336338223234507d4'], + }), + ('HWxtest', '1.1.7', { + 'checksums': ['7cfcf7860d655945f9d3bbda4590374d3100bb5da6b49956f2e701b910a20e0c'], + }), + ('diveRsity', '1.9.90', { + 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], + }), + ('doSNOW', '1.0.16', { + 'checksums': ['161434ecd55f04d6b070da784b222a7686c914b73de558eef6048a229022398e'], + }), + ('phangorn', '2.4.0', { + 'checksums': ['31d0ea035b48d3940013f369e514351db19f9f92b2832c53f09f752b4a998875'], + }), + ('geepack', '1.2-1', { + 'checksums': ['7effe67381129a48154c445704490ea3b5f2e1adedb66cb65f61369dd1f8d38d'], + }), + ('biom', '0.3.12', { + 'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'], + }), + ('pim', '2.0.1', { + 'checksums': ['174568a01f68b9601a4ea89ca5857bf4888242f00e4212bfb7a422d6292300d5'], + }), + ('minpack.lm', '1.2-1', { + 'checksums': ['14cb7dba3ef2b46da0479b46d46c76198e129a31f6157cd8b37f178adb15d5a3'], + }), + ('rootSolve', '1.7', { + 'checksums': ['08b3bb63f04fc0b065cb615b6ca1ef95eb6df7a813eb9eb625bc15c6de332c22'], + }), + ('diagram', '1.6.4', { + 'checksums': ['7c2bc5d5d634c3b8ca7fea79fb463e412962d88f47a77a74c811cc62f375ce38'], + }), + ('FME', '1.3.5', { + 'checksums': ['3619d88df2a41ca8819b93bb7dff3b8233f76ff8ab0ca67c664f530f835935e4'], + }), + ('bmp', '0.3', { + 'checksums': ['bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649'], + }), + ('tiff', '0.1-5', { + 'checksums': ['9514e6a9926fcddc29ce1dd12b1072ad8265900373f738de687ef4a1f9124e2b'], + }), + ('readbitmap', '0.1.5', { + 'checksums': ['737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291'], + }), + ('imager', '0.41.1', { + 'patches': ['imager-0.41.1_icpc-wd308.patch'], + 'checksums': [ + 'afb42fdd3f62c41007eafa205f671cc4af6d165dc813a7cac194124251bc4849', # imager_0.41.1.tar.gz + '3e314bf545c40adfeb62a1aff6895e45083e8c9541116f9e771b16bc943451bf', # imager-0.41.1_icpc-wd308.patch + ], + }), + ('signal', '0.7-6', { + 'checksums': ['6b60277b07cf0167f8272059b128cc82f27a9bab1fd33d74c2a9e1f2abca5def'], + }), + ('tuneR', '1.3.3', { + 'checksums': ['bdc3c2017b162d2ba0a249e80361a4f47202e763c21aecfc57380a482a3a692b'], + }), + ('pastecs', '1.3.21', { + 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], + }), + ('audio', '0.1-5.1', { + 'checksums': ['4d7977783d307a88d2323466ab8511a5ea9c8ac52815bffee79b053b0815b0c6'], + }), + ('fftw', '1.0-4', { + 'checksums': ['80413901ce751c0700ac53283366cfcfe3cbeec2982d29721a0275f9fb9de204'], + }), + ('seewave', '2.1.0', { + 'checksums': ['5ea4fd79fe99f094c6bb9092e6048490175e9bedcd6d6e97badc1143df861f44'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('oce', '0.9-23', { + 'checksums': ['390fd082710ee1586074ff20df61208df4c76b9f2dc0c9b1125aade4c934b04c'], + }), + ('ineq', '0.2-13', { + 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], + }), + ('soundecology', '1.3.3', { + 'checksums': ['276164d5eb92c78726c647be16232d2443acbf7061371ddde2672b4fdb7a069a'], + }), + ('memuse', '4.0-0', { + 'checksums': ['fbf8716a1388692ee439f69ac99643fa427eb100027d8911ff0fbfdcb5b6c3bc'], + }), + ('pinfsc50', '1.1.0', { + 'checksums': ['b6b9b6365a3f408533264d7ec820494f57eccaf362553e8478a46a8e5b474aba'], + }), + ('vcfR', '1.8.0', { + 'checksums': ['5ffcf9980c1936b9be41b92d5887c56a7ec6e3cf197e5ef7c78aefa8aba20499'], + }), + ('glmmML', '1.0.3', { + 'checksums': ['93a43621cb533b6f95cdf7c880ec28803b022b2729388f3f4b39ba4c4ee46aeb'], + }), + ('ucminf', '1.1-4', { + 'checksums': ['a2eb382f9b24e949d982e311578518710f8242070b3aa3314a331c1e1e7f6f07'], + }), + ('ordinal', '2018.4-19', { + 'checksums': ['ab7fc4527e22460d74ec1198450222e7c6e9940ca1fd2c5e04a939a925a9d711'], + }), + ('Rtsne', '0.13', { + 'patches': ['Rtsne-0.13_icpc-wd308.patch'], + 'checksums': [ + '1c3bffe3bd11733ee4fe01749c293669daafda1af2ec74f9158f6080625b999d', # Rtsne_0.13.tar.gz + '89d435412c6e9e9721b2a5d8a7065fda6faed7db34c06ad05ecad7065b958fd4', # Rtsne-0.13_icpc-wd308.patch + ], + }), + ('cowplot', '0.9.3', { + 'checksums': ['3e10475fd7506ea9297ed72eb1a3acf858c6fa99d26e46fc39654eba000c3dcb'], + }), + ('tsne', '0.1-3', { + 'checksums': ['66fdf5d73e69594af529a9c4f261d972872b9b7bffd19f85c1adcd66afd80c69'], + }), + ('RcppProgress', '0.4.1', { + 'checksums': ['11764105922f763d4c75c502599ec7dcc2fd629a029964caf53f98b41d0c607a'], + }), + ('sn', '1.5-2', { + 'checksums': ['2f2a83f39e58b110336546c3d66796b68d17f9b7fd5787d740bbc8ff91c9fc99'], + }), + ('tclust', '1.4-1', { + 'checksums': ['4b0be612c8ecd7b4eb19a44ab6ac8f5d40515600ae1144c55989b6b41335ad9e'], + }), + ('ranger', '0.10.1', { + 'checksums': ['327ce1f603aa3a66f66494bb85ad92aaf7622bb0949976a96325d7f6663fe68b'], + }), + ('hexbin', '1.27.2', { + 'checksums': ['46d47b1efef75d6f126af686a4dd614228b60418b9a5bde9e9e5d11200a0ee52'], + }), + ('pryr', '0.1.4', { + 'checksums': ['d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b'], + }), + ('moments', '0.14', { + 'checksums': ['2a3b81e60dafdd092d2bdd3513d7038855ca7d113dc71df1229f7518382a3e39'], + }), + ('laeken', '0.4.6', { + 'checksums': ['465174263f2d495162bf1ee8ab35b362dae8088e458c162ce517813267d813e6'], + }), + ('VIM', '4.7.0', { + 'checksums': ['cdd64cbdca23c097efa8d5084bfc1c0d1449744e90a41680a5246db979d14cee'], + }), + ('proxy', '0.4-22', { + 'checksums': ['aa866ccbfc81253e3651963b5ba482feeb5d1a0449e818486271d79a23720e50'], + }), + ('smoother', '1.1', { + 'checksums': ['91b55b82f805cfa1deedacc0a4e844a2132aa59df593f3b05676954cf70a195b'], + }), + ('dynamicTreeCut', '1.63-1', { + 'checksums': ['831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9'], + }), + ('DT', '0.4', { + 'checksums': ['3daa96b819ca54e5fbc2c7d78cb3637982a2d44be58cea0683663b71cfc7fa19'], + }), + ('beeswarm', '0.2.3', { + 'checksums': ['0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843'], + }), + ('vipor', '0.4.5', { + 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], + }), + ('ggbeeswarm', '0.6.0', { + 'checksums': ['bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333'], + }), + ('shinydashboard', '0.7.0', { + 'checksums': ['0b7b102e9e5bea78ddc4da628d072a358270f2db9b63a6ebe4d8bdce3066d883'], + }), + ('rrcov', '1.4-4', { + 'checksums': ['8569e00ec8a86db8db4fcb8a74bc81314ef2b53fa3a284a02ad37f103782c572'], + }), + ('WriteXLS', '4.0.0', { + 'checksums': ['a0541da45e16bc4bf994cdf3f07a0e202c38d52386460c64e27fe6c1cd889d5b'], + }), + ('bst', '0.3-15', { + 'checksums': ['d08570927d9d1b1748c8c8520546a1b591f54ac515be0c40af5a818782466708'], + }), + ('mpath', '0.3-5', { + 'checksums': ['b5c921aaddc0b2590dfd7b011dc480836ecdae6225d2f0b263a50d780dbd64fb'], + }), + ('timereg', '1.9.2', { + 'checksums': ['b0b969807e72003cc537c979f01b62e6199fa335baca4cf92473babcd19cac35'], + }), + ('peperr', '1.1-7', { + 'checksums': ['73e0422c71f2df59cd4a0f820c87dd828f2952b60df2d6c58f62a35559d74605'], + }), + ('heatmap3', '1.1.1', { + 'checksums': ['055e30a2fee0e8b6e499cdc5ccb7e37e5615ed3d52cc7058fc5ca5fc808cf393'], + }), + ('GlobalOptions', '0.1.0', { + 'checksums': ['567a0a51f6b7b14127302f00e6e4944befd4964c069f96a9e61256e8c3c79ef2'], + }), + ('circlize', '0.4.4', { + 'checksums': ['9c638b3a2b798fe6f8affa344a81dbd695bed4ebcc661d52f8899488a3aa48d0'], + }), + ('GetoptLong', '0.1.7', { + 'checksums': ['b9a98881db407eae9b711c4fa9170168fd5f3be1f8485cd8f28d0a60ace083ba'], + }), + ('dendextend', '1.8.0', { + 'checksums': ['30b72fbbb63555d65f8991c7347400f4df57a07c1342d00666bc8b21d8b039ee'], + }), + ('RInside', '0.2.14', { + 'checksums': ['8de5340993fe879ca00fa559c5b1b27b408ba78bfc5f67d36d6f0b8d8e8649cf'], + }), + ('limSolve', '1.5.5.3', { + 'checksums': ['2f27c03411e0d771ad50d5412125bf4fa0ba461051610edc77e20d28488e86d2'], + }), + ('dbplyr', '1.2.2', { + 'checksums': ['9d410bb0055fffe10f1f8da55a5b24d98322c7b571d74df61427d5888332bc48'], + }), + ('modelr', '0.1.2', { + 'checksums': ['6a9831c510967551a6064716dfd4db48b59dc056dcf1c7f1d2cce05ef0789027'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('clipr', '0.4.1', { + 'checksums': ['1bebc57ddad830c469415a99b13124aee14b91f4b1701fd20defb04623413d18'], + }), + ('reprex', '0.2.0', { + 'checksums': ['69a3fa8ceabb2fa001d91e03a8a28391d2a1af2c2f9b3de694e08d1f65bf84d0'], + }), + ('selectr', '0.4-1', { + 'checksums': ['8bd42f167629344e485e586f9b05fed342746132489079084d82133d7b3ee2ca'], + }), + ('rvest', '0.3.2', { + 'checksums': ['0d6e8837fb1df79b1c83e7b48d8f1e6245f34a10c4bb6952e7bec7867e4abb12'], + }), + ('tidyverse', '1.2.1', { + 'checksums': ['ad67a27bb4e89417a15338fe1a40251a7b5dedba60e9b72637963d3de574c37b'], + }), + ('R.cache', '0.13.0', { + 'checksums': ['d3d4a99a676734ea53e96747d87857fa69615e59858804e92f8ad9ddcf62c5c1'], + }), + ('R.rsp', '0.42.0', { + 'checksums': ['a02ebd3857849896f30993ed8306c88b03116250261d9d85dcee48103f0498fd'], + }), + ('listenv', '0.7.0', { + 'checksums': ['6126020b111870baea08b36afa82777cd578e88c17db5435cd137f11b3964555'], + }), + ('globals', '0.12.1', { + 'checksums': ['2a72473375bac80a8e882b5e2534f0fc073594a565a09263a1b68396b7edcff9'], + }), + ('future', '1.9.0', { + 'checksums': ['d807c19d85dc47a28dd391eab3d67b8d1b91070ffb26a8b2b987c6c447d0cd14'], + }), + ('gdistance', '1.2-2', { + 'checksums': ['c8c923f02ae4e9ef8376d1b195e0246b6941356c8c790c0a5673c5009eee1753'], + }), + ('vioplot', '0.2', { + 'checksums': ['601f043630999e0498f0fba213d3d3fefd6ff0abf8fdb22119199b3d8d58939b'], + }), + ('emulator', '1.2-17', { + 'checksums': ['28be9a86883e7bc319d78a53efec2e8abe445519774b723466d3aa8f537a1e94'], + }), + ('gmm', '1.6-2', { + 'checksums': ['b12f888276c2d480f17ae2711e4915bb253574e3fc36531349f1c2f2c8ad715d'], + }), + ('tmvtnorm', '1.4-10', { + 'checksums': ['1a9f35e9b4899672e9c0b263affdc322ecb52ec198b2bb015af9d022faad73f0'], + }), + ('IDPmisc', '1.1.17', { + 'checksums': ['18ec9db0aab1de526b8e57ac1f0223811806a814777149b793722b999e6f7c59'], + }), + ('gap', '1.1-22', { + 'checksums': ['71a691aac9ce29bfcf1159eacba1866c8571b781f68fb32a3e52fb8584f03ef7'], + }), + ('qrnn', '2.0.3', { + 'checksums': ['4f10a22d1e064f75dd17f7bceea0c34aeeda3f803c2cb61a328152728c7c8151'], + }), + ('TMB', '1.7.14', { + 'checksums': ['b499644b4bbc89f191101639ff8d9d9ec90b896ca24ca650e6aea36f0928ec2e'], + }), + ('glmmTMB', '0.2.2.0', { + 'checksums': ['c5176f4f00ca4b900f49d3744bbcc6772fc31f431bcbf2431db64a5da99c97b2'], + }), + ('DHARMa', '0.2.0', { + 'checksums': ['3422c9d733e7203d17d88761422e242a72309928bc3b01378810fde7c50f004a'], + }), + ('bridgesampling', '0.4-0', { + 'checksums': ['9577b535535b46022d06a7372ee309e2eb2ef0d045d65e2f3ed507f9b88062bf'], + }), + ('BayesianTools', '0.1.5', { + 'checksums': ['f32548f15fe8c625823eb2098165b680e07704356525e631c7bb129f8297bc0a'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.1', { + 'checksums': ['f1069bf920e9bc3da6bf43542a3a7ccc3142544d759945115ecade69dd5ccde0'], + }), + ('dummies', '1.5.6', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '1.1.2', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3', { + 'checksums': ['e377effe345987850ece985eabf79750ca1979d75469d17a323c21515ad1dda8'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.4.1', { + 'checksums': ['6f585cb622cc52e2b7f3efddb7a363e91771bff80b8facb554755c2b33b7f402'], + }), + ('Rssa', '1.0', { + 'checksums': ['9cc20a7101d8dff4c6cfb789f9bdc14e2b3bb128d7613a67b0f9633cf006902a'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.32', { + 'checksums': ['23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1'], + }), + ('DistributionUtils', '0.5-1', { + 'checksums': ['e92a29003d5e5974f53e40bdb8417e2bdabe784304e21360d7a1cbec7818853f'], + }), + ('gapfill', '0.9.6', { + 'checksums': ['850d0be9d05e3f3620f0f5143496321f1004ed966299bffd6a67a9abd8d9040d'], + }), + ('gee', '4.13-19', { + 'checksums': ['ebd3eb754b338dc8d89a35fff149af57c1be3aa2eb6162912c7cc52a8572c292'], + }), + ('Matching', '4.9-3', { + 'checksums': ['1fbf346d75a079f5b23137dd7bc112207db8d64adfd197826ae6b5748600bc02'], + }), + ('MatchIt', '3.0.2', { + 'checksums': ['782b159a2b5172e758e3993177930d604140ae668fd8a7c98c30792df80de9de'], + }), + ('RItools', '0.1-16', { + 'checksums': ['749fd32e93826ed047ba080542cdde8178d3f8cf4ae12b34890c597de97f4567'], + }), + ('optmatch', '0.9-10', { + 'patches': ['optmatch-0.9-10_icpc-wd308.patch'], + 'checksums': [ + 'e1fcc23ab969a4018ef33ca22a210c14f8ca81840bee8e5e2e1c3179729adbca', # optmatch_0.9-10.tar.gz + '1f0f2a6665267e7c5693f858afddc80a9912301e82c62a5b58c5694d28f3f7ec', # optmatch-0.9-10_icpc-wd308.patch + ], + }), + ('SKAT', '1.3.2.1', { + 'checksums': ['7442408ccd1b9d2abb3f3dbd27e1b46e50b87042195bc46ce25fe0d887f98e7a'], + }), + ('GillespieSSA', '0.5-4', { + 'checksums': ['d88c09e598cabfa3bcb28c12e0809439b8ea9a439292f4c8d9d9a7bad133412f'], + }), + ('startupmsg', '0.9.5', { + 'checksums': ['102ad504bc3e7d1927f99c82587c4cefb68d8f6002b70e013b44e15352f6c7b6'], + }), + ('distr', '2.7.0', { + 'checksums': ['90d7d58843092a8c968e8fcb93a87ddc54f3e35696b21826320322598317027d'], + }), + ('distrEx', '2.7.0', { + 'checksums': ['eda1f11afa07fa7e88fded42702eb24db802fe48df4d168ce8c86fde5d3a0e56'], + }), + ('KODAMA', '1.4', { + 'checksums': ['126bc85c5fe08c06fe1d4dda230da2d7574d57bda3b8fa36b2a87d498d7cf763'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-2', { + 'checksums': ['e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179'], + }), + ('dtw', '1.20-1', { + 'checksums': ['43ca1a47a7c81a2b5d5054da1be8b8af79a85d6f9ce7b4512e9ed91f790f60f0'], + }), + ('SDMTools', '1.1-221', { + 'checksums': ['a6da297a670f756ee964ffd99c3b212c55c297d385583fd0e767435dd5cd4ccd'], + }), + ('later', '0.7.4', { + 'checksums': ['c4d49aa91f5154ef54ea0498b17f230b8bf99da62541b64417e0c8971261bf88'], + }), + ('promises', '1.0.1', { + 'checksums': ['c2dbc7734adf009377a41e570dfe0d82afb91335c9d0ca1ef464b9bdcca65558'], + }), + ('ggridges', '0.5.0', { + 'checksums': ['124bc84044e56728fa965682f8232fc868f2af7d3eb7276f6b0df53be8d2dbfe'], + }), + ('bibtex', '0.4.2', { + 'checksums': ['1f06ab3660c940405230ad16ff6e4ba38d4418a59cd9b16d78a4349f8b488372'], + }), + ('gbRd', '0.4-11', { + 'checksums': ['0251f6dd6ca987a74acc4765838b858f1edb08b71dbad9e563669b58783ea91b'], + }), + ('Rdpack', '0.9-0', { + 'checksums': ['2bb4f64c416f89166d3d2433257da2dbf981a8550d956ed99f10a83f0d07fc18'], + }), + ('metap', '1.0', { + 'checksums': ['50a014cd52c30d55cf219cc37864323c4d1b44c3c26ff948b10e4dff1dde3fa3'], + }), + ('lsei', '1.2-0', { + 'checksums': ['4781ebd9ef93880260d5d5f23066580ac06061e95c1048fb25e4e838963380f6'], + }), + ('npsurv', '0.4-0', { + 'checksums': ['404cf7135dc40a04e9b81224a543307057a8278e11109ba1fcaa28e87c6204f3'], + }), + ('fitdistrplus', '1.0-11', { + 'checksums': ['861b986529d21a1c5de3e7e22848167704848f60b3f31770827fc8e2c79b0c8a'], + }), + ('reticulate', '1.10', { + 'checksums': ['58e36d3b8a67d01194c4e5099499657d017f77fc2081213633964b1d57a7e32f'], + }), + ('hdf5r', '1.0.0', { + 'patches': ['hdf5r-1.0.0_fix-HDF5-1.10.2.patch'], + 'preinstallopts': "unset LIBS && ", + 'checksums': [ + '6a5fb0c4ac7129405e993ce461db908d51bc0ea2b717e8ca306c26902423d7e8', # hdf5r_1.0.0.tar.gz + 'a01ffc5aa37dc3df375638c78ac02bb7e518eb0e41447a25e77a6da6f4e92608', # hdf5r-1.0.0_fix-HDF5-1.10.2.patch + ], + }), + ('DTRreg', '1.3', { + 'checksums': ['835df542d0ec55368834bc4173dc4aa90f1c0ff146ab243d6e377bba309b8484'], + }), + ('pulsar', '0.3.4', { + 'checksums': ['d7230b2286d0fbfa59bbd4f7314ee6e7b77f929f41a8b42bd95af0a7e354cb1c'], + }), + ('bayesm', '3.1-0.1', { + 'checksums': ['5879823b7fb6e6df0c0fe98faabc1044a4149bb65989062df4ade64e19d26411'], + }), + ('energy', '1.7-5', { + 'checksums': ['24c2cf080939f8f56cd9cda06d2dfc30d0389cd3ec7250af4f9a09a4c06b6996'], + }), + ('compositions', '1.40-2', { + 'checksums': ['110d71ae000561987cb73fc76cd953bd69d37562cb401ed3c36dca137d01b78a'], + }), + ('tweenr', '0.1.5', { + 'checksums': ['d8b6f85459796319b8bf0cb71478a17b5d3a0ace580ba3c8ebbb4a4a3bdc001a'], + }), + ('units', '0.6-1', { + 'checksums': ['f180c56241c2b6dc6406eabf983a2bcb6e88db7936ad599bbd75bf845aa04e3d'], + }), + ('ggforce', '0.1.3', { + 'checksums': ['c4ea83a674793836eac876f8cfdf363ea677d9a947b4461226883a6d7cedcd73'], + }), + ('ggrepel', '0.8.0', { + 'checksums': ['6386606e716d326354a29fcb6cd09f9b3d3b5e7c5ba0d5f7ff35416b1a4177d4'], + }), + ('ggraph', '1.0.2', { + 'checksums': ['4c24739ecabfc65c290a11980491a20bdaac675392a98dc30ccde76ac4b8f53a'], + }), + ('tidygraph', '1.1.0', { + 'checksums': ['6419cfdfb7a160e8f032c62cd68ab12dbd870994a53a182443baa878438c15b3'], + }), + ('clustree', '0.2.2', { + 'checksums': ['10242fbfd607e08c0eba52642a9a49dbfef461cc6f4a2ac999c66400c481c492'], + }), + ('plotly', '4.8.0', { + 'checksums': ['78f90282c831bbbb675ed4811fb506a98dd05e37251fabd42ebc263c80bae8a6'], + }), + ('tweedie', '2.3.2', { + 'checksums': ['9a6226e64e3d56eb7eb2a408f8b825c2ad6ee0ea203a9220e85e7789514adb81'], + }), + ('RcppGSL', '0.3.6', { + 'checksums': ['35e8a8e3c0837df58b7f710d7b4c38a9b63d2522cb3e35ca6a499c30f055ed9a'], + }), + ('mvabund', '3.13.1', { + 'checksums': ['d2b21443a7a791f25340c9c7cad6439b1a9cc5154ca7387be00722b67e920bfd'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.0', { + 'checksums': ['072c2c581dedd29e76e5e4c1363f9f840a302592a3b091d7ba82be67c9e61dae'], + }), + ('grpreg', '3.2-0', { + 'checksums': ['15ad18d851305c85ad9015fb93f132c10d2e0fb26886afdcf942e053616d734b'], + }), + ('trust', '0.1-7', { + 'checksums': ['e3d15aa84a71becd2824253d4a8156bdf1ab9ac3b72ced0cd53f3bb370ac6f04'], + }), + ('ergm', '3.9.4', { + 'checksums': ['548d783b8f752984436b8ebf7fd828e1afb3d3e6642bcdd2d4209a6b8c82bd2e'], + }), + ('networkDynamic', '0.9.0', { + 'checksums': ['e951d4bc892f96d867a8f5822d662633f9206f2dadf46caaa6083fc0d97289a4'], + }), + ('tergm', '3.5.2', { + 'checksums': ['65b4f80799342a596ea5b14371f3982f1b611faa02ecabbfd5c79a9b4a66f85c'], + }), + ('ergm.count', '3.3.0', { + 'checksums': ['e14b4c973d3bde3adc15ebbda5443866678f3919bf5e942bf7a8b6bcd4ea93a0'], + }), + ('tsna', '0.2.0', { + 'checksums': ['a26b0564490e78cdb55bc4ad36fda6e7cedc0bb6b21d278513dbe620bf0c0027'], + }), + ('statnet', '2018.10', { + 'checksums': ['387ae8294b6d41d747a62d726a21e10a70ad2a9e612c311658e97f6ce54214ec'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('NMF', '0.21.0', { + 'checksums': ['3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '0.3.1', { + 'checksums': ['86c8c16411e4e20396fc0287a72dfe45499be4c81d28c972cda0a0fe12d16d4f'], + }), + ('mcmc', '0.9-5', { + 'checksums': ['c676ae0006a52fb527e9dbd3af0684943c3af157d34aaf5b89705d042f5479c4'], + }), + ('MCMCpack', '1.4-4', { + 'checksums': ['97e193d628f7161e59288ed594a313af3a520bf30d5a95f1ede0cb2a567cf9f7'], + }), + ('shinythemes', '1.1.2', { + 'checksums': ['2e13d4d5317fc61082e8f3128b15e0b10ed9736ce81e152dd7ae7f6109f9b18a'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.11', { + 'checksums': ['982b9f34dbcf98136a8406b9ce4717faf155c7d5d923dcdf0dca6a9d53e27219'], + }), + ('liquidSVM', '1.2.2', { + 'checksums': ['96f545e5878d2cce27f37185757945607b00fdeaa43258f0884a578be6c3688a'], + }), + ('oddsratio', '1.0.3', { + 'checksums': ['b33861d8beae189c66e6b94d59cc698bf08aeafb47262b5f7a1d2e88a2b2b8cd'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.22.1.1', { + 'checksums': ['e4c9d50d2a6a42ffecb15aa1561495599b206a7edd77db95501c7d09253fc412'], + }), + ('mlegp', '3.1.7', { + 'checksums': ['d4845eaf9260f8b8112726dd7ceb5c2f5ce75125fa313191db9de121f2ee15e0'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.4.2', { + 'checksums': ['28a5f7363325021bd93f9bd060cc48f20c689dae2f2f6f7100faae66d7651f80'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.0', { + 'checksums': ['af326f918bd46f3f653be1907e01551025fd961077ca719c861ab0f29d14d516'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.1.3', { + 'checksums': ['020005634099a057207a614928ced57900acd4952f147bebe6718034ea82e755'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/kohonen-3.0.6_intel-wd308.patch b/easybuild/easyconfigs/r/R/kohonen-3.0.6_intel-wd308.patch new file mode 100644 index 00000000000..c087131cd82 --- /dev/null +++ b/easybuild/easyconfigs/r/R/kohonen-3.0.6_intel-wd308.patch @@ -0,0 +1,17 @@ +add -wd308 compiler option to avoid compiler warning #308 being treated as an error +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -Nur kohonen.orig/MD5 kohonen/MD5 +--- kohonen.orig/MD5 2018-08-17 17:20:03.000000000 +0200 ++++ kohonen/MD5 2019-04-02 11:02:48.179308525 +0200 +@@ -65,3 +65,4 @@ + 25ac1ecf2fd6446650632602f73ee35c *src/neighbourhood-functions.h + a08c489f9b9a7fe83f5389456d2df1f6 *src/pbatch-supersom.cpp + 417171759d5123bf75830bd818230fa2 *src/supersom.cpp ++30917495af4f0aac85eec6eba684d25b *src/Makevars +diff -Nur kohonen.orig/src/Makevars kohonen/src/Makevars +--- kohonen.orig/src/Makevars 1970-01-01 01:00:00.000000000 +0100 ++++ kohonen/src/Makevars 2019-04-02 10:46:28.538719778 +0200 +@@ -0,0 +1,3 @@ ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CFLAGS = -wd308 ++PKG_CXXFLAGS = -wd308 diff --git a/easybuild/easyconfigs/r/R/liquidSVM-1.2.2_intel.patch b/easybuild/easyconfigs/r/R/liquidSVM-1.2.2_intel.patch new file mode 100644 index 00000000000..6519d895e2a --- /dev/null +++ b/easybuild/easyconfigs/r/R/liquidSVM-1.2.2_intel.patch @@ -0,0 +1,35 @@ +fix intel compiler error: identifier "_mm_hint" is undefined cache_prefetch(sample1.x_csv+i, PREFETCH_L1) +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ur liquidSVM.orig/MD5 liquidSVM/MD5 +--- liquidSVM.orig/MD5 2019-01-10 21:10:03.000000000 +0100 ++++ liquidSVM/MD5 2019-04-03 16:15:56.458387551 +0200 +@@ -162,7 +162,7 @@ + cbd209324ad752e19be10d8975d65e2f *src/sources/shared/system_support/os_specifics.h + 54e8583d2e8e269ff2b6d7a79d57cbd5 *src/sources/shared/system_support/parallel_control.cpp + fd14e7613065d218f8f4af60d9a86e92 *src/sources/shared/system_support/parallel_control.h +-a13c47e6412181278450927da739ee0d *src/sources/shared/system_support/simd_basics.h ++2fc61f25da6f44b203a6cf3d79e82681 *src/sources/shared/system_support/simd_basics.h + 16556dabd9a86100c4238bf47c1472de *src/sources/shared/system_support/simd_basics.ins.cpp + 43de099c1955a3670fbf6688d5c0b4ab *src/sources/shared/system_support/thread_manager.cpp + 76ef26f0446a6dcdd7c68d913b821534 *src/sources/shared/system_support/thread_manager.h +diff -ur liquidSVM.orig/src/sources/shared/system_support/simd_basics.h liquidSVM/src/sources/shared/system_support/simd_basics.h +--- liquidSVM.orig/src/sources/shared/system_support/simd_basics.h 2019-01-10 20:28:51.000000000 +0100 ++++ liquidSVM/src/sources/shared/system_support/simd_basics.h 2019-04-03 16:15:05.802202840 +0200 +@@ -63,7 +63,7 @@ + + #define simdd__ __m256d + #define SIMD_WORD_SIZE 4 +- #if defined(__MACH__) || defined __clang__ ++ #if defined(__MACH__) || defined __clang__ || defined __INTEL_COMPILER + #define cache_prefetch(address, hint) _mm_prefetch(address, hint) + #elif defined(_WIN32) && !defined(__MINGW32__) + #define cache_prefetch(address, hint) _mm_prefetch( (char*)((void*)(address)), int(hint)) +@@ -98,7 +98,7 @@ + + #define simdd__ __m128d + #define SIMD_WORD_SIZE 2 +- #if defined(__MACH__) || defined __clang__ ++ #if defined(__MACH__) || defined __clang__ || defined __INTEL_COMPILER + #define cache_prefetch(address, hint) _mm_prefetch(address, hint) + #elif defined(_WIN32) && !defined(__MINGW32__) + #define cache_prefetch(address, hint) _mm_prefetch( (char*)((void*)(address)), int(hint)) From 7f9d2f331ecf8df81d976bc7556430e416230615 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 5 Apr 2019 16:22:16 +0200 Subject: [PATCH 1095/5331] fix MD5 sum --- easybuild/easyconfigs/r/R/kohonen-3.0.6_intel-wd308.patch | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/kohonen-3.0.6_intel-wd308.patch b/easybuild/easyconfigs/r/R/kohonen-3.0.6_intel-wd308.patch index c087131cd82..281a4fb0e4c 100644 --- a/easybuild/easyconfigs/r/R/kohonen-3.0.6_intel-wd308.patch +++ b/easybuild/easyconfigs/r/R/kohonen-3.0.6_intel-wd308.patch @@ -2,15 +2,15 @@ add -wd308 compiler option to avoid compiler warning #308 being treated as an er Author: Samuel Moors, Vrije Universiteit Brussel (VUB) diff -Nur kohonen.orig/MD5 kohonen/MD5 --- kohonen.orig/MD5 2018-08-17 17:20:03.000000000 +0200 -+++ kohonen/MD5 2019-04-02 11:02:48.179308525 +0200 ++++ kohonen/MD5 2019-04-05 16:19:20.927622744 +0200 @@ -65,3 +65,4 @@ 25ac1ecf2fd6446650632602f73ee35c *src/neighbourhood-functions.h a08c489f9b9a7fe83f5389456d2df1f6 *src/pbatch-supersom.cpp 417171759d5123bf75830bd818230fa2 *src/supersom.cpp -+30917495af4f0aac85eec6eba684d25b *src/Makevars ++04d564ce60a31fc98e7a5b6159a78c3c *src/Makevars diff -Nur kohonen.orig/src/Makevars kohonen/src/Makevars --- kohonen.orig/src/Makevars 1970-01-01 01:00:00.000000000 +0100 -+++ kohonen/src/Makevars 2019-04-02 10:46:28.538719778 +0200 ++++ kohonen/src/Makevars 2019-04-05 16:18:01.699296172 +0200 @@ -0,0 +1,3 @@ +# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' +PKG_CFLAGS = -wd308 From 101468c9c9cf9b8de6323418b8ea6037c229ef1d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 5 Apr 2019 16:45:16 +0200 Subject: [PATCH 1096/5331] add GDAL and PROJ deps --- .../R/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb | 51 +++++++++++++++++++ .../easyconfigs/r/R/PROJ-5.0.0-intel-2018b.eb | 31 +++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/r/R/PROJ-5.0.0-intel-2018b.eb diff --git a/easybuild/easyconfigs/r/R/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/R/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..2523cf04fa3 --- /dev/null +++ b/easybuild/easyconfigs/r/R/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['a328d63d476b3653f5a25b5f7971e87a15cdf8860ab0729d4b1157ba988b8d0b'] + +dependencies = [ + ('Python', '3.6.6'), + ('netCDF', '4.6.1'), + ('expat', '2.2.5'), + ('GEOS', '3.6.2', '-Python-%(pyver)s'), + ('SQLite', '3.24.0'), + ('libxml2', '2.9.8'), + ('libpng', '1.6.34'), + ('libjpeg-turbo', '2.0.0'), + ('JasPer', '2.0.14'), + ('LibTIFF', '4.0.9'), + ('zlib', '1.2.11'), + ('cURL', '7.60.0'), + ('PCRE', '8.41'), + ('PROJ', '5.0.0'), + ('libgeotiff', '1.4.2'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/R/PROJ-5.0.0-intel-2018b.eb b/easybuild/easyconfigs/r/R/PROJ-5.0.0-intel-2018b.eb new file mode 100644 index 00000000000..95bdc197845 --- /dev/null +++ b/easybuild/easyconfigs/r/R/PROJ-5.0.0-intel-2018b.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '5.0.0' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b30df08d736e69744cb255828721abb545b494d6032c13a96520f3219a444cd2'] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' From 65b04fd397c98ead6fcfe46ff1a88a71dd171ab0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 5 Apr 2019 16:50:13 +0200 Subject: [PATCH 1097/5331] adding easyconfigs: Kent_tools-20190326-linux.x86_64.eb --- .../Kent_tools-20190326-linux.x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb new file mode 100644 index 00000000000..b8a2632a841 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb @@ -0,0 +1,31 @@ +easyblock = 'BinariesTarball' + +name = 'Kent_tools' +version = '20190326' +versionsuffix = '-linux.x86_64' + +homepage = 'http://genome.cse.ucsc.edu/' +description = """Kent tools: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Check the last modified date at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64 +# Then and pack into tarball with: +# mkdir Kent_tools +# rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ Kent_tools +# tar cfvz Kent_tools-20190326.tar.gz Kent_tools +# +sources = [SOURCE_TAR_GZ] +checksums = ['ce9da071e4e31abdda5ecff882fa9799ef879a4fc9a7d43a0799cff2de965444'] + +postinstallcmds = [ + "cp -a %(builddir)s/Kent_tools/blat/{blat,gfClient,gfServer} %(installdir)s/bin", + "cp -a %(builddir)s/Kent_tools/blat/FOOTER.txt %(installdir)s/bin/FOOTER_blat.txt", +] + +sanity_check_paths = { + 'files': ['bin/blat', 'bin/getRna', 'bin/liftOver', 'bin/mafGene', 'bin/splitFile', 'bin/twoBitToFa'], + 'dirs': [], +} + +moduleclass = 'bio' From eca3b0a2cb8b8bed54679ed90c69faa3aeb92ea3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 5 Apr 2019 17:02:23 +0200 Subject: [PATCH 1098/5331] move GDAL and PROJ to correct directories --- .../{r/R => g/GDAL}/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb | 0 easybuild/easyconfigs/{r/R => p/PROJ}/PROJ-5.0.0-intel-2018b.eb | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{r/R => g/GDAL}/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb (100%) rename easybuild/easyconfigs/{r/R => p/PROJ}/PROJ-5.0.0-intel-2018b.eb (100%) diff --git a/easybuild/easyconfigs/r/R/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb similarity index 100% rename from easybuild/easyconfigs/r/R/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb rename to easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/r/R/PROJ-5.0.0-intel-2018b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-5.0.0-intel-2018b.eb similarity index 100% rename from easybuild/easyconfigs/r/R/PROJ-5.0.0-intel-2018b.eb rename to easybuild/easyconfigs/p/PROJ/PROJ-5.0.0-intel-2018b.eb From 2f7f174913e28e12238a5f1eb4696a07fb47ce4e Mon Sep 17 00:00:00 2001 From: install Date: Fri, 5 Apr 2019 08:51:52 -0700 Subject: [PATCH 1099/5331] adding easyconfigs: amask-20190404-foss-2018b.eb --- .../a/amask/amask-20190404-foss-2018b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/amask/amask-20190404-foss-2018b.eb diff --git a/easybuild/easyconfigs/a/amask/amask-20190404-foss-2018b.eb b/easybuild/easyconfigs/a/amask/amask-20190404-foss-2018b.eb new file mode 100644 index 00000000000..c5bd66da81e --- /dev/null +++ b/easybuild/easyconfigs/a/amask/amask-20190404-foss-2018b.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'amask' +commit = '25b56e3' +version = '20190404' + +homepage = 'https://github.com/TACC/amask' +description = """amask is a set of tools to to determine the affinity of MPI processes and OpenMP threads + in a parallel environment.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/TACC/amask/archive/'] +sources = [{'download_filename': '%s.tar.gz' % commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['c8cb80814872bb3da681a135320653feb30c1b9de1e90673cfb164a90e6f22e4'] + +buildopts = 'CC_SER="$CXX -g" CC_MPI="$MPICXX -g" CC_OMP="$CXX -fopenmp -g" CC_HYB="$MPICXX -fopenmp -g" ' +buildopts += 'LD_MPI="$MPICXX -g" LD_OMP="$CXX -fopenmp -g" LD_HYB="$MPICXX -fopenmp -g" ' + +files_to_copy = ['bin', 'lib'] + +sanity_check_paths = { + 'files': ['bin/amask_hybrid', 'bin/amask_mpi', 'bin/amask_omp', 'lib/amask.a'], + 'dirs': [], +} + +moduleclass = 'tools' From adccdfb1f20f389606f8dfb8ad55604436bf91c0 Mon Sep 17 00:00:00 2001 From: install Date: Fri, 5 Apr 2019 09:32:18 -0700 Subject: [PATCH 1100/5331] adding easyconfigs: nvtop-1.0.0-fosscuda-2018b.eb --- .../n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb new file mode 100644 index 00000000000..c8db06e2080 --- /dev/null +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'nvtop' +version = '1.0.0' + +homepage = 'https://github.com/Syllo/nvtop' +description = 'htop-like GPU usage monitor' + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['https://github.com/Syllo/nvtop/archive/'] +sources = ['https://github.com/Syllo/nvtop/archive/1.0.0.tar.gz'] +checksums = ['de3d7b6a889f886f3bc28c15c3c34cfb6fcb7cb7ebc9a0cc36c3c77d837029b1'] + +dependencies = [ + ('CUDA', '9.2.88'), + ('ncurses', '6.1'), +] + +builddependencies = [ + ('CMake', '3.12.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/nvtop'], + 'dirs': [], +} + +moduleclass = 'tools' From d9083e1703d3e9d5bd3b7c7df3a1cc50d7d458da Mon Sep 17 00:00:00 2001 From: install Date: Fri, 5 Apr 2019 09:39:31 -0700 Subject: [PATCH 1101/5331] adding easyconfigs: gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb --- ...stat-0.5.0-fosscuda-2018b-Python-2.7.15.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..b99312bbdd1 --- /dev/null +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'gpustat' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/wookayin/gpustat' +description = 'dstat-like utilization monitor for NVIDIA GPUs' + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2f43421dbcd9ebd8caf179aeb5f78ac123786033fb9a4310ce0f8e18b25eb03e'] + +dependencies = [ + ('Python', '2.7.15'), + ('CUDA', '9.2.88'), +] + +options = { 'modulename': 'gpustat' } + +sanity_check_paths = { + 'files': ['bin/gpustat'], + 'dirs': [], +} + +moduleclass = 'tools' From 4d2d50c11cb39bbd71744678817f5e31ba4ef710 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 5 Apr 2019 19:27:33 +0200 Subject: [PATCH 1102/5331] add libgeotiff dep --- .../libgeotiff-1.4.2-intel-2018b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.4.2-intel-2018b.eb diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.4.2-intel-2018b.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.4.2-intel-2018b.eb new file mode 100644 index 00000000000..151946174fd --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.4.2-intel-2018b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.4.2' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = "Library for reading and writing coordinate system information from/to GeoTIFF files" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [ + 'http://download.osgeo.org/geotiff/libgeotiff/', + 'ftp://ftp.remotesensing.org/pub/libgeotiff/', +] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['ad87048adb91167b07f34974a8e53e4ec356494c29f1748de95252e8f81a5e6e'] + +dependencies = [ + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.9'), + ('PROJ', '5.0.0'), + ('libjpeg-turbo', '2.0.0'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 4394929ce2b924ecc776ff54b8e5a4d0246feb8d Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 5 Apr 2019 12:34:27 -0500 Subject: [PATCH 1103/5331] adding easyconfigs: libxc-4.0.1-foss-2017b.eb --- .../l/libxc/libxc-4.0.1-foss-2017b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb b/easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb new file mode 100644 index 00000000000..6525ab4d7af --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.0.1-foss-2017b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '4.0.1' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +# Tests also fail with Intel Compilers on Haswell when optarch is enabled. +toolchainopts = {'lowopt': True, 'optarch': False} + +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] +checksums = [ + '836cb2f529bb9d1979a347d4d5460bf9a18c64f39b8127e88f3004471a72ab30', # libxc-4.0.1.tar.gz + '588631b4a18f1f64e6c8e9ff701f15fec0e34c0871e402b8a934fcd97c3d043b', # libxc-4.0_no-longdouble.patch +] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' From c154b2b0b64b4d27a4dd32bb412edd29b05c6128 Mon Sep 17 00:00:00 2001 From: install Date: Fri, 5 Apr 2019 11:40:00 -0700 Subject: [PATCH 1104/5331] adding easyconfigs: psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb --- ...util-5.6.1-fosscuda-2018b-Python-2.7.15.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..2d4311d151e --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'psutil' +version = '5.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'] + +dependencies = [ + ('Python', '2.7.15'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 35896ebf4f97a5e679bc368f246998953a5457f8 Mon Sep 17 00:00:00 2001 From: install Date: Fri, 5 Apr 2019 12:12:07 -0700 Subject: [PATCH 1105/5331] Converted to a PythonBundle and explicitly include all python module dependencies in the bundle. --- ...stat-0.5.0-fosscuda-2018b-Python-2.7.15.eb | 32 +++++++++++++++---- 1 file changed, 25 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb index b99312bbdd1..5a04663a5dc 100644 --- a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'gpustat' version = '0.5.0' @@ -9,20 +9,38 @@ description = 'dstat-like utilization monitor for NVIDIA GPUs' toolchain = {'name': 'fosscuda', 'version': '2018b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['2f43421dbcd9ebd8caf179aeb5f78ac123786033fb9a4310ce0f8e18b25eb03e'] - dependencies = [ ('Python', '2.7.15'), ('CUDA', '9.2.88'), ] -options = { 'modulename': 'gpustat' } +exts_list = [ + ('psutil', '5.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], + }), + ('blessings', '1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blessings'], + 'checksums': ['98e5854d805f50a5b58ac2333411b0482516a8210f23f43308baeb58d77c157d'], + }), + ('nvidia-ml-py', '7.352.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nvidia-ml-py'], + 'checksums': ['b4a342ba52a51ff794af38279ce62f78b278ba5f50c13103af52c4f6113ff65e'], + 'modulename': 'pynvml', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gpustat'], + 'checksums': ['2f43421dbcd9ebd8caf179aeb5f78ac123786033fb9a4310ce0f8e18b25eb03e'], + }), +] + +download_dep_fail = True + +options = {'modulename': 'gpustat'} sanity_check_paths = { 'files': ['bin/gpustat'], - 'dirs': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } moduleclass = 'tools' From e030488b69b8552d1a08d7d2d5337b3ee0b496d1 Mon Sep 17 00:00:00 2001 From: install Date: Fri, 5 Apr 2019 14:41:23 -0700 Subject: [PATCH 1106/5331] Wild stab at trying to satisfy the pipeline by explicitly setting 'download_dep_fail' to True and 'use_pip' to False where neither was set at all before. No great hope those will satisfy the tests, but hopefully the new output will give some better hint how to proceed? --- .../p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb index 2d4311d151e..1ceec65c79e 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb @@ -17,6 +17,9 @@ dependencies = [ ('Python', '2.7.15'), ] +download_dep_fail = True +use_pip = False + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 658213a1726b7b1bd949e62259fe4465bc6ec3aa Mon Sep 17 00:00:00 2001 From: install Date: Fri, 5 Apr 2019 14:56:26 -0700 Subject: [PATCH 1107/5331] Cargo-culting from the test-passing #8017 which is also a PythonBundle and seems to have 'use_pip = True' and no mention of 'download_dep_fail' --- .../g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb index 5a04663a5dc..b9082ccc60f 100644 --- a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb @@ -14,6 +14,8 @@ dependencies = [ ('CUDA', '9.2.88'), ] +use_pip = True + exts_list = [ ('psutil', '5.6.1', { 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], @@ -34,10 +36,6 @@ exts_list = [ }), ] -download_dep_fail = True - -options = {'modulename': 'gpustat'} - sanity_check_paths = { 'files': ['bin/gpustat'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 20aab66daea3bace626d175a34eb7aa4a3134835 Mon Sep 17 00:00:00 2001 From: install Date: Fri, 5 Apr 2019 15:22:50 -0700 Subject: [PATCH 1108/5331] Working from success in #8025 (in turn from looking at #8017 and #7273) removed 'download_dep_fail' and set 'use_pip = True' --- .../p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb index 1ceec65c79e..f47c4f5bec4 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb @@ -13,13 +13,12 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'] +use_pip = True + dependencies = [ ('Python', '2.7.15'), ] -download_dep_fail = True -use_pip = False - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 691c800c186da682ef1355512c24beb534a4532d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 6 Apr 2019 09:24:28 +0200 Subject: [PATCH 1109/5331] update checksum for kohonen --- easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb index 5681b50d007..df383c41996 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb @@ -1222,7 +1222,7 @@ exts_list = [ 'patches': ['kohonen-3.0.6_intel-wd308.patch'], 'checksums': [ '8bdddc9d51635580256c80e801bb7dc9981d637eeaf2cffcbd83ec64641a202c', # kohonen_3.0.6.tar.gz - '9c63b853cebd07417133a541375fc24ea30e1bc42bf99cdf67597ed1a6cdc8f1', # kohonen-3.0.6_intel-wd308.patch + '03c15c42c62f10b31c40d1d68da787621081647eab7e64a16c2ced98f1aa7914', # kohonen-3.0.6_intel-wd308.patch ], }), ('base64', '2.0', { From dfd1deeb3aee5a30d93d6613a53b194e8b1b257c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 7 Apr 2019 22:48:20 +0200 Subject: [PATCH 1110/5331] add missing patches --- easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb index df383c41996..4005df888c4 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb @@ -2078,7 +2078,11 @@ exts_list = [ 'checksums': ['c676ae0006a52fb527e9dbd3af0684943c3af157d34aaf5b89705d042f5479c4'], }), ('MCMCpack', '1.4-4', { - 'checksums': ['97e193d628f7161e59288ed594a313af3a520bf30d5a95f1ede0cb2a567cf9f7'], + 'patches': ['MCMCpack-1.4-4_intel_wd308.patch'], + 'checksums': [ + '97e193d628f7161e59288ed594a313af3a520bf30d5a95f1ede0cb2a567cf9f7', # MCMCpack_1.4-4.tar.gz + '8820c9153c4717614ed5f3fce9b8507fca1194d4296ea3426e0a3ca7b92bb74a', # MCMCpack-1.4-4_intel_wd308.patch + ], }), ('shinythemes', '1.1.2', { 'checksums': ['2e13d4d5317fc61082e8f3128b15e0b10ed9736ce81e152dd7ae7f6109f9b18a'], @@ -2093,7 +2097,11 @@ exts_list = [ 'checksums': ['982b9f34dbcf98136a8406b9ce4717faf155c7d5d923dcdf0dca6a9d53e27219'], }), ('liquidSVM', '1.2.2', { - 'checksums': ['96f545e5878d2cce27f37185757945607b00fdeaa43258f0884a578be6c3688a'], + 'patches': ['liquidSVM-1.2.2_intel.patch'], + 'checksums': [ + '96f545e5878d2cce27f37185757945607b00fdeaa43258f0884a578be6c3688a', # liquidSVM_1.2.2.tar.gz + 'a670a6de7c8a7755a9f6f0cc658772f40aebe342512be4a20dea6c56595ff44e', # liquidSVM-1.2.2_intel.patch + ], }), ('oddsratio', '1.0.3', { 'checksums': ['b33861d8beae189c66e6b94d59cc698bf08aeafb47262b5f7a1d2e88a2b2b8cd'], From ba94113a939c98cfd4983f8e421a2e0d9935123f Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Apr 2019 11:01:24 +0200 Subject: [PATCH 1111/5331] Fix dask --- .../bokeh-1.0.4-foss-2018b-Python-3.6.6.eb | 5 + .../bokeh-1.0.4-intel-2018b-Python-3.6.6.eb | 48 ++++++++++ .../dask-1.0.0-foss-2018b-Python-3.6.6.eb | 95 +++++++++++++++++++ .../dask-1.0.0-intel-2018b-Python-3.6.6.eb | 8 ++ 4 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb index fbfb07f1342..26e6fe6c5b0 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-foss-2018b-Python-3.6.6.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [ ('Python', '3.6.6'), ('PyYAML', '3.13', versionsuffix), + ('Pillow', '5.3.0', versionsuffix), ] use_pip = True @@ -29,6 +30,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], }), + ('packaging', '19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + 'checksums': ['0c98a5d0be38ed775798ece1b9727178c4469d9c3b4ada66e8e6b7849f8732af'], + }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], 'checksums': ['ceeb6a75afc1b2de00c2b8b6da121dec3fb77031326897b80d4375a70e96aebf'], diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..dad8cde51de --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-1.0.4-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '1.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('PyYAML', '3.13', versionsuffix), + ('Pillow', '5.3.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('tornado', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], + }), + ('packaging', '19.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + 'checksums': ['0c98a5d0be38ed775798ece1b9727178c4469d9c3b4ada66e8e6b7849f8732af'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/b/bokeh'], + 'checksums': ['ceeb6a75afc1b2de00c2b8b6da121dec3fb77031326897b80d4375a70e96aebf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..2764b9118db --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,95 @@ +easyblock = 'Bundle' + +name = 'dask' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/dask/dask/' +description = """Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms + and task scheduling.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('PyYAML', '3.13', versionsuffix), + ('bokeh', '1.0.4', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('toolz', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toolz'], + 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], + }), + ('HeapDict', version, { + 'source_urls': ['https://pypi.python.org/packages/source/h/HeapDict'], + 'checksums': ['40c9e3680616cfdf942f77429a3a9e0a76f31ce965d62f4ffbe63a83a5ef1b5a'], + }), + ('zict', '0.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/z/zict'], + 'checksums': ['63377f063086fc92e5c16e4d02162c571f6470b9e796cf3411ef9e815c96b799'], + }), + ('tornado', '5.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], + }), + ('tblib', '1.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tblib'], + 'checksums': ['436e4200e63d92316551179dc540906652878df4ff39b43db30fcf6400444fe7'], + }), + ('sortedcontainers', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sortedcontainers'], + 'checksums': ['974e9a32f56b17c1bac2aebd9dcf197f3eb9cd30553c5852a3187ad162e1a03a'], + }), + ('psutil', '5.4.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'checksums': ['6e265c8f3da00b015d24b842bfeb111f856b13d24f2c57036582568dc650d6c3'], + }), + ('msgpack-python', '0.5.6', { + 'modulename': 'msgpack', + 'source_urls': ['https://pypi.python.org/packages/source/s/msgpack-python'], + 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], + }), + ('msgpack', '0.5.6', { + 'source_urls': ['https://pypi.python.org/packages/source/m/msgpack'], + 'checksums': ['0ee8c8c85aa651be3aa0cd005b5931769eaa658c948ce79428766f1bd46ae2c3'], + }), + ('cloudpickle', '0.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle'], + 'checksums': ['f169a8523a40eb0a3452e1878aac31da6759409fbafa51dd50d89d4a6b42bcf1'], + }), + ('Click', '7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/d/dask'], + 'checksums': ['a1fa4a3b2d7ce4dd0c68db4b68dadf2c283ff54d98bd72c556fc462000449ff7'], + }), + ('distributed', '1.25.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], + 'checksums': ['7d892c7aeb28ba4903eef6735851e7c6e20baeb6a4b4c159c27cae53f4b8064e'], + }), + ('docrep', '0.2.5', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docrep'], + }), + ('dask-jobqueue', '0.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/dask-jobqueue'], + 'modulename': 'dask_jobqueue', + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'remote', 'scheduler', 'ssh', 'submit', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb index 862c2f14a12..4bb290afe5c 100644 --- a/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'intel', 'version': '2018b'} dependencies = [ ('Python', '3.6.6'), ('PyYAML', '3.13', versionsuffix), + ('bokeh', '1.0.4', versionsuffix), ] exts_defaultclass = 'PythonPackage' @@ -75,6 +76,13 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/d/distributed'], 'checksums': ['7d892c7aeb28ba4903eef6735851e7c6e20baeb6a4b4c159c27cae53f4b8064e'], }), + ('docrep', '0.2.5', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docrep'], + }), + ('dask-jobqueue', '0.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/dask-jobqueue'], + 'modulename': 'dask_jobqueue', + }), ] sanity_check_paths = { From 0ac2b08cc40aa70eb61d4bb44d6a3445c53b2659 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Mon, 8 Apr 2019 11:55:12 +0200 Subject: [PATCH 1112/5331] Use PythonBundle for dask --- .../d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb | 10 ++-------- .../d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb | 10 ++-------- 2 files changed, 4 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb index 2764b9118db..2a73f7da31b 100644 --- a/easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/dask/dask-1.0.0-foss-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'dask' version = '1.0.0' @@ -16,11 +16,7 @@ dependencies = [ ('bokeh', '1.0.4', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('toolz', '0.9.0', { @@ -90,6 +86,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb index 4bb290afe5c..7c031f4e0d4 100644 --- a/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/dask/dask-1.0.0-intel-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'dask' version = '1.0.0' @@ -16,11 +16,7 @@ dependencies = [ ('bokeh', '1.0.4', versionsuffix), ] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True exts_list = [ ('toolz', '0.9.0', { @@ -90,6 +86,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'data' From aa3f499dd812e0209c769e6883947636d5d23524 Mon Sep 17 00:00:00 2001 From: wapoelma Date: Mon, 8 Apr 2019 12:04:19 +0200 Subject: [PATCH 1113/5331] adding easyconfigs: cyvcf2-0.10.10-foss-2018b-Python-3.6.6.eb --- .../cyvcf2-0.10.10-foss-2018b-Python-3.6.6.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.10.10-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.10.10-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.10.10-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..2fac33807b4 --- /dev/null +++ b/easybuild/easyconfigs/c/cyvcf2/cyvcf2-0.10.10-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'cyvcf2' +version = '0.10.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/brentp/cyvcf2' +description = """cython + htslib == fast VCF and BCF processing""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('HTSlib', '1.9'), +] + +use_pip = True + +exts_list = [ + ('Click', '7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/click/'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('humanfriendly', '4.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/h/humanfriendly/'], + 'checksums': ['ed1e98ae056b597f15b41bddcc32b9f21e6ab4f3445f9faad1668675de759f7b'], + }), + ('coloredlogs', '10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/coloredlogs/'], + 'checksums': ['b869a2dda3fa88154b9dd850e27828d8755bfab5a838a1c97fbc850c6e377c36'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/cyvcf2'], + 'checksums': ['14a469567992c218d1f1b8ab76b93ec5c1bf56c9f071cf93a3affdaabc9268e0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cyvcf2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From d5227167473506d6bee6eff34dd55046b638b4f8 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Mon, 8 Apr 2019 14:45:24 +0200 Subject: [PATCH 1114/5331] adding easyconfigs: sep-1.0.3-foss-2018b-Python-2.7.15.eb, sep-1.0.3-intel-2018b-Python-2.7.15.eb --- .../sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb | 29 +++++++++++++++++++ .../sep-1.0.3-intel-2018b-Python-2.7.15.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..43e9a582cdc --- /dev/null +++ b/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'sep' +version = '1.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sep.readthedocs.io/en/v1.0.x/' +description = """Python and C library for Source Extraction and Photometry. +( this easyconfig provides python library only )""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['a35704cffadbd042f931899a5564c539835fa7049d0cafff407d7ec7727d3aaa'] + +dependencies = [ + ('Python', '2.7.15'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..c5636f45fd5 --- /dev/null +++ b/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'sep' +version = '1.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sep.readthedocs.io/en/v1.0.x/' +description = """Python and C library for Source Extraction and Photometry. +( this easyconfig provides python library only )""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['a35704cffadbd042f931899a5564c539835fa7049d0cafff407d7ec7727d3aaa'] + +dependencies = [ + ('Python', '2.7.15'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'astro' From f5739483ed9986cc119ffccfb6932255ab26adc0 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Mon, 8 Apr 2019 14:53:10 +0200 Subject: [PATCH 1115/5331] adding easyconfigs: statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb, statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb --- ...tsmodels-0.9.0-foss-2018b-Python-2.7.15.eb | 36 +++++++++++++++++++ ...smodels-0.9.0-intel-2018b-Python-2.7.15.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..d214f1f9101 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.statsmodels.org' +description = """Statsmodels is a Python module that provides classes and functions +for the estimation of many different statistical models, as well as for conducting +statistical tests, and statistical data exploration.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [('Python', '2.7.15')] + +use_pip = True + +exts_list = [ + ('patsy', '0.5.1', { + 'source_urls': [PYPI_SOURCE], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..dd54047abb6 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.statsmodels.org' +description = """Statsmodels is a Python module that provides classes and functions +for the estimation of many different statistical models, as well as for conducting +statistical tests, and statistical data exploration.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [('Python', '2.7.15')] + +use_pip = True + +exts_list = [ + ('patsy', '0.5.1', { + 'source_urls': [PYPI_SOURCE], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From 88ef0bbc764cd476ec971400e7481d15553eb162 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 8 Apr 2019 16:36:20 +0200 Subject: [PATCH 1116/5331] adding easyconfigs: Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb --- .../Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pyke3/Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/Pyke3/Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pyke3/Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..348a8979f2d --- /dev/null +++ b/easybuild/easyconfigs/p/Pyke3/Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,27 @@ +easyblock = "PythonPackage" + +name = 'Pyke3' +version = '1.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sourceforge.net/projects/pyke/' +description = """Pyke introduces a form of Logic Programming (inspired by Prolog) +to the Python community by providing a knowledge-based inference engine +(expert system) written in 100% Python.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://download.sourceforge.net/pyke/'] +sources = [SOURCELOWER_ZIP] +checksums = ['b877b390e70a2eacc01d97c3a992fde947276afc2798ca3ac6c6f74c796cb6dc'] + +dependencies = [('Python', '3.6.6')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pyke'], +} + +options = {'modulename': 'pyke'} + +moduleclass = 'data' From aadf8d5464153b38a79417e8494457df76ed0c0f Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 8 Apr 2019 15:14:06 +0000 Subject: [PATCH 1117/5331] Apply mit-shm patch to fosscuda Mesa too. --- easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb index 428bb968c41..ab53c0069d4 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-fosscuda-2018b.eb @@ -28,10 +28,14 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] sources = [SOURCELOWER_TAR_XZ] -patches = ['Mesa-17.3.6_fix-strip-llvm-flags.patch'] +patches = [ + 'Mesa-17.3.6_fix-strip-llvm-flags.patch', + 'Mesa-18.1.1-query-mit-shm.patch', +] checksums = [ 'd3312a2ede5aac14a47476b208b8e3a401367838330197c4588ab8ad420d7781', # mesa-18.1.1.tar.xz '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.3.6_fix-strip-llvm-flags.patch + 'a9df2759758318d917debbfcc2cb15f6525b3dce41bd1e481d16e2eaa592a24e', # Mesa-18.1.1-query-mit-shm.patch ] builddependencies = [ From 84f0935aafb8c64ce9962996e97de7fa73e01886 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 8 Apr 2019 10:30:06 -0500 Subject: [PATCH 1118/5331] adding easyconfigs: RELION-3.0.4-foss-2017b.eb, RELION-3.0.4-intel-2017b.eb --- .../r/RELION/RELION-3.0.4-foss-2017b.eb | 36 +++++++++++++++++++ .../r/RELION/RELION-3.0.4-intel-2017b.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb create mode 100644 easybuild/easyconfigs/r/RELION/RELION-3.0.4-intel-2017b.eb diff --git a/easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb new file mode 100644 index 00000000000..e82327f2b40 --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'RELION' +version = '3.0.4' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/3dem/relion/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['2580d66088923a644bc7d3b02efd154b775a3ec3d010426f382bb3be5db9c98b'] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('X11', '20171023'), + ('FLTK', '1.3.4'), + ('LibTIFF', '4.0.9'), + ('tbb', '2018_U5'), +] + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-lpthread' -DMPI_INCLUDE_PATH=$EBROOTOPENMPI/include " +configopts += "-DMPI_C_COMPILER=$EBROOTOPENMPI/bin/mpicc -DMPI_CXX_COMPILER=$EBROOTOPENMPI/bin/mpicxx " +configopts += "-DCUDA=OFF -DCudaTexture=OFF " +configopts += "-DALTCPU=ON -DMKLFFT=ON -DFORCE_OWN_TBB=OFF " + +sanity_check_paths = { + 'files': ['bin/relion'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RELION/RELION-3.0.4-intel-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-3.0.4-intel-2017b.eb new file mode 100644 index 00000000000..464110af96d --- /dev/null +++ b/easybuild/easyconfigs/r/RELION/RELION-3.0.4-intel-2017b.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'RELION' +version = '3.0.4' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' +description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer + program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class + averages in electron cryo-microscopy (cryo-EM).""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://github.com/3dem/relion/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['2580d66088923a644bc7d3b02efd154b775a3ec3d010426f382bb3be5db9c98b'] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('X11', '20171023'), + ('FLTK', '1.3.4'), + ('LibTIFF', '4.0.9'), + ('tbb', '2018_U5'), +] + +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-lpthread' -DMPI_INCLUDE_PATH=$EBROOTIMPI/include64 " +configopts += "-DMPI_C_COMPILER=$EBROOTIMPI/bin64/mpiicc -DMPI_CXX_COMPILER=$EBROOTIMPI/bin64/mpiicpc " +configopts += "-DCUDA=OFF -DCudaTexture=OFF " +configopts += "-DALTCPU=ON -DMKLFFT=ON -DFORCE_OWN_TBB=OFF " + +sanity_check_paths = { + 'files': ['bin/relion'], + 'dirs': [] +} + +moduleclass = 'bio' From 296451ecfb9eda30be7eca5189cd0180b2205e5e Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 8 Apr 2019 17:31:55 +0200 Subject: [PATCH 1119/5331] adding easyconfigs: OpenSSL-1.1.1b-GCCcore-8.2.0.eb --- .../o/OpenSSL/OpenSSL-1.1.1b-GCCcore-8.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1b-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1b-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1b-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..671485bbe0d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1b-GCCcore-8.2.0.eb @@ -0,0 +1,25 @@ +name = 'OpenSSL' +version = '1.1.1b' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.openssl.org/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c557b023230413dfb0756f3137a13e6d726838ccd1430888ad15bfb2b43ea4b'] + +dependencies = [('zlib', '1.2.11')] + +builddependencies = [ + ('Perl', '5.28.1'), + ('binutils', '2.31.1'), +] + +runtest = 'test' + +moduleclass = 'system' From 49d010ea1525e1c3dcb56062159ea512964100d5 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 8 Apr 2019 17:40:00 +0200 Subject: [PATCH 1120/5331] Fix sanity check dir --- .../easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb index dacf4ccb704..52ade1ce7d1 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb @@ -21,7 +21,7 @@ dependencies = [('Python', '3.7.2')] sanity_check_paths = { 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } moduleclass = 'devel' From d324bf119bc3412f903a058e2f089ce16bedace9 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Mon, 8 Apr 2019 11:58:35 -0500 Subject: [PATCH 1121/5331] Added OpenMP toolchain opts --- easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb | 1 + easybuild/easyconfigs/r/RELION/RELION-3.0.4-intel-2017b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb index e82327f2b40..43dcf86d3c2 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb @@ -9,6 +9,7 @@ description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely averages in electron cryo-microscopy (cryo-EM).""" toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'openmp': True} source_urls = ['https://github.com/3dem/relion/archive'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/r/RELION/RELION-3.0.4-intel-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-3.0.4-intel-2017b.eb index 464110af96d..afbb41a0a43 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-3.0.4-intel-2017b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-3.0.4-intel-2017b.eb @@ -9,6 +9,7 @@ description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely averages in electron cryo-microscopy (cryo-EM).""" toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'openmp': True} source_urls = ['https://github.com/3dem/relion/archive'] sources = ['%(version)s.tar.gz'] From 0f03d232a0d610cc280c4997ce726e97d578c343 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 8 Apr 2019 20:54:48 +0200 Subject: [PATCH 1122/5331] add download_dep_fail, use_pip --- .../p/Pyke3/Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/Pyke3/Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pyke3/Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb index 348a8979f2d..493c006e077 100644 --- a/easybuild/easyconfigs/p/Pyke3/Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Pyke3/Pyke3-1.1.1-intel-2018b-Python-3.6.6.eb @@ -17,6 +17,9 @@ checksums = ['b877b390e70a2eacc01d97c3a992fde947276afc2798ca3ac6c6f74c796cb6dc'] dependencies = [('Python', '3.6.6')] +download_dep_fail = True +use_pip = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/pyke'], From fabfc770015ae09ff663a446929ad007609b3192 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 8 Apr 2019 22:55:38 +0200 Subject: [PATCH 1123/5331] update to 19.0.1 --- .../easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-8.2.0.eb | 2 +- ...19.0.0-GCCcore-8.2.0.eb => Mesa-19.0.1-GCCcore-8.2.0.eb} | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/m/Mesa/{Mesa-19.0.0-GCCcore-8.2.0.eb => Mesa-19.0.1-GCCcore-8.2.0.eb} (94%) diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-8.2.0.eb index d02e3bb817d..cd73a103d6c 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-8.2.0.eb @@ -16,7 +16,7 @@ checksums = ['1f7ad0d379a722fcbd303aa5650c6d7d5544fde83196b42a73d1193568a4df12'] builddependencies = [('binutils', '2.31.1')] dependencies = [ - ('Mesa', '18.1.1'), + ('Mesa', '19.0.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb similarity index 94% rename from easybuild/easyconfigs/m/Mesa/Mesa-19.0.0-GCCcore-8.2.0.eb rename to easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb index bccaac10e6b..48cfba0fe1b 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'Mesa' -version = '19.0.0' +version = '19.0.1' homepage = 'http://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - @@ -30,7 +30,7 @@ source_urls = [ sources = [SOURCELOWER_TAR_XZ] patches = ['Mesa-17.3.6_fix-strip-llvm-flags.patch'] checksums = [ - '5a549dfb40ec31e5c36c47aadac04554cb2e2a8d144a046a378fc16da57e38f8', # mesa-19.0.0.tar.xz + '6884163c0ea9e4c98378ab8fecd72fe7b5f437713a14471beda378df247999d4', # mesa-19.0.1.tar.xz '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.3.6_fix-strip-llvm-flags.patch ] @@ -40,7 +40,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('Autotools', '20180311'), ('pkg-config', '0.29.2'), - ('Mako', '1.0.7', '-Python-3.7.2'), + ('Mako', '1.0.7'), ('libxml2', '2.9.8'), ('expat', '2.2.6'), ] From fb07aec7b490303ad4990a92a175e0de3b97a737 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 8 Apr 2019 22:59:51 +0200 Subject: [PATCH 1124/5331] use multideps --- ...on-3.7.2.eb => Mako-1.0.7-GCCcore-8.2.0-Python-%(pyver)s.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/Mako/{Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb => Mako-1.0.7-GCCcore-8.2.0-Python-%(pyver)s.eb} (93%) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-%(pyver)s.eb similarity index 93% rename from easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb rename to easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-%(pyver)s.eb index 52ade1ce7d1..f189d0fbaa4 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-%(pyver)s.eb @@ -17,7 +17,7 @@ download_dep_fail = True use_pip = True builddependencies = [('binutils', '2.31.1')] -dependencies = [('Python', '3.7.2')] +multi_deps = {'Python': ['3.7.2', '2.7.15']} sanity_check_paths = { 'files': ['bin/mako-render'], From 755bc7eb3b55315df4d9b05ce7fddfec62d6451e Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 8 Apr 2019 23:02:04 +0200 Subject: [PATCH 1125/5331] remove suffix --- .../m/Mako/Mako-1.0.7-GCCcore-8.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..fffbeac31bb --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.7' + +homepage = 'http://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] + +download_dep_fail = True +use_pip = True + +builddependencies = [('binutils', '2.31.1')] +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'devel' From f1cefa072755046337c337fa553780d6dca35dbb Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 8 Apr 2019 23:05:14 +0200 Subject: [PATCH 1126/5331] Remove scrap file (from --update-pr fail) --- ...ko-1.0.7-GCCcore-8.2.0-Python-%(pyver)s.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-%(pyver)s.eb diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-%(pyver)s.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-%(pyver)s.eb deleted file mode 100644 index f189d0fbaa4..00000000000 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0-Python-%(pyver)s.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Mako' -version = '1.0.7' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.makotemplates.org' -description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" - -toolchain = {'name': 'GCCcore', 'version': '8.2.0'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] - -download_dep_fail = True -use_pip = True - -builddependencies = [('binutils', '2.31.1')] -multi_deps = {'Python': ['3.7.2', '2.7.15']} - -sanity_check_paths = { - 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -moduleclass = 'devel' From 1b0aaf0b4e098814cfd5e8b8f1fe06d6dd1c9fdd Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 8 Apr 2019 23:11:18 +0200 Subject: [PATCH 1127/5331] Update to 1.0.8 --- ...ako-1.0.7-GCCcore-8.2.0.eb => Mako-1.0.8-GCCcore-8.2.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/m/Mako/{Mako-1.0.7-GCCcore-8.2.0.eb => Mako-1.0.8-GCCcore-8.2.0.eb} (85%) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.8-GCCcore-8.2.0.eb similarity index 85% rename from easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0.eb rename to easybuild/easyconfigs/m/Mako/Mako-1.0.8-GCCcore-8.2.0.eb index fffbeac31bb..9ec7a294e9b 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.8-GCCcore-8.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'Mako' -version = '1.0.7' +version = '1.0.8' homepage = 'http://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] +checksums = ['04092940c0df49b01f43daea4f5adcecd0e50ef6a4b222be5ac003d5d84b2843'] download_dep_fail = True use_pip = True From b4b1250d43fef85aee24c6a309b1fd745e24d7a5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Apr 2019 09:17:09 +0200 Subject: [PATCH 1128/5331] fix checking of binutils build dep in easyconfig tests --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 1a7b8eacc3b..8b06f97fc44 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -560,7 +560,7 @@ def template_easyconfig_test(self, spec): requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) if requires_binutils: - dep_names = [d['name'] for d in ec['builddependencies']] + dep_names = [d['name'] for d in ec.builddependencies()] self.assertTrue('binutils' in dep_names, "binutils is a build dep in %s: %s" % (spec, dep_names)) # make sure all patch files are available From 4c52702f45823081eb235d770a3e9fa417eb48a9 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 9 Apr 2019 10:49:13 +0200 Subject: [PATCH 1129/5331] sep: style improvement --- .../easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb | 2 +- .../easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb index 43e9a582cdc..680e8a774e1 100644 --- a/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb @@ -6,7 +6,7 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://sep.readthedocs.io/en/v1.0.x/' description = """Python and C library for Source Extraction and Photometry. -( this easyconfig provides python library only )""" + (this easyconfig provides python library only)""" toolchain = {'name': 'foss', 'version': '2018b'} diff --git a/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb index c5636f45fd5..3aeac1e9c84 100644 --- a/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb @@ -4,9 +4,10 @@ name = 'sep' version = '1.0.3' versionsuffix = '-Python-%(pyver)s' +homepage = 'https://sep.readthedocs.io/en/v1.0.x/' homepage = 'https://sep.readthedocs.io/en/v1.0.x/' description = """Python and C library for Source Extraction and Photometry. -( this easyconfig provides python library only )""" + (this easyconfig provides python library only)""" toolchain = {'name': 'intel', 'version': '2018b'} From 30265423025a5418eede73547dc72fc4dfa035f8 Mon Sep 17 00:00:00 2001 From: wapoelma Date: Tue, 9 Apr 2019 10:57:11 +0200 Subject: [PATCH 1130/5331] adding easyconfigs: ARGoS-3.0.0-beta53-foss-2018b.eb, FreeImage-3.18.0-GCCcore-7.3.0.eb, Lua-5.2.4-GCCcore-7.3.0.eb and patches: FreeImage-3.18.0-fix-makefile.patch, Lua-5.2.4-fix-makefile.patch --- .../a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b.eb | 35 ++++++++++++ .../FreeImage-3.18.0-GCCcore-7.3.0.eb | 39 ++++++++++++++ .../FreeImage-3.18.0-fix-makefile.patch | 54 +++++++++++++++++++ .../l/Lua/Lua-5.2.4-GCCcore-7.3.0.eb | 39 ++++++++++++++ .../l/Lua/Lua-5.2.4-fix-makefile.patch | 18 +++++++ 5 files changed, 185 insertions(+) create mode 100644 easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b.eb create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile.patch create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.2.4-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.2.4-fix-makefile.patch diff --git a/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b.eb b/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b.eb new file mode 100644 index 00000000000..300f6acdfde --- /dev/null +++ b/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'ARGoS' +version = '3.0.0-beta53' + +homepage = 'http://www.argos-sim.info' +description = """A parallel, multi-engine simulator for heterogeneous swarm robotics""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/ilpincy/argos3/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['849ebb1af31d01519a1f3d9731064eaa8041b2ed140bb699096912de1272214c'] + +dependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Lua', '5.2.4'), + ('FreeImage', '3.18.0'), + ('Qt5', '5.10.1'), + ('freeglut', '3.0.0'), +] + +start_dir = 'src' +separate_build_dir = True +configopts = '-DARGOS_DOCUMENTATION=OFF -DARGOS_INSTALL_LDSOCONF=OFF' + +sanity_check_paths = { + 'files': ['include/argos3/core/config.h', 'lib/argos3/libargos3core_simulator.%s' % SHLIB_EXT], + 'dirs': ['share/argos3'] +} + +modextrapaths = {'LD_LIBRARY_PATH': 'lib/argos3'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..cd1604d56ff --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-7.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FreeImage' +version = '3.18.0' + +homepage = 'http://freeimage.sourceforge.net' +description = """FreeImage is an Open Source library project for developers who would like to support popular graphics +image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to +use, fast, multithreading safe.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(name)s%s.zip' % ''.join(version.split('.'))] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip + '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # FreeImage-3.18.0-fix-makefile.patch +] + +builddependencies = [('binutils', '2.30')] + +skipsteps = ['configure'] + +buildopts = ['', '-f Makefile.fip'] +installopts = [ + 'INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib', + '-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib' +] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['include/FreeImage.h', 'include/FreeImagePlus.h', 'lib/libfreeimage.a', 'lib/libfreeimage.%s' % SHLIB_EXT, + 'lib/libfreeimageplus.a', 'lib/libfreeimageplus.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile.patch b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile.patch new file mode 100644 index 00000000000..ac35040d4d6 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-fix-makefile.patch @@ -0,0 +1,54 @@ +# Do not install files to root user +# wpoely86@gmail.com +diff -ur FreeImage.orig/Makefile.fip FreeImage/Makefile.fip +--- FreeImage.orig/Makefile.fip 2015-03-10 09:03:56.000000000 +0100 ++++ FreeImage/Makefile.fip 2019-04-09 10:32:42.052332853 +0200 +@@ -11,7 +11,7 @@ + # Converts cr/lf to just lf + DOS2UNIX = dos2unix + +-LIBRARIES = -lstdc++ ++LIBRARIES = -lstdc++ $(LIBS) + + MODULES = $(SRCS:.c=.o) + MODULES := $(MODULES:.cpp=.o) +@@ -72,10 +72,10 @@ + + install: + install -d $(INCDIR) $(INSTALLDIR) +- install -m 644 -o root -g root $(HEADER) $(INCDIR) +- install -m 644 -o root -g root $(HEADERFIP) $(INCDIR) +- install -m 644 -o root -g root $(STATICLIB) $(INSTALLDIR) +- install -m 755 -o root -g root $(SHAREDLIB) $(INSTALLDIR) ++ install -m 644 $(HEADER) $(INCDIR) ++ install -m 644 $(HEADERFIP) $(INCDIR) ++ install -m 644 $(STATICLIB) $(INSTALLDIR) ++ install -m 755 $(SHAREDLIB) $(INSTALLDIR) + ln -sf $(SHAREDLIB) $(INSTALLDIR)/$(VERLIBNAME) + ln -sf $(VERLIBNAME) $(INSTALLDIR)/$(LIBNAME) + +diff -ur FreeImage.orig/Makefile.gnu FreeImage/Makefile.gnu +--- FreeImage.orig/Makefile.gnu 2015-03-10 09:04:00.000000000 +0100 ++++ FreeImage/Makefile.gnu 2019-04-09 10:31:59.066052732 +0200 +@@ -11,7 +11,7 @@ + # Converts cr/lf to just lf + DOS2UNIX = dos2unix + +-LIBRARIES = -lstdc++ ++LIBRARIES = -lstdc++ $(LIBS) + + MODULES = $(SRCS:.c=.o) + MODULES := $(MODULES:.cpp=.o) +@@ -71,9 +71,9 @@ + + install: + install -d $(INCDIR) $(INSTALLDIR) +- install -m 644 -o root -g root $(HEADER) $(INCDIR) +- install -m 644 -o root -g root $(STATICLIB) $(INSTALLDIR) +- install -m 755 -o root -g root $(SHAREDLIB) $(INSTALLDIR) ++ install -m 644 $(HEADER) $(INCDIR) ++ install -m 644 $(STATICLIB) $(INSTALLDIR) ++ install -m 755 $(SHAREDLIB) $(INSTALLDIR) + ln -sf $(SHAREDLIB) $(INSTALLDIR)/$(VERLIBNAME) + ln -sf $(VERLIBNAME) $(INSTALLDIR)/$(LIBNAME) + # ldconfig diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.2.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.2.4-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..63cbaae6789 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.2.4-GCCcore-7.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = "Lua" +version = "5.2.4" + +homepage = "http://www.lua.org/" +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.lua.org/ftp/'] +sources = ['lua-%s.tar.gz' % version.replace('-', '.')] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + 'b9e2e4aad6789b3b63a056d442f7b39f0ecfca3ae0f1fc0ae4e9614401b69f4b', # lua-5.2.4.tar.gz + '63092210748fd2c3ef55b7b3d9277a84fa615bfec312421d7c4513e7d68f286d', # Lua-5.2.4-fix-makefile.patch +] + +skipsteps = ['configure'] +prebuildopts = 'MYCFLAGS=$CFLAGS MYLIBS=$LIBS MYLDFLAGS=$LDFLAGS' +buildopts = 'linux' +installopts = 'linux INSTALL_TOP=%(installdir)s' + +builddependencies = [('binutils', '2.30')] + +dependencies = [('libreadline', '7.0')] + +sanity_check_paths = { + 'files': ["bin/lua"], + 'dirs': [] +} + +moduleclass = "lang" diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.2.4-fix-makefile.patch b/easybuild/easyconfigs/l/Lua/Lua-5.2.4-fix-makefile.patch new file mode 100644 index 00000000000..ac88dd6def7 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.2.4-fix-makefile.patch @@ -0,0 +1,18 @@ +# Do not put custom makefiles flags to empty by default (so EB can overwrite them) +# wpoely86@gmail.com +diff -ur lua-5.2.4.orig/src/Makefile lua-5.2.4/src/Makefile +--- lua-5.2.4.orig/src/Makefile 2013-11-11 12:45:49.000000000 +0100 ++++ lua-5.2.4/src/Makefile 2019-04-09 10:04:57.701119382 +0200 +@@ -19,9 +19,9 @@ + SYSLDFLAGS= + SYSLIBS= + +-MYCFLAGS= +-MYLDFLAGS= +-MYLIBS= ++MYCFLAGS?= ++MYLDFLAGS?= ++MYLIBS?= + MYOBJS= + + # == END OF USER SETTINGS -- NO NEED TO CHANGE ANYTHING BELOW THIS LINE ======= From 498e1257db094227413932d95dabc5de26184565 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 9 Apr 2019 11:00:19 +0200 Subject: [PATCH 1131/5331] pytest: +sha256sums --- .../p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb | 8 ++++++++ .../p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb | 8 ++++++++ .../p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb | 8 ++++++++ .../p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb | 8 ++++++++ 4 files changed, 32 insertions(+) diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb index 58ba996f18d..502bedc4461 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-2.7.15.eb @@ -16,29 +16,37 @@ use_pip = True exts_list = [ ('py', '1.8.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('attrs', '19.1.0', { 'modulename': 'attr', 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('pluggy', '0.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], }), ('atomicwrites', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { 'modulename': 'more_itertools', 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('scandir', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], }), ('pathlib2', '2.3.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + 'checksums': ['f21d2f1fb8200830dcbb5d8ec466a9c9120e20d8b53c7585d180125cce1d297a'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb index be7a5f440d2..103ad368022 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-foss-2018b-Python-3.6.6.eb @@ -16,29 +16,37 @@ use_pip = True exts_list = [ ('py', '1.8.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('attrs', '19.1.0', { 'modulename': 'attr', 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('pluggy', '0.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], }), ('atomicwrites', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { 'modulename': 'more_itertools', 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('scandir', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], }), ('pathlib2', '2.3.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + 'checksums': ['f21d2f1fb8200830dcbb5d8ec466a9c9120e20d8b53c7585d180125cce1d297a'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb index 64f8adb7723..0898a7655d0 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-2.7.15.eb @@ -16,29 +16,37 @@ use_pip = True exts_list = [ ('py', '1.8.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('attrs', '19.1.0', { 'modulename': 'attr', 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('pluggy', '0.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], }), ('atomicwrites', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { 'modulename': 'more_itertools', 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('scandir', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], }), ('pathlib2', '2.3.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + 'checksums': ['f21d2f1fb8200830dcbb5d8ec466a9c9120e20d8b53c7585d180125cce1d297a'], }), ] diff --git a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb index 5a69c143e85..9698a8bafd9 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-4.4.0-intel-2018b-Python-3.6.6.eb @@ -16,29 +16,37 @@ use_pip = True exts_list = [ ('py', '1.8.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/py/'], + 'checksums': ['dc639b046a6e2cff5bbe40194ad65936d6ba360b52b3c3fe1d08a82dd50b5e53'], }), ('attrs', '19.1.0', { 'modulename': 'attr', 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], }), ('pluggy', '0.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'], + 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], }), ('atomicwrites', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'], + 'checksums': ['75a9445bac02d8d058d5e1fe689654ba5a6556a1dfd8ce6ec55a0ed79866cfa6'], }), ('more-itertools', '5.0.0', { 'modulename': 'more_itertools', 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), ('scandir', '1.10.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], }), ('pathlib2', '2.3.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + 'checksums': ['25199318e8cc3c25dcb45cbe084cc061051336d5a9ea2a12448d3d8cb748f742'], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'], + 'checksums': ['f21d2f1fb8200830dcbb5d8ec466a9c9120e20d8b53c7585d180125cce1d297a'], }), ] From 3d9c24d9500a65641339a993aa254b598bfe599a Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 9 Apr 2019 11:12:28 +0200 Subject: [PATCH 1132/5331] sep: style improvement --- .../easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb | 2 +- .../easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb index 680e8a774e1..3eab596a57a 100644 --- a/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/sep/sep-1.0.3-foss-2018b-Python-2.7.15.eb @@ -4,7 +4,7 @@ name = 'sep' version = '1.0.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://sep.readthedocs.io/en/v1.0.x/' +homepage = 'https://sep.readthedocs.io' description = """Python and C library for Source Extraction and Photometry. (this easyconfig provides python library only)""" diff --git a/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb index 3aeac1e9c84..31bc313c363 100644 --- a/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/sep/sep-1.0.3-intel-2018b-Python-2.7.15.eb @@ -4,8 +4,7 @@ name = 'sep' version = '1.0.3' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://sep.readthedocs.io/en/v1.0.x/' -homepage = 'https://sep.readthedocs.io/en/v1.0.x/' +homepage = 'https://sep.readthedocs.io' description = """Python and C library for Source Extraction and Photometry. (this easyconfig provides python library only)""" From 9b951b34752a5e2f678476e498d6410e5cf9062e Mon Sep 17 00:00:00 2001 From: wapoelma Date: Tue, 9 Apr 2019 12:24:36 +0200 Subject: [PATCH 1133/5331] adding easyconfigs: GMAP-GSNAP-2019-03-15-foss-2018b.eb, rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb and patches: GMAP-GSNAP-2019-03-15-fix-avx512.patch --- .../GMAP-GSNAP-2019-03-15-fix-avx512.patch | 14 ++++ .../GMAP-GSNAP-2019-03-15-foss-2018b.eb | 45 ++++++++++++ ...rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb | 69 +++++++++++++++++++ 3 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2019-03-15-fix-avx512.patch create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2019-03-15-foss-2018b.eb create mode 100644 easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2019-03-15-fix-avx512.patch b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2019-03-15-fix-avx512.patch new file mode 100644 index 00000000000..ad1dcf06f94 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2019-03-15-fix-avx512.patch @@ -0,0 +1,14 @@ +# use 256bit version of call +# wpoely86@gmail.com +diff -ur gmap-2019-03-15.orig/src/merge-uint8.c gmap-2019-03-15/src/merge-uint8.c +--- gmap-2019-03-15.orig/src/merge-uint8.c 2018-10-07 18:38:05.000000000 +0200 ++++ gmap-2019-03-15/src/merge-uint8.c 2019-04-09 12:10:14.232828157 +0200 +@@ -69,7 +69,7 @@ + /* print_vector(vTmp,"Tmp 4"); */ + /* print_vector(vMin,"Min 4"); */ + +- *vMergedB = _mm_max_epu64(vTmp, vMax); ++ *vMergedB = _mm256_max_epu64(vTmp, vMax); + *vMergedA = _mm256_alignr_epi64(vMin, vMin, 1); + + return; diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2019-03-15-foss-2018b.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2019-03-15-foss-2018b.eb new file mode 100644 index 00000000000..9c5e6a2d9c1 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2019-03-15-foss-2018b.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2019-03-15' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s-fix-avx512.patch'] +checksums = [ + 'a6c2cd10833e27e6e0465f43432aecc872529bbb056da7b621aafa081b9b4b7a', # gmap-gsnap-2019-03-15.tar.gz + '0cd05c66062086727aa0abc1e806dadfeab7bb478c3516d63a26fc7d178d7be9', # GMAP-GSNAP-2019-03-15-fix-avx512.patch +] + +# with these deps you can use standard compressed files +# to support files in gobby format take a look at README for extra dependencies +# http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +# you can change the MAX_READLENGTH for GSNAP with something like this. +# details in the README http://research-pub.gene.com/gmap/src/README +# configopts = 'MAX_READLENGTH=250' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..06d1bc0cac6 --- /dev/null +++ b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,69 @@ +easyblock = 'Tarball' + +name = 'rnaQUAST' +version = '1.5.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://cab.spbu.ru/software/rnaquast/' +description = """rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. +In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality +assessment using third-party software.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://cab.spbu.ru/files/rnaquast/release%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['7286cd766127c65de032e7c4d38ff874a217bee29dadff7f5dbad5785a550d79'] + +dependencies = [ + ('Python', '2.7.15'), + ('GMAP-GSNAP', '2019-03-15'), + ('Biopython', '1.72', versionsuffix), + ('matplotlib', '2.2.3', versionsuffix), + ('BLAST+', '2.8.1'), +] + +postinstallcmds = [ + 'chmod -x %(installdir)s/README %(installdir)s/VERSION' +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('simplejson', '3.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], + }), + ('argh', '0.26.2', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argh'], + 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], + }), + ('argcomplete', '1.9.5', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argcomplete'], + 'checksums': ['94423d1a56cdec2ef47699e02c9a48cf8827b9c4465b836c0cefb30afe85e59a'], + }), + ('pyfaidx', '0.5.5.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyfaidx'], + 'checksums': ['9ac22bdc7b9c5d995d32eb9dc278af9ba970481636ec75c0d687d38c26446caa'], + }), + ('gffutils', '0.9', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gffutils/'], + 'checksums': ['e1b0bf2b422ec3491be13d77bf7baf71d274abd844e8f8b6c1217a95b236218b'], + }), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_paths = { + 'files': ['rnaQUAST.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' From 2cc127f5a5ef704fd08b2f99af708a4f68b700f8 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 9 Apr 2019 12:25:07 +0200 Subject: [PATCH 1134/5331] statsmodels: fixed source_urls --- .../statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb | 11 ++++++----- .../statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb | 11 ++++++----- 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb index d214f1f9101..e239e733c91 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb @@ -17,20 +17,21 @@ use_pip = True exts_list = [ ('patsy', '0.5.1', { - 'source_urls': [PYPI_SOURCE], - 'sources': ['%(name)s-%(version)s.tar.gz'], + 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), (name, version, { - 'source_urls': [PYPI_SOURCE], - 'sources': ['%(name)s-%(version)s.tar.gz'], + 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], }), ] sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/patsy', + 'lib/python%(pyshortver)s/site-packages/statsmodels' + ], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb index dd54047abb6..9e52a206129 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb @@ -17,20 +17,21 @@ use_pip = True exts_list = [ ('patsy', '0.5.1', { - 'source_urls': [PYPI_SOURCE], - 'sources': ['%(name)s-%(version)s.tar.gz'], + 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], }), (name, version, { - 'source_urls': [PYPI_SOURCE], - 'sources': ['%(name)s-%(version)s.tar.gz'], + 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], }), ] sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/patsy', + 'lib/python%(pyshortver)s/site-packages/statsmodels' + ], } moduleclass = 'math' From c6fecee994d3da7b70da8f0838eacd7ceb632491 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 9 Apr 2019 12:58:42 +0200 Subject: [PATCH 1135/5331] Fix correct version of BLAST+ for 2018b toolchain --- .../r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb index 06d1bc0cac6..bf84cbd7b91 100644 --- a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-1.5.2-foss-2018b-Python-2.7.15.eb @@ -20,7 +20,7 @@ dependencies = [ ('GMAP-GSNAP', '2019-03-15'), ('Biopython', '1.72', versionsuffix), ('matplotlib', '2.2.3', versionsuffix), - ('BLAST+', '2.8.1'), + ('BLAST+', '2.7.1'), ] postinstallcmds = [ From b8cae53cb57d8708f5fb4bada82e738917467d27 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 9 Apr 2019 13:00:05 +0200 Subject: [PATCH 1136/5331] Fix style issue --- .../easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-7.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-7.3.0.eb index cd1604d56ff..8fd999c6cbd 100644 --- a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-7.3.0.eb @@ -32,7 +32,7 @@ dependencies = [('zlib', '1.2.11')] sanity_check_paths = { 'files': ['include/FreeImage.h', 'include/FreeImagePlus.h', 'lib/libfreeimage.a', 'lib/libfreeimage.%s' % SHLIB_EXT, - 'lib/libfreeimageplus.a', 'lib/libfreeimageplus.%s' % SHLIB_EXT], + 'lib/libfreeimageplus.a', 'lib/libfreeimageplus.%s' % SHLIB_EXT], 'dirs': [] } From 66b3bf27392e4b319d4a25bf76db559940f2f6cd Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 9 Apr 2019 13:03:02 +0200 Subject: [PATCH 1137/5331] Fix multiple Lua version in toolchain --- ...ss-2018b.eb => ARGoS-3.0.0-beta53-foss-2018b-Lua-5.2.4.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/a/ARGoS/{ARGoS-3.0.0-beta53-foss-2018b.eb => ARGoS-3.0.0-beta53-foss-2018b-Lua-5.2.4.eb} (92%) diff --git a/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b.eb b/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b-Lua-5.2.4.eb similarity index 92% rename from easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b.eb rename to easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b-Lua-5.2.4.eb index 300f6acdfde..4369a3eece2 100644 --- a/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b.eb +++ b/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b-Lua-5.2.4.eb @@ -2,6 +2,8 @@ easyblock = 'CMakeMake' name = 'ARGoS' version = '3.0.0-beta53' +luaver = '5.2.4' +versionsuffix = '-Lua-%s' % luaver homepage = 'http://www.argos-sim.info' description = """A parallel, multi-engine simulator for heterogeneous swarm robotics""" @@ -15,7 +17,7 @@ checksums = ['849ebb1af31d01519a1f3d9731064eaa8041b2ed140bb699096912de1272214c'] dependencies = [('CMake', '3.12.1')] dependencies = [ - ('Lua', '5.2.4'), + ('Lua', luaver), ('FreeImage', '3.18.0'), ('Qt5', '5.10.1'), ('freeglut', '3.0.0'), From 202f5d7d0ebad01f2029663e5df9c50f8188e177 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Apr 2019 13:20:06 +0200 Subject: [PATCH 1138/5331] {chem}[intel/2018b] PyRETIS v2.1.0 + MDTraj v1.9.2 w/ Python 3.6.6 --- .../MDTraj-1.9.2-intel-2018b-Python-3.6.6.eb | 32 +++++++ .../PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb | 58 ++++++++++++ .../Sphinx-1.8.1-intel-2018b-Python-3.6.6.eb | 88 +++++++++++++++++++ 3 files changed, 178 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.2-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.2-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.2-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..1e6a3c151a8 --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.2-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'MDTraj' +version = '1.9.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/mdtraj/mdtraj/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['9a77cdf080e5c000c493f625a4a1c140d1c0b3ae1fd0299fa3204209befc5c18'] + +dependencies = [ + ('Python', '3.6.6'), + ('zlib', '1.2.11'), +] + +download_dep_fail = True +#use_pip = True + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..229c975e88a --- /dev/null +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'PyRETIS' +version = '2.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pyretis.org' +description = """PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based + on transition interface sampling and replica exchange transition interface sampling.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('Sphinx', '1.8.1', versionsuffix), + ('matplotlib', '3.0.0', versionsuffix), + ('MDTraj', '1.9.2', versionsuffix), +] + +#use_pip = True + +exts_list = [ + # PyRETIS requires more recent setuptools due to use of find_namespace_packages (added in setuptools v40.1.0) + ('setuptools', '41.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['79d30254b6fe7a8e672e43cd85f13a9f3f2a50080bc81d851143e2219ef0dcb1'], + }), + # PyRETIS requires Cython 0.29.* + ('Cython', '0.29.6', { + 'source_urls': ['https://pypi.python.org/packages/source/C/Cython/'], + 'checksums': ['6c5d33f1b5c864382fbce810a8fd9e015447869ae42e98e6301e977b8165e7ae'], + }), + ('colorama', '0.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], + 'checksums': ['05eed71e2e327246ad6b38c540c4a3117230b19679b875190486ddd2d721422d'], + }), + ('tqdm', '4.31.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tqdm/'], + 'checksums': ['e22977e3ebe961f72362f6ddfb9197cc531c9737aaf5f607ef09740c849ecd05'], + }), + ('sphinx-bootstrap-theme', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx-bootstrap-theme/'], + 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], + }), + (name, version, { + 'source_tmpl': 'pyretis-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyretis'], + 'checksums': ['fbacc3c69d0c57e279992a4d01e80f84af3fd191a7bdfebd032391133c540d07'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyretisanalyse', 'bin/pyretisrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..e21f7196125 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx/Sphinx-1.8.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,88 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx' +version = '1.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sphinx.pocoo.org/' +description = """Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. + It was originally created for the new Python documentation, and it has excellent facilities for the + documentation of Python projects, but C/C++ is already supported as well, and it is planned to add + special support for other languages as well.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [('Python', '3.6.6')] + +use_pip = True + +exts_list = [ + ('packaging', '18.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], + 'checksums': ['0886227f54515e592aaa2e5a553332c73962917f2831f1b0f9b9f4380a4b9807'], + }), + ('MarkupSafe', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], + 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], + }), + ('sphinxcontrib-websupport', '1.1.0', { + 'modulename': 'sphinxcontrib.websupport', + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinxcontrib-websupport/'], + 'checksums': ['9de47f375baf1ea07cdb3436ff39d7a9c76042c10a769c52353ec46e4e8fc3b9'], + # can't use pip here because it doesn't support namespaces + # cfr. https://github.com/pypa/pip/issues/1924 + 'use_pip': False, + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], + 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], + }), + ('imagesize', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imagesize/'], + 'checksums': ['f3832918bc3c66617f92e35f5d70729187676313caa60c187eb0f28b8fe5e3b5'], + }), + ('Docutils', '0.14', { + 'source_tmpl': 'docutils-%(version)s.tar.gz', + 'source_urls': [('http://sourceforge.net/projects/docutils/files/docutils/%(version)s/', 'download')], + 'checksums': ['51e64ef2ebfb29cae1faa133b3710143496eca21c530f3f71424d77687764274'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('snowballstemmer', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/snowballstemmer/'], + 'checksums': ['919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128'], + }), + ('Babel', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + 'checksums': ['8cba50f48c529ca3fa18cf81fa9403be176d374ac4d60738b839122dfaaa3d23'], + }), + ('alabaster', '0.7.12', { + 'source_urls': ['https://pypi.python.org/packages/source/a/alabaster/'], + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.6.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/typing/'], + 'checksums': ['4027c5f6127a6267a435201981ba156de91ad0d1d98e9ddc2aa173453453492d'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/S/Sphinx/'], + 'checksums': ['652eb8c566f18823a022bb4b6dbc868d366df332a11a0226b5bc3a798a479f17'], + }), + ('sphinx_rtd_theme', '0.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx_rtd_theme/'], + 'checksums': ['02f02a676d6baabb758a20c7a479d58648e0f64f13e07d1b388e9bb2afe86a09'], + }), + ('numpydoc', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpydoc/'], + 'checksums': ['61f4bf030937b60daa3262e421775838c945dcdd671f37b69e8e4854c7eb5ffd'], + }), +] + +sanity_check_paths = { + 'files': ['bin/sphinx-%s' % x for x in ['apidoc', 'autogen', 'build', 'quickstart']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' From 07fc3954a47b2c41cffc28a83ec3f7754376e3c2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 9 Apr 2019 13:59:40 +0200 Subject: [PATCH 1139/5331] Try to pass multi dep test --- test/easyconfigs/easyconfigs.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 8b06f97fc44..f2fcdd44b21 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -248,6 +248,13 @@ def check_dep_vars(dep, dep_vars): if re.search('^version: %s' % old_dep_versions[dep], key): dep_vars.pop(key) + # filter out Lua versionsuffixes + lua_dep_vars = [v for v in dep_vars.keys() if '-Lua' in v] + if len(dep_vars) > len(lua_dep_vars): + for key in dep_vars.keys(): + if re.search('; versionsuffix: .*-Lua-[0-9.]+', key): + dep_vars.pop(key) + # only single variant is always OK if len(dep_vars) == 1: res = True From 93bc967531f95ca8e4d6565cfe95a324f24bd2c2 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 9 Apr 2019 14:03:23 +0200 Subject: [PATCH 1140/5331] Another try to get it to pass --- test/easyconfigs/easyconfigs.py | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f2fcdd44b21..b4ae4e10b30 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -197,7 +197,7 @@ def check_dep_vars(dep, dep_vars): # for some dependencies, we allow exceptions for software that depends on a particular version, # as long as that's indicated by the versionsuffix - elif dep in ['Boost', 'R', 'PLUMED'] and len(dep_vars) > 1: + elif dep in ['Boost', 'R', 'PLUMED', 'Lua'] and len(dep_vars) > 1: for key in dep_vars.keys(): dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') # filter out dep version if all easyconfig filenames using it include specific dep version @@ -248,13 +248,6 @@ def check_dep_vars(dep, dep_vars): if re.search('^version: %s' % old_dep_versions[dep], key): dep_vars.pop(key) - # filter out Lua versionsuffixes - lua_dep_vars = [v for v in dep_vars.keys() if '-Lua' in v] - if len(dep_vars) > len(lua_dep_vars): - for key in dep_vars.keys(): - if re.search('; versionsuffix: .*-Lua-[0-9.]+', key): - dep_vars.pop(key) - # only single variant is always OK if len(dep_vars) == 1: res = True From 8efaf73b9f2348ec07514bc890c8d1ad46db8822 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Apr 2019 14:21:33 +0200 Subject: [PATCH 1141/5331] enable use_pip in MDTraj and PyRETIS easyconfigs --- .../m/MDTraj/MDTraj-1.9.2-intel-2018b-Python-3.6.6.eb | 2 +- .../p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.2-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.2-intel-2018b-Python-3.6.6.eb index 1e6a3c151a8..5b15ee34011 100644 --- a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.2-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.2-intel-2018b-Python-3.6.6.eb @@ -19,7 +19,7 @@ dependencies = [ ] download_dep_fail = True -#use_pip = True +use_pip = True # The unit tests of MDTraj are a pain to get to work: they require # a massive number of extra dependencies. See diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb index 229c975e88a..b5e094b367b 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.1.0-intel-2018b-Python-3.6.6.eb @@ -17,7 +17,7 @@ dependencies = [ ('MDTraj', '1.9.2', versionsuffix), ] -#use_pip = True +use_pip = True exts_list = [ # PyRETIS requires more recent setuptools due to use of find_namespace_packages (added in setuptools v40.1.0) From cd62c125870f89c0e15cd8467d09e9b2a0879791 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 9 Apr 2019 16:05:59 +0200 Subject: [PATCH 1142/5331] Update to Mako 1.0.8 --- easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb index 48cfba0fe1b..a47526504a5 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb @@ -40,7 +40,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('Autotools', '20180311'), ('pkg-config', '0.29.2'), - ('Mako', '1.0.7'), + ('Mako', '1.0.8'), ('libxml2', '2.9.8'), ('expat', '2.2.6'), ] From e0bbef1df63877b81a820d1d2042231d14c379d6 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Tue, 9 Apr 2019 16:46:46 +0200 Subject: [PATCH 1143/5331] statsmodels: sanity_check_paths not needed for exts in PythonBundle --- .../statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb | 8 -------- .../statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb | 8 -------- 2 files changed, 16 deletions(-) diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb index e239e733c91..9415f9c9e2e 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb @@ -26,12 +26,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/patsy', - 'lib/python%(pyshortver)s/site-packages/statsmodels' - ], -} - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb index 9e52a206129..bfad00f9922 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb @@ -26,12 +26,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/patsy', - 'lib/python%(pyshortver)s/site-packages/statsmodels' - ], -} - moduleclass = 'math' From fbcdf54090d77ced0149c4c27b70e041452907d3 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 9 Apr 2019 16:57:05 +0200 Subject: [PATCH 1144/5331] adding easyconfigs: Meson-0.50.0-GCCcore-8.2.0-Python-3.7.2.eb --- ...Meson-0.50.0-GCCcore-8.2.0-Python-3.7.2.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.50.0-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.50.0-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/m/Meson/Meson-0.50.0-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..0b0b5ac20ef --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.50.0-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.50.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['13e034b8e74fd39cb4a833915343bcb291b0337374d0537b76922605dad28648'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('Ninja', '1.9.0'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 38d1f5771d5f7f7f13f9751c850116234ce4ca64 Mon Sep 17 00:00:00 2001 From: install Date: Tue, 9 Apr 2019 09:44:02 -0700 Subject: [PATCH 1145/5331] Set 'download_dep_fail = True' --- .../p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb index f47c4f5bec4..55bc2e064ce 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.6.1-fosscuda-2018b-Python-2.7.15.eb @@ -14,6 +14,7 @@ sources = [SOURCE_TAR_GZ] checksums = ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'] use_pip = True +download_dep_fail = True dependencies = [ ('Python', '2.7.15'), From ebab6a40c776d0aa2cd61456327769c59a38f0ab Mon Sep 17 00:00:00 2001 From: install Date: Tue, 9 Apr 2019 09:55:09 -0700 Subject: [PATCH 1146/5331] Updated sources to use 's' and removed explict CUDA dependency since it's already implied by 'fosscuda' --- easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb index c8db06e2080..2effe8d520c 100644 --- a/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb @@ -9,11 +9,10 @@ description = 'htop-like GPU usage monitor' toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = ['https://github.com/Syllo/nvtop/archive/'] -sources = ['https://github.com/Syllo/nvtop/archive/1.0.0.tar.gz'] +sources = ['https://github.com/Syllo/nvtop/archive/%(version)s.tar.gz'] checksums = ['de3d7b6a889f886f3bc28c15c3c34cfb6fcb7cb7ebc9a0cc36c3c77d837029b1'] dependencies = [ - ('CUDA', '9.2.88'), ('ncurses', '6.1'), ] From 4aaeecd24d562d1a66e5a44ae7028fb5fbbc58d6 Mon Sep 17 00:00:00 2001 From: install Date: Tue, 9 Apr 2019 10:00:00 -0700 Subject: [PATCH 1147/5331] Removed explict CUDA dependency since it's already implied by 'fosscuda' --- .../g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb index b9082ccc60f..7ff8e499d58 100644 --- a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} dependencies = [ ('Python', '2.7.15'), - ('CUDA', '9.2.88'), ] use_pip = True From 9cca65b80ed67a25e924ef4a960384a068bfce09 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 9 Apr 2019 14:04:48 -0500 Subject: [PATCH 1148/5331] No MKL in foss --- easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb b/easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb index 43dcf86d3c2..812a9bfd629 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-3.0.4-foss-2017b.eb @@ -27,7 +27,7 @@ dependencies = [ configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-lpthread' -DMPI_INCLUDE_PATH=$EBROOTOPENMPI/include " configopts += "-DMPI_C_COMPILER=$EBROOTOPENMPI/bin/mpicc -DMPI_CXX_COMPILER=$EBROOTOPENMPI/bin/mpicxx " configopts += "-DCUDA=OFF -DCudaTexture=OFF " -configopts += "-DALTCPU=ON -DMKLFFT=ON -DFORCE_OWN_TBB=OFF " +configopts += "-DALTCPU=ON -DFORCE_OWN_TBB=OFF " sanity_check_paths = { 'files': ['bin/relion'], From 43b0a6a8ba59c0ec0379396b85b1e0c51cea8da1 Mon Sep 17 00:00:00 2001 From: Toon Verstraelen Date: Wed, 10 Apr 2019 11:48:26 +0200 Subject: [PATCH 1149/5331] Add pretestopts to CheMPS2 easyconfig --- easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2018b.eb | 1 + easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2018b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2018b.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2018b.eb index 90f6c396925..3de9441a5ac 100644 --- a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2018b.eb +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2018b.eb @@ -19,6 +19,7 @@ dependencies = [ ('HDF5', '1.10.2') ] +pretestopts = 'export OMP_NUM_THREADS=1 && ' runtest = 'test' separate_build_dir = True diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2018b.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2018b.eb index c3c7728d4b1..c55ca636382 100644 --- a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2018b.eb +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2018b.eb @@ -19,6 +19,7 @@ dependencies = [ ('HDF5', '1.10.2') ] +pretestopts = 'export OMP_NUM_THREADS=1 && ' runtest = 'test' separate_build_dir = True From 43e60f116aa49bc94473763594fc638c46982f02 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Wed, 10 Apr 2019 15:33:43 +0200 Subject: [PATCH 1150/5331] statsmodels: code-style --- .../statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb | 4 ++-- .../statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb index 9415f9c9e2e..9806418887c 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-foss-2018b-Python-2.7.15.eb @@ -6,8 +6,8 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.statsmodels.org' description = """Statsmodels is a Python module that provides classes and functions -for the estimation of many different statistical models, as well as for conducting -statistical tests, and statistical data exploration.""" + for the estimation of many different statistical models, as well as for conducting + statistical tests, and statistical data exploration.""" toolchain = {'name': 'foss', 'version': '2018b'} diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb index bfad00f9922..15441771e45 100644 --- a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.9.0-intel-2018b-Python-2.7.15.eb @@ -6,8 +6,8 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.statsmodels.org' description = """Statsmodels is a Python module that provides classes and functions -for the estimation of many different statistical models, as well as for conducting -statistical tests, and statistical data exploration.""" + for the estimation of many different statistical models, as well as for conducting + statistical tests, and statistical data exploration.""" toolchain = {'name': 'intel', 'version': '2018b'} From 4f6820750f879827580a7aa3dcd1b18f14246401 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 10 Apr 2019 11:05:54 -0500 Subject: [PATCH 1151/5331] add an additional env variable of GRACE_HOME, so that to locate the font dir --- .../easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb | 4 ++++ .../easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb index e5386963e73..73d656f3336 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb @@ -34,4 +34,8 @@ sanity_check_paths = { 'dirs': ['include', 'fonts', 'templates'], } +modextravars = { + 'GRACE_HOME': '%(installdir)s', +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb index 29fc9ea0cf3..84971e4a5a2 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb @@ -34,4 +34,8 @@ sanity_check_paths = { 'dirs': ['include', 'fonts', 'templates'], } +modextravars = { + 'GRACE_HOME': '%(installdir)s', +} + moduleclass = 'vis' From 20d8d23998752e6d4c91d4c9ffa4511b18b881dd Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 10 Apr 2019 11:41:05 -0500 Subject: [PATCH 1152/5331] adding easyconfigs: IPython-5.8.0-foss-2017b-Python-2.7.14.eb, IPython-5.8.0-foss-2017b-Python-3.6.3.eb, IPython-5.8.0-intel-2017b-Python-2.7.14.eb, IPython-5.8.0-intel-2017b-Python-3.6.3.eb --- .../IPython-5.8.0-foss-2017b-Python-2.7.14.eb | 235 ++++++++++++++++++ .../IPython-5.8.0-foss-2017b-Python-3.6.3.eb | 226 +++++++++++++++++ ...IPython-5.8.0-intel-2017b-Python-2.7.14.eb | 235 ++++++++++++++++++ .../IPython-5.8.0-intel-2017b-Python-3.6.3.eb | 226 +++++++++++++++++ 4 files changed, 922 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..cb290c7ccf7 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,235 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '5.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [ + ('Python', '2.7.14'), + ('ZeroMQ', '4.2.2'), + ('matplotlib', '2.1.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('pyzmq', '17.0.0', { + 'modulename': 'zmq', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], + 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], + }), + ('nbformat', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('certifi', '2018.4.16', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('futures', '3.2.0', { + 'modulename': 'concurrent.futures', + 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], + 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], + }), + ('tornado', '5.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], + }), + ('MarkupSafe', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], + }), + ('mistune', '0.8.3', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], + }), + ('ptyprocess', '0.5.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], + }), + ('terminado', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('ipython_genutils', 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['7d6143d10e9b026df888e0b2936ceff1827ef2f2087646b4dd475c8dcef58606'], + }), + ('widgetsnbextension', '3.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], + }), + ('requests', '2.21.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], + }), + ('urllib3', '1.24.1', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('widgetsnbextension', '3.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "ipython notebook --help", + "iptest", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..a196af4552f --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,235 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '5.8.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [ + ('Python', '2.7.14'), + ('ZeroMQ', '4.2.2'), + ('matplotlib', '2.1.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('pyzmq', '17.0.0', { + 'modulename': 'zmq', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], + 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], + }), + ('nbformat', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('certifi', '2018.4.16', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('futures', '3.2.0', { + 'modulename': 'concurrent.futures', + 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], + 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], + }), + ('tornado', '5.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + 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and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [ + ('Python', '3.6.3'), + ('ZeroMQ', '4.2.2'), + ('matplotlib', '2.1.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('pyzmq', '17.0.0', { + 'modulename': 'zmq', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyzmq/'], + 'checksums': ['0145ae59139b41f65e047a3a9ed11bbc36e37d5e96c64382fcdff911c4d8c3f0'], + }), + ('nbformat', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], + }), + ('Pygments', '2.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'checksums': ['dbae1046def0efb574852fab9e90209b23f556367b5a320c0bcb871c77c3e8cc'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('certifi', '2018.4.16', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('tornado', '5.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + 'checksums': ['1b83d5c10550f2653380b4c77331d6f8850f287c4f67d7ce1e1c639d9222fbc7'], + }), + ('MarkupSafe', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('jsonschema', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], + }), + ('mistune', '0.8.3', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + 'checksums': ['bc10c33bfdcaa4e749b779f62f60d6e12f8215c46a292d05e486b869ae306619'], + }), + ('ptyprocess', '0.5.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + 'checksums': ['e64193f0047ad603b71f202332ab5527c5e52aa7c8b609704fc28c0dc20c4365'], + }), + ('terminado', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('ipython_genutils', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('scandir', '1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], + 'checksums': ['b2d55be869c4f716084a19b1e16932f0769711316ba62de941320bf2be84763d'], + }), + ('pathlib2', '2.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + 'checksums': ['8eb170f8d0d61825e09a95b38be068299ddeda82f35e96c3301a8a5e7604cb83'], + }), + ('pickleshare', '0.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + 'checksums': ['84a9257227dfdd6fe1b4be1319096c20eb85ff1e82c7932f36efccfe1b09737b'], + }), + ('traitlets', '4.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], + }), + ('jupyter_core', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], + }), + ('jupyter_client', '5.2.3', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + 'checksums': ['27befcf0446b01e29853014d6a902dd101ad7d7f94e2252b1adca17c3466b761'], + }), + ('pexpect', '4.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + 'checksums': ['9f8eb3277716a01faafaba553d629d3d60a1a624c7cf45daa600d2148c30020c'], + }), + ('pandocfilters', '1.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], + 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], + }), + ('configparser', '3.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], + 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], + }), + ('entrypoints', '0.2.3', { + 'source_urls': ['https://pypi.python.org/packages/source/e/entrypoints/'], + 'checksums': ['d2d587dde06f99545fb13a383d2cd336a8ff1f359c5839ce3a64c917d10c029f'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], + }), + ('testpath', '0.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], + 'checksums': ['0d5337839c788da5900df70f8e01015aec141aa3fe7936cb0d0a2953f7ac7609'], + }), + ('wcwidth', '0.1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + }), + ('prompt_toolkit', '1.0.15', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], + 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], + }), + ('ipykernel', '4.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + 'checksums': ['c091449dd0fad7710ddd9c4a06e8b9e15277da306590bc07a3a1afa6b4453c8f'], + }), + ('ipywidgets', '7.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + 'checksums': ['ab9869cda5af7ba449d8f707b29b7e97a7db97d6366805d6b733338f51096f54'], + }), + ('Send2Trash', '1.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/Send2Trash/'], + 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], + }), + ('webencodings', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/webencodings/'], + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/h/html5lib/'], + 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], + }), + ('bleach', '2.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bleach/'], + 'checksums': ['eb7386f632349d10d9ce9d4a838b134d4731571851149f9cc2c05a9a837a9a44'], + }), + ('nbconvert', '5.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'checksums': ['12b1a4671d4463ab73af6e4cbcc965b62254e05d182cd54995dda0d0ef9e2db9'], + }), + ('parso', '0.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parso/'], + 'checksums': ['5815f3fe254e5665f3c5d6f54f086c2502035cb631a91341591b5a564203cffb'], + }), + ('jedi', '0.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], + 'checksums': ['d6e799d04d1ade9459ed0f20de47c32f2285438956a677d083d3c98def59fa97'], + }), + ('backcall', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backcall/'], + 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], + }), + ('notebook', '5.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + 'checksums': ['7d6143d10e9b026df888e0b2936ceff1827ef2f2087646b4dd475c8dcef58606'], + }), + ('widgetsnbextension', '3.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], + }), + ('requests', '2.21.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + 'checksums': ['502a824f31acdacb3a35b6690b5fbf0bc41d63a24a45c4004352b0242707598e'], + }), + ('urllib3', '1.24.1', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['de9529817c93f27c8ccbfead6985011db27bd0ddfcdb2d86f3f663385c6a9c22'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('widgetsnbextension', '3.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + 'checksums': ['5417789ee6064ff515fd10be24870660af3561c02d3d48b26f6f44285d0f70cc'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "ipython notebook --help", + "iptest", +] + +moduleclass = 'tools' From 4183cf4d465f00e4b1bee74ac530f37056a3c28d Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Wed, 10 Apr 2019 11:42:18 -0500 Subject: [PATCH 1153/5331] correct style problem --- .../easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb | 2 +- .../easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb index 73d656f3336..0879fd8c8d5 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb @@ -34,7 +34,7 @@ sanity_check_paths = { 'dirs': ['include', 'fonts', 'templates'], } -modextravars = { +modextravars = { 'GRACE_HOME': '%(installdir)s', } diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb index 84971e4a5a2..a224be48e35 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb @@ -34,7 +34,7 @@ sanity_check_paths = { 'dirs': ['include', 'fonts', 'templates'], } -modextravars = { +modextravars = { 'GRACE_HOME': '%(installdir)s', } From f1585d6ed314977d3434cbf24e71ebb091d5e02f Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 10 Apr 2019 11:43:16 -0500 Subject: [PATCH 1154/5331] Add dependency --- .../z/ZeroMQ/ZeroMQ-4.2.2-foss-2017b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017b.eb diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017b.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017b.eb new file mode 100644 index 00000000000..9497534bcf4 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.2-foss-2017b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.2.2' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5b23f4ca9ef545d5bd3af55d305765e3ee06b986263b31967435d285a3e6df6b'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.31'), + ('libsodium', '1.0.13'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From 185ed209f0dba630d0804b6fc6bb9b3813f295a6 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 10 Apr 2019 11:44:04 -0500 Subject: [PATCH 1155/5331] Fix source URL --- .../easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb index 247097915a2..fd09c972029 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.13-GCCcore-6.4.0.eb @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.libsodium.org/libsodium/releases/'] +source_urls = ['https://download.libsodium.org/libsodium/releases/old'] sources = [SOURCE_TAR_GZ] checksums = ['9c13accb1a9e59ab3affde0e60ef9a2149ed4d6e8f99c93c7a5b97499ee323fd'] From 9ba3dbebb9565422e414e33d2b5166cbe66feb5d Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 10 Apr 2019 15:11:56 -0500 Subject: [PATCH 1156/5331] adding easyconfigs: IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb, IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb --- ...0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb | 58 +++++++++++++++++++ ....8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb | 58 +++++++++++++++++++ 2 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb new file mode 100644 index 00000000000..7a2d0b648d9 --- /dev/null +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'IRkernel' +version = '0.8.15' +versionsuffix = '-R-%(rver)s-Python-%(pyver)s' + +homepage = 'https://irkernel.github.io' +description = """The R kernel for the 'Jupyter' environment executes R code + which the front-end (Jupyter Notebook or other front-ends) submits to the + kernel via the network.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [ + ('R', '3.4.3', '-X11-20171023'), + ('Python', '2.7.14'), + ('IPython', '5.8.0', '-Python-%(pyver)s'), + ('ZeroMQ', '4.2.2'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.rstudio.com/src/contrib/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('repr', '0.19.2', { + 'checksums': ['dd4d766d95e8e75f90c05e50e44e759139a47b1477748f4cf9683d35a7fa10d6'], + }), + ('IRdisplay', '0.7.0', { + 'checksums': ['91eac9acdb92ed0fdc58e5da284aa4bb957ada5eef504fd89bec136747999089'], + }), + ('pbdZMQ', '0.3-3', { + 'checksums': ['ae26c13400e2acfb6463ff9b67156847a22ec79f3b53baf65119efaba1636eca'], + }), + (name, version, { + 'checksums': ['469969622d1048d3d1377f89d8def064a6f90b2064097aee7a0ec9a8ee6016d8'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +# The R kernel spec must be installed in order for Jupyter to see it +# This ensures that it is installed in the user local directory at module load +modluafooter = 'execute {cmd="R --slave -e \'library(IRkernel); IRkernel::installspec()\'", modeA={"load"}}' + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb new file mode 100644 index 00000000000..6d3d60c6168 --- /dev/null +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'IRkernel' +version = '0.8.15' +versionsuffix = '-R-%(rver)s-Python-%(pyver)s' + +homepage = 'https://irkernel.github.io' +description = """The R kernel for the 'Jupyter' environment executes R code + which the front-end (Jupyter Notebook or other front-ends) submits to the + kernel via the network.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [ + ('R', '3.4.3', '-X11-20171023'), + ('Python', '2.7.14'), + ('IPython', '5.8.0', '-Python-%(pyver)s'), + ('ZeroMQ', '4.2.2'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.rstudio.com/src/contrib/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('repr', '0.19.2', { + 'checksums': ['dd4d766d95e8e75f90c05e50e44e759139a47b1477748f4cf9683d35a7fa10d6'], + }), + ('IRdisplay', '0.7.0', { + 'checksums': ['91eac9acdb92ed0fdc58e5da284aa4bb957ada5eef504fd89bec136747999089'], + }), + ('pbdZMQ', '0.3-3', { + 'checksums': ['ae26c13400e2acfb6463ff9b67156847a22ec79f3b53baf65119efaba1636eca'], + }), + (name, version, { + 'checksums': ['469969622d1048d3d1377f89d8def064a6f90b2064097aee7a0ec9a8ee6016d8'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +# The R kernel spec must be installed in order for Jupyter to see it +# This ensures that it is installed in the user local directory at module load +modluafooter = 'execute {cmd="R --slave -e \'library(IRkernel); IRkernel::installspec()\'", modeA={"load"}}' + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'tools' From e254f2d50a664f935165a47de93bddb3646f3f96 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 10 Apr 2019 16:17:21 -0500 Subject: [PATCH 1157/5331] adding easyconfigs: CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb, CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb, CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb, CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb --- .../CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb | 34 +++++++++++++++++++ .../CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb | 34 +++++++++++++++++++ ...CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb | 34 +++++++++++++++++++ .../CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb | 34 +++++++++++++++++++ 4 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..79bd3e32c99 --- /dev/null +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'CONCOCT' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/BinPro/CONCOCT' +description = """A program for unsupervised binning of metagenomic contigs by using nucleotide + composition, coverage data in multiple samples and linkage data from paired end reads.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/BinPro/CONCOCT/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['4428a1d7bce5c7546106bea0a0ff6c2168e3680f6422adce5ef523bce46dc180'] + +dependencies = [ + ('GSL', '2.4'), + ('Python', '2.7.14'), + ('Biopython', '1.70', versionsuffix), + ('scikit-learn', '0.19.1', versionsuffix) +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'concoct'} + +sanity_check_paths = { + 'files': ['bin/concoct', 'bin/concoct_refine'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/concoct'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..d7e39c28363 --- /dev/null +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'CONCOCT' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/BinPro/CONCOCT' +description = """A program for unsupervised binning of metagenomic contigs by using nucleotide + composition, coverage data in multiple samples and linkage data from paired end reads.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/BinPro/CONCOCT/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['4428a1d7bce5c7546106bea0a0ff6c2168e3680f6422adce5ef523bce46dc180'] + +dependencies = [ + ('GSL', '2.4'), + ('Python', '3.6.3'), + ('Biopython', '1.70', versionsuffix), + ('scikit-learn', '0.19.1', versionsuffix) +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'concoct'} + +sanity_check_paths = { + 'files': ['bin/concoct', 'bin/concoct_refine'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/concoct'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..2d584ba802e --- /dev/null +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'CONCOCT' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/BinPro/CONCOCT' +description = """A program for unsupervised binning of metagenomic contigs by using nucleotide + composition, coverage data in multiple samples and linkage data from paired end reads.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://github.com/BinPro/CONCOCT/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['4428a1d7bce5c7546106bea0a0ff6c2168e3680f6422adce5ef523bce46dc180'] + +dependencies = [ + ('GSL', '2.4'), + ('Python', '2.7.14'), + ('Biopython', '1.70', versionsuffix), + ('scikit-learn', '0.19.1', versionsuffix) +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'concoct'} + +sanity_check_paths = { + 'files': ['bin/concoct', 'bin/concoct_refine'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/concoct'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..cad571feaad --- /dev/null +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'CONCOCT' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/BinPro/CONCOCT' +description = """A program for unsupervised binning of metagenomic contigs by using nucleotide + composition, coverage data in multiple samples and linkage data from paired end reads.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://github.com/BinPro/CONCOCT/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['4428a1d7bce5c7546106bea0a0ff6c2168e3680f6422adce5ef523bce46dc180'] + +dependencies = [ + ('GSL', '2.4'), + ('Python', '3.6.3'), + ('Biopython', '1.70', versionsuffix), + ('scikit-learn', '0.19.1', versionsuffix) +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'concoct'} + +sanity_check_paths = { + 'files': ['bin/concoct', 'bin/concoct_refine'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/concoct'], +} + +moduleclass = 'bio' From 956eb9836717fbbc44e37aa25f1dbf1608656a18 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 10 Apr 2019 16:18:14 -0500 Subject: [PATCH 1158/5331] Add dependency --- ...t-learn-0.19.1-foss-2017b-Python-2.7.14.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..de44a56868f --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.19.1-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.19.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5ca0ad32ee04abe0d4ba02c8d89d501b4e5e0304bdf4d45c2e9875a735b323a0'] + +dependencies = [ + ('Python', '2.7.14'), + ('matplotlib', '2.1.0', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' From d12500ada63c607f51a213a899fc5da9429d141c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Apr 2019 08:09:35 +0200 Subject: [PATCH 1159/5331] fix checksum for nlme in R 3.5.* easyconfigs --- easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb index 5faab3cefd6..ee5a16f71d1 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb @@ -429,7 +429,7 @@ exts_list = [ 'checksums': ['2723523e8581cc0e2215435ac773033577a16087a3f41d111757dd96b8c5559d'], }), ('nlme', '3.1-137', { - 'checksums': ['01049bb9c53826ff4ec5ba7117d766b17a0108c85f80871a5adb0c0b58ef7e87'], + 'checksums': ['ac82a5d15233dfca2a1aaf9f3ceee018adfe2983344750023dd433ed49b07ba8'], }), ('minqa', '1.2.4', { 'checksums': ['cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c'], diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index 02a6c98cee2..d17b5098e9d 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -397,7 +397,7 @@ exts_list = [ 'checksums': ['41366f777d8adb83d0bdbac1392a1ab118b36217ca648d3bb9db763aa7ff4686'], }), ('nlme', '3.1-137', { - 'checksums': ['01049bb9c53826ff4ec5ba7117d766b17a0108c85f80871a5adb0c0b58ef7e87'], + 'checksums': ['ac82a5d15233dfca2a1aaf9f3ceee018adfe2983344750023dd433ed49b07ba8'], }), ('mgcv', '1.8-24', { 'checksums': ['a9f8e9823f6d6a4a568d151f2fa619bb2811df73c013e9a105720d9b32b4740c'], diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 38041a1bb7e..6d2e61ebf7d 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -395,7 +395,7 @@ exts_list = [ 'checksums': ['41366f777d8adb83d0bdbac1392a1ab118b36217ca648d3bb9db763aa7ff4686'], }), ('nlme', '3.1-137', { - 'checksums': ['01049bb9c53826ff4ec5ba7117d766b17a0108c85f80871a5adb0c0b58ef7e87'], + 'checksums': ['ac82a5d15233dfca2a1aaf9f3ceee018adfe2983344750023dd433ed49b07ba8'], }), ('mgcv', '1.8-24', { 'checksums': ['a9f8e9823f6d6a4a568d151f2fa619bb2811df73c013e9a105720d9b32b4740c'], From 7e7b846d55b190126dd7bb0b3dc7be865320723e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Apr 2019 08:18:40 +0200 Subject: [PATCH 1160/5331] also fix checksum for boot 1.3-20 extension in older R easyconfigs --- easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb index 3792661502d..51fbf775b80 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb @@ -462,7 +462,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], + 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb index 8160b831f0a..2e2c0888d0c 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb @@ -470,7 +470,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], + 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb index 6b1a391603b..69285fca419 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb @@ -489,7 +489,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], + 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb index 221e6835916..f30b361b36b 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb @@ -489,7 +489,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], + 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb index 779850e09b1..70aa7bbf4c7 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb @@ -489,7 +489,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], + 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb index 5faab3cefd6..eb03347dddb 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb @@ -552,7 +552,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], + 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], From 385bc0a65aa204d79e1b637991204f9adc018c60 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 11 Apr 2019 12:04:20 +0100 Subject: [PATCH 1161/5331] Update PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb --- .../p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb index f9f38c56be6..6de7fae4fc3 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb @@ -216,7 +216,8 @@ download_dep_fail = True # This environment is needed to prevent setup.py from invoking git to determine version. prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' -prebuildopts += ' CFLAGS="-ldl"' +prebuildopts += ' LDFLAGS="$LDFLAGS -ldl"' +preinstallopts = 'VERBOSE=1 LDFLAGS="$LDFLAGS -ldl"' runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/build/lib.linux-x86_64-%(pyshortver)s:$PYTHONPATH ' # skip test subsuites that include hanging/failing tests for now From b5a771daab8877ed7d072f9611e717fde14f7d24 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 11 Apr 2019 12:08:31 +0100 Subject: [PATCH 1162/5331] Update PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb --- .../p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb index 2e19fdd3fa5..c93da010136 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -217,7 +217,8 @@ download_dep_fail = True # This environment is needed to prevent setup.py from invoking git to determine version. prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' -prebuildopts += ' CFLAGS="-ldl"' +prebuildopts += ' LDFLAGS="$LDFLAGS -ldl"' +preinstallopts = 'VERBOSE=1 LDFLAGS="$LDFLAGS -ldl"' # you can choice here: either give a list of CUDA cc version or tell it All # by default it does autodetect of the GPU on the local machine From c866f486a1d18697daf45e04c0bd192fdaac6034 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 11 Apr 2019 15:20:54 +0200 Subject: [PATCH 1163/5331] First guess at meson configuration --- .../m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb index a47526504a5..48da122e449 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb @@ -7,7 +7,7 @@ # it will try to use the llvmpipe by default. It you want swr, do: # GALLIUM_DRIVER=swr -easyblock = 'ConfigureMake' +easyblock = 'MesonNinja' name = 'Mesa' version = '19.0.1' @@ -28,14 +28,16 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] sources = [SOURCELOWER_TAR_XZ] -patches = ['Mesa-17.3.6_fix-strip-llvm-flags.patch'] +#patches = ['Mesa-17.3.6_fix-strip-llvm-flags.patch'] checksums = [ '6884163c0ea9e4c98378ab8fecd72fe7b5f437713a14471beda378df247999d4', # mesa-19.0.1.tar.xz - '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.3.6_fix-strip-llvm-flags.patch +# '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.3.6_fix-strip-llvm-flags.patch ] builddependencies = [ ('binutils', '2.31.1'), + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), ('flex', '2.6.4'), ('Bison', '3.0.5'), ('Autotools', '20180311'), @@ -54,12 +56,14 @@ dependencies = [ ('libunwind', '1.3.1'), ] -# GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" -configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" -configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " +configopts = " --Dosmesa=gallium -Dglx=gallium-xlib --Ddri3=false" +configopts += " --Dgbm=false --Dglx-direct=false --Dgallium-drivers='swrast,swr' -Degl=false" +configopts += " --Dosmesa-bits=32 --Dllvm=true --Dshared-llvm=true" +configopts += " --Dlibunwind=true" +# No equivalent to this: +#configopts += " --enable-texture-float " -buildopts = 'V=1' +#buildopts = 'V=1' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, From 521094d01ac28d1198242ba5d0ceca0e20332c64 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 11 Apr 2019 11:27:33 -0500 Subject: [PATCH 1164/5331] adding easyconfigs: MEGAHIT-1.1.3-foss-2017b-Python-2.7.14.eb, MEGAHIT-1.1.3-foss-2017b-Python-3.6.3.eb --- .../MEGAHIT-1.1.3-foss-2017b-Python-2.7.14.eb | 42 +++++++++++++++++++ .../MEGAHIT-1.1.3-foss-2017b-Python-3.6.3.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.3-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.3-foss-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.3-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.3-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..ef409d75433 --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.3-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'MEGAHIT' +version = '1.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex + metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b6eefdee075aaf7a8f9090e2e8b08b770caff90aa43a255e0e220d82ce71c492'] + +dependencies = [ + ('Python', '2.7.14'), +] + +# This is the CPU-only version. +# +# We're specifying 'version' because otherwise the Makefile will try to +# guess it using 'git describe --tag', which seems less reliable. +buildopts = 'version=v%(version)s verbose=1 use_gpu=0' + +files_to_copy = [ + (['%(namelower)s', '%(namelower)s_asm_core', '%(namelower)s_sdbg_build', '%(namelower)s_toolkit'], 'bin'), + 'LICENSE', + 'README.md', +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s_asm_core', 'bin/%(namelower)s_sdbg_build'], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s -v'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.3-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.3-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..5e78b0ac3ff --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.3-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'MEGAHIT' +version = '1.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex + metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b6eefdee075aaf7a8f9090e2e8b08b770caff90aa43a255e0e220d82ce71c492'] + +dependencies = [ + ('Python', '3.6.3'), +] + +# This is the CPU-only version. +# +# We're specifying 'version' because otherwise the Makefile will try to +# guess it using 'git describe --tag', which seems less reliable. +buildopts = 'version=v%(version)s verbose=1 use_gpu=0' + +files_to_copy = [ + (['%(namelower)s', '%(namelower)s_asm_core', '%(namelower)s_sdbg_build', '%(namelower)s_toolkit'], 'bin'), + 'LICENSE', + 'README.md', +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s_asm_core', 'bin/%(namelower)s_sdbg_build'], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s -v'] + +moduleclass = 'bio' From 4de6dc6eaae995f5cf522b8fe1c3206bafb21c85 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 11 Apr 2019 11:47:07 -0500 Subject: [PATCH 1165/5331] adding easyconfigs: parallel-20171122-foss-2017b.eb --- .../parallel/parallel-20171122-foss-2017b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20171122-foss-2017b.eb diff --git a/easybuild/easyconfigs/p/parallel/parallel-20171122-foss-2017b.eb b/easybuild/easyconfigs/p/parallel/parallel-20171122-foss-2017b.eb new file mode 100644 index 00000000000..63670f728c0 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20171122-foss-2017b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20171122' + +homepage = 'http://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['41b46add38eecad3026e0086c1fb01cfa13c7cc24ecf91cd595e22f83fca82a6'] + +dependencies = [ + ('Perl', '5.26.0'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +moduleclass = 'tools' From caff2db9ff02c693a7da0f6c752601ea4caa5c8a Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 11 Apr 2019 12:47:15 -0500 Subject: [PATCH 1166/5331] adding easyconfigs: CheckM-1.0.13-foss-2017b-Python-2.7.14.eb, CheckM-1.0.13-foss-2017b-Python-3.6.3.eb, CheckM-1.0.13-intel-2017b-Python-2.7.14.eb, CheckM-1.0.13-intel-2017b-Python-3.6.3.eb --- .../CheckM-1.0.13-foss-2017b-Python-2.7.14.eb | 39 +++++++++++++++++++ .../CheckM-1.0.13-foss-2017b-Python-3.6.3.eb | 39 +++++++++++++++++++ ...CheckM-1.0.13-intel-2017b-Python-2.7.14.eb | 39 +++++++++++++++++++ .../CheckM-1.0.13-intel-2017b-Python-3.6.3.eb | 39 +++++++++++++++++++ 4 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..7575b126f79 --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'CheckM' +version = '1.0.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Ecogenomics/CheckM' +description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, + single cells, or metagenomes.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [ + ('Python', '2.7.14'), + ('pplacer', '1.1.alpha19', '', True), + ('prodigal', '2.6.3'), + ('HMMER', '3.1b2'), +] + +use_pip = True + +exts_list = [ + ('DendroPy', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/D/DendroPy'], + 'checksums': ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'], + }), + ('checkm-genome', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/checkm-genome'], + 'checksums': ['ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e'], + 'modulename': 'checkm', + }), +] + +sanity_check_paths = { + 'files': ['bin/checkm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..21f54e3815e --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'CheckM' +version = '1.0.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Ecogenomics/CheckM' +description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, + single cells, or metagenomes.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +dependencies = [ + ('Python', '3.6.3'), + ('pplacer', '1.1.alpha19', '', True), + ('prodigal', '2.6.3'), + ('HMMER', '3.1b2'), +] + +use_pip = True + +exts_list = [ + ('DendroPy', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/D/DendroPy'], + 'checksums': ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'], + }), + ('checkm-genome', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/checkm-genome'], + 'checksums': ['ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e'], + 'modulename': 'checkm', + }), +] + +sanity_check_paths = { + 'files': ['bin/checkm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..870a15df966 --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'CheckM' +version = '1.0.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Ecogenomics/CheckM' +description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, + single cells, or metagenomes.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [ + ('Python', '2.7.14'), + ('pplacer', '1.1.alpha19', '', True), + ('prodigal', '2.6.3'), + ('HMMER', '3.1b2'), +] + +use_pip = True + +exts_list = [ + ('DendroPy', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/D/DendroPy'], + 'checksums': ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'], + }), + ('checkm-genome', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/checkm-genome'], + 'checksums': ['ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e'], + 'modulename': 'checkm', + }), +] + +sanity_check_paths = { + 'files': ['bin/checkm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..0264c0a0aeb --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'CheckM' +version = '1.0.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Ecogenomics/CheckM' +description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, + single cells, or metagenomes.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +dependencies = [ + ('Python', '3.6.3'), + ('pplacer', '1.1.alpha19', '', True), + ('prodigal', '2.6.3'), + ('HMMER', '3.1b2'), +] + +use_pip = True + +exts_list = [ + ('DendroPy', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/D/DendroPy'], + 'checksums': ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'], + }), + ('checkm-genome', version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/checkm-genome'], + 'checksums': ['ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e'], + 'modulename': 'checkm', + }), +] + +sanity_check_paths = { + 'files': ['bin/checkm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From e81b51b841ba5a44f52425ae9e49bf06dab65e1c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 11 Apr 2019 12:47:59 -0500 Subject: [PATCH 1167/5331] Add dependency --- .../prodigal/prodigal-2.6.3-GCCcore-6.4.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..b5fceee31a4 --- /dev/null +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'prodigal' +version = '2.6.3' + +homepage = 'http://prodigal.ornl.gov/' + +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f'] + +builddependencies = [('binutils', '2.28')] + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +moduleclass = 'bio' From 51f667148aa75eb5cff1d44c90f6e8f9141f969a Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 11 Apr 2019 16:11:15 -0500 Subject: [PATCH 1168/5331] Delete CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb --- ...CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb deleted file mode 100644 index 2d584ba802e..00000000000 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-2.7.14.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'CONCOCT' -version = '1.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/BinPro/CONCOCT' -description = """A program for unsupervised binning of metagenomic contigs by using nucleotide - composition, coverage data in multiple samples and linkage data from paired end reads.""" - -toolchain = {'name': 'intel', 'version': '2017b'} - -source_urls = ['https://github.com/BinPro/CONCOCT/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['4428a1d7bce5c7546106bea0a0ff6c2168e3680f6422adce5ef523bce46dc180'] - -dependencies = [ - ('GSL', '2.4'), - ('Python', '2.7.14'), - ('Biopython', '1.70', versionsuffix), - ('scikit-learn', '0.19.1', versionsuffix) -] - -use_pip = True -download_dep_fail = True - -options = {'modulename': 'concoct'} - -sanity_check_paths = { - 'files': ['bin/concoct', 'bin/concoct_refine'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/concoct'], -} - -moduleclass = 'bio' From aac65322dd880fd7ce01ba9bdc6a9ab849d7ee14 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 11 Apr 2019 16:11:26 -0500 Subject: [PATCH 1169/5331] Delete CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb --- .../CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb deleted file mode 100644 index cad571feaad..00000000000 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-intel-2017b-Python-3.6.3.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'CONCOCT' -version = '1.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/BinPro/CONCOCT' -description = """A program for unsupervised binning of metagenomic contigs by using nucleotide - composition, coverage data in multiple samples and linkage data from paired end reads.""" - -toolchain = {'name': 'intel', 'version': '2017b'} - -source_urls = ['https://github.com/BinPro/CONCOCT/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['4428a1d7bce5c7546106bea0a0ff6c2168e3680f6422adce5ef523bce46dc180'] - -dependencies = [ - ('GSL', '2.4'), - ('Python', '3.6.3'), - ('Biopython', '1.70', versionsuffix), - ('scikit-learn', '0.19.1', versionsuffix) -] - -use_pip = True -download_dep_fail = True - -options = {'modulename': 'concoct'} - -sanity_check_paths = { - 'files': ['bin/concoct', 'bin/concoct_refine'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/concoct'], -} - -moduleclass = 'bio' From d2a1352fa9590796c259963d9e8eead9bbfd1734 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 11 Apr 2019 16:17:11 -0500 Subject: [PATCH 1170/5331] Add dependencies and uniform style --- .../CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb | 19 ++++++++++++++----- .../CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb | 19 ++++++++++++++----- 2 files changed, 28 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb index 79bd3e32c99..6b1b02e8197 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb @@ -4,9 +4,10 @@ name = 'CONCOCT' version = '1.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://github.com/BinPro/CONCOCT' -description = """A program for unsupervised binning of metagenomic contigs by using nucleotide - composition, coverage data in multiple samples and linkage data from paired end reads.""" +homepage = 'https://concoct.readthedocs.io' +description = """Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning + of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data + from paired end reads.""" toolchain = {'name': 'foss', 'version': '2017b'} @@ -15,10 +16,18 @@ sources = ['%(version)s.tar.gz'] checksums = ['4428a1d7bce5c7546106bea0a0ff6c2168e3680f6422adce5ef523bce46dc180'] dependencies = [ - ('GSL', '2.4'), ('Python', '2.7.14'), + ('GSL', '2.4'), ('Biopython', '1.70', versionsuffix), - ('scikit-learn', '0.19.1', versionsuffix) + ('scikit-learn', '0.19.1', versionsuffix), + ('MEGAHIT', '1.1.3', versionsuffix), + ('BEDTools', '2.27.1'), + ('picard', '2.18.27', '-Java-1.8', True), + ('SAMtools', '1.6'), + ('Bowtie2', '2.3.4.1'), + ('parallel', '20171122'), + ('Pysam', '0.14', versionsuffix), + ('CheckM', '1.0.13', versionsuffix), ] use_pip = True diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb index d7e39c28363..30bfadb038e 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb @@ -4,9 +4,10 @@ name = 'CONCOCT' version = '1.0.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://github.com/BinPro/CONCOCT' -description = """A program for unsupervised binning of metagenomic contigs by using nucleotide - composition, coverage data in multiple samples and linkage data from paired end reads.""" +homepage = 'https://concoct.readthedocs.io' +description = """Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning + of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data + from paired end reads.""" toolchain = {'name': 'foss', 'version': '2017b'} @@ -15,10 +16,18 @@ sources = ['%(version)s.tar.gz'] checksums = ['4428a1d7bce5c7546106bea0a0ff6c2168e3680f6422adce5ef523bce46dc180'] dependencies = [ - ('GSL', '2.4'), ('Python', '3.6.3'), + ('GSL', '2.4'), ('Biopython', '1.70', versionsuffix), - ('scikit-learn', '0.19.1', versionsuffix) + ('scikit-learn', '0.19.1', versionsuffix), + ('MEGAHIT', '1.1.3', versionsuffix), + ('BEDTools', '2.27.1'), + ('picard', '2.18.27', '-Java-1.8', True), + ('SAMtools', '1.6'), + ('Bowtie2', '2.3.4.1'), + ('parallel', '20171122'), + ('Pysam', '0.14', versionsuffix), + ('CheckM', '1.0.13', versionsuffix), ] use_pip = True From 618b2d31d900a52055c0b60bdf63487d111acd61 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 12 Apr 2019 09:49:45 +0800 Subject: [PATCH 1171/5331] prepare release notes for eb390 --- RELEASE_NOTES | 78 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 78 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 818073f5bdb..fab0ca023dc 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,84 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 10,358 easyconfig files, for 1,643 different software packages, 31 different (compiler) toolchains, 13 software bundles and 1 meta-package. +v3.9.0 (April 12th 2019) +------------------------ + +feature release +- added example easyconfig files for 68 new software packages: + - arrow (#8007), ACT (#7928), aiohttp (#7728), at-spi2-atk and at-spi2-core (#7658), BCEL (#7937), Bader (#7804), + BlobTools (#7565), barrnap (#7738), biscuit (#5868), bitarray (#7772), bmtagger (#7890), bsddb3 (#7642), + CONCOCT (#7891), Cheetah (#7952), CheckM (#7712), cyvcf2 (#8031), DAS_Tool (#7741), ExaBayes (#7801), + FastANI (#7992), Flask (#7734), fastp (#7693), GRASS (#7489), GTDB-Tk (#7995), Giza (#7843), giflib (#7663), + glew (#7685), gpustat (#8025), HPCX (#7725), IntelPython (#7920), KNIME (#7554), KronaTools (#7721), + KyotoCabinet (#7955), Leptonica (#7932), libepoxy (#7655), libpsl (#7666), MAGMA (#7829), MATLAB-Engine (#7758), + MaxBin (#7767), MetaBAT (#7746), MinPath (#7763), NGSadmix (#7524), NIMBLE (#7564), ncdu (#7505), PCAngsd (#7727), + Ploticus (#7545), POT (#8011), ProjectQ (#7576), PyRETIS (#8041), pizzly (#7724), pocl (#7681), pullseq (#7740), + pyBigWig (#7600), Pyke3 (#8034), RDKit (#7973), RNAIndel (#8009), SPLASH (#7843), SRPRISM (#7890), SciPy-bundle (#7922), + SqueezeMeta (#7771), scikit-optimize (#7613), sep (#8032), slidingwindow (#7909), TensorRT (#7584), Transrate (#5108), + taxator-tk (#7894), tesseract (#7932), VCF-kit (#7786), VV (#7297) +- added additional easyconfigs for various supported software packages, including: + - ABySS 2.0.2, ABySS 2.0.3, ABySS 2.0.3, ACT 18.0.2, AFNI 19.0.01, AFNI 19.0.01, AMOS 3.1.0, ATK 2.28.1, AUGUSTUS 3.3.2, AUGUSTUS 3.3.2, AUGUSTUS 3.3.2, AUGUSTUS 3.3.2, Advisor 2019_update2.eb, Amber 16, Amber 16, Amber 16, Amber 16, Amber 16, Amber 16, Amber 16, Amber 18, Amber 18, Arrow 0.7.1, Autoconf 2.69, Automake 1.16.1, Autotools 20180311, aiohttp 3.5.4, angsd 0.925, ant 1.10.1, astropy 2.0.12, astropy 2.0.12, at spi2, at spi2, BCEL 5.2, BCFtools 1.6, BLAST+ 2.2.31.eb, BLAST+ 2.6.0, BLAST+ 2.7.1, BLAST+ 2.8.1, BLAST 2.8.1, BUSCO 3.0.2, Bader 1.02, Bader 1.03, BamTools 2.5.1, Bazel 0.20.0, Biopython 1.70, Biopython 1.70, Biopython 1.70, Bismark 0.20.1, Bison 3.3.2, Bison 3.3.2.eb, BlobTools 20180528, Boost.Python 1.65.1, Boost.Python 1.67.0, Bowtie2 2.3.4.2, barrnap 0.9, basemap 1.2.0, beagle lib, binutils 2.32, binutils 2.32.eb, biscuit 0.1.4, bitarray 0.8.3, bitarray 0.8.3, bmtagger 3.101, bokeh 1.0.4, bsddb3 6.2.6, buildenv default, bx python, CD HIT, CDO 1.9.5, CDO 1.9.5, CLAPACK 3.2.1, CLAPACK 3.2.1, CLHEP 2.3.4.3, CLHEP 2.4.1.0, CLHEP 2.4.1.0, CONCOCT 1.0.0, CUDA 10.1.105.eb, CellRanger 3.0.2.eb, CheckM 1.0.13, Clang 6.0.1, Clang 7.0.1, cftime 1.0.1, cuDNN 7.0.5.15, cuDNN 7.0.5.15, cuDNN 7.4.2.24, DAS_Tool 1.1.1, DBG2OLC 20180221, DBG2OLC 20180221, DBus 1.13.8, Doxygen 1.8.15, dask 0.19.4, dbus glib, EMBOSS 6.6.0, EasyBuild 3.8.1.eb, ExaBayes 1.5, Exonerate 2.4.0, Exonerate 2.4.0, ecCodes 2.9.2, ecCodes 2.9.2, expat 2.2.6, FFTW 3.3.6, FFmpeg 4.1, FLTK 1.3.4, FLTK 1.3.4, FLTK 1.3.4, FTGL 2.1.3, FUSE 3.4.1, Flask 1.0.2, FragGeneScan 1.31, FreeXL 1.0.5, FriBidi 1.0.5, fastp 0.19.7, flex 2.6.4, fontconfig 2.13.1, freetype 2.9.1, future 0.16.0, GATE 8.0, GATK 4.0.1.2, GATK 4.1.0.0, GCC 8.3.0, GCCcore 8.3.0.eb, GConf 3.2.6, GDB 8.0.1, GDB 8.0.1, GEOS 3.6.2, GLPK 4.65, GMP 6.1.2, GObject Introspection, GObject Introspection, GRASS 7.6.0, GROMACS 2018.4, GROMACS 2018.4, GST plugins, GStreamer 0.10.36, GStreamer 1.15.1, GTK+ 3.22.30, GTS 0.7.6, Gdk Pixbuf, Gdk Pixbuf, Geant4 10.03.p03, Geant4 10.5, Geant4 10.5, GffCompare 0.10.6, GitPython 2.1.11, Giza 1.1.0, Go 1.11.5.eb, Go 1.12.1, Go 1.12.eb, Guile 1.8.8, gc 7.6.10, gettext 0.19.8.1, gffread 0.10.6, gflags 2.2.1, giflib 5.1.4, git lfs, git 2.21.0, glew 2.1.0, glog 0.3.5, gnuplot 5.2.6, gperf 3.1, gzip 1.10, HDF5 1.10.1, HDF5 1.10.1, HDF5 1.10.5, HDF5 1.10.5, HISAT2 2.1.0, HISAT2 2.1.0, HISAT2 2.1.0, HMMER 3.1b2, HMMER 3.1b2, HPCX 2.3.0, HPL 2.3, HPL 2.3, HTSeq 0.11.2, HTSeq 0.9.1, HTSeq 0.9.1, HTSeq 0.9.1, HTSeq 0.9.1, HTSlib 1.6, HTSlib 1.9, HarfBuzz 1.9.0, HarfBuzz 2.2.0, h5py 2.7.1, h5py 2.7.1, h5py 2.7.1, h5py 2.8.0, help2man 1.47.8, hwloc 2.0.3, IGVTools 2.4.18, IPython 7.2.0, ImageJ 1.51a.eb, Inspector 2019_update2.eb, IntelPython 2.7.15, IntelPython 3.6.8, icc 2019.2.187, icc 2019.3.199, iccifort 2019.2.187, iccifort 2019.3.199, ifort 2019.2.187, ifort 2019.3.199, iimpi 2019.02.eb, iimpi 2019.03.eb, imbalanced learn, imkl 2019.2.187, imkl 2019.3.199, impi 2019.2.187, impi 2019.3.199, intel 2019.02.eb, intel 2019.03.eb, intltool 0.51.0, ispc 1.10.0.eb, itac 2019.2.026.eb, JUnit 4.12, JasPer 1.900.1, JasPer 2.0.14, Java 1.8.0_202.eb, Java 1.9.0.4.eb, Java 11.0.2.eb, Java 11.eb, Jellyfish 1.1.12, Jellyfish 1.1.12, KNIME 3.6.2.eb, Keras 2.2.0, Keras 2.2.0, Kraken 1.1, Kraken2 2.0.7, KronaTools 2.7, LIBSVM 3.23, LLVM 5.0.0, LLVM 5.0.0, LLVM 7.0.1, LZO 2.10, Leptonica 1.77.0, LibTIFF 4.0.10, LoFreq 2.1.3.1, LoFreq 2.1.3.1, LocARNA 1.9.2.2, lftp 4.8.4, libGLU 9.0.0, libGLU 9.0.0, libGLU 9.0.0, libcerf 1.11, libcerf 1.11, libdrm 2.4.97, libepoxy 1.5.3, libffi 3.2.1, libgcrypt 1.8.4, libgd 2.2.5, libgpg error, libgpuarray 0.7.5, libgpuarray 0.7.5, libgpuarray 0.7.5, libgpuarray 0.7.5, libharu 2.3.0, libidn 1.35, libjpeg turbo, libmatheval 1.1.11, libpciaccess 0.14, libpng 1.6.36, libpsl 0.20.2, libreadline 8.0, libspatialite 4.3.0a, libtasn1 4.13, libtool 2.4.6, libunistring 0.9.10, libunwind 1.2.1, libwebp 1.0.2, libxml2 2.9.9, libxslt 1.1.33, lpsolve 5.5.2.5, lpsolve 5.5.2.5, lpsolve 5.5.2.5, M4 1.4.18, MACS2 2.1.2.1, MACS2 2.1.2.1, MAGMA 1.07b, MATLAB Engine, MATLAB Engine, MATLAB Enginet 4.0.0, UCX 1.5.0rc1, UDUNITS 2.2. +- minor enhancements, including: + - Python: add ujson extension (#7517) + - add 'asnipe' as extension to R 3.5.1 easyconfigs (#7572) + - add liquidSVM extension to R 3.5.1 (#7597) + - add libunwind dependency to recent Mesa easyconfig when building with foss/GCC (#7629) + - add oddsratio/mltools/h2o extensions to R 3.5.1 easyconfigs (#7744) + - run various checks on easyconfigs that are touched in pull requests and involve Python packages (#7754) + - add mlegp extension in R 3.5.1 easyconfigs (#7814) + - replace ncurses-devel OS dependency in CMake easyconfigs using dummy toolchain with proper ncurses dependency (#7834) + - add 'bartMachine' and 'lqa' extensions to R 3.5.1 (#7865) + - add cpan minus extension to recent perl easyconfigs (#7866) + - add PresenceAbsence, GUTS, GenSA extensions to R 3.5.1 easyconfigs (#7905) + - add parsedate extension to R 3.5.1 easyconfigs (#7935) + - prefer https:// over ftp:// for source_urls in recent GROMACS easyconfigs (#7948) + - add 'circular' extension to R 3.5.1 easyconfigs (#7975) + - add missing configopts in GATE 8.1 easyconfig to enable Davis feature (#8000) +- various bug fixes, including: + - Mesa-18.1.1: add patch to detect MIT-SHM (#7536) + - add proper description to MINC-2.4.03 (#7551) + - Blobtools: pre-download taxdump (#7583) + - add/reorder missing/misplaced extensions in Python 2.7.15 and 3.6.6 easyconfigs (#7696) + - add Python versionsuffix, follow up for pr #7702 (#7708) + - fix Jellyfish dependency in easyconfig for Kraken 1.0 (Jellyfish 1.x is required) (#7743) + - use https in most recent XZ easyconfigs (#7782) + - add patch for OpenMPI 3.1.x to fix ib-query 'Invalid argument' error (#7789) + - restore checksums check for R-* easyconfigs (#7792) + - build OpenBLAS with -fno-tree-vectorize (asm constraint bugs for <0.3.6) + cleanup & SHA256 checksums (#7790 and #7793) + - fix Travis config to test with both Python 2.6 & 2.7 (#7798) + - extra patch for TensorFlow 1.12.0 to remove -B/usr/bin from linker_bin_path_flag in cuda_configure.bzl (#7800) + - fix STAR-Fusion-1.5.0 (#7802) + - fix checksum for boot extension in R 3.5.1 easyconfigs (#7814) + - add add_ompi_datatype_attribute_to_release_ucp_datatype.patch to older OpenMPI-3.x versions (#7824) + - use PythonBundle for snakemake-5.2.4-foss-2018b-Python-3.6.6.eb (+ fix moduleclass) (#7842) + - use correct buildopts + add missing zlib dependency in StringTie 1.3.5 easyconfig (#7845) + - stick to intervaltree 2.1.0 as required extension for VCF-kit + fix stripping out of hardcoded versions for dependencies (#7882) + - fix typo in comment in pplacer easyconfig (#7885) + - update GStreamer to not enable dw and fix some missing dependencies (#7889) + - add missing XZ dependency to most recent Pysam easyconfigs (#7897) + - remove outdated 'typing' Python package from Python 3.7.2 easyconfig (#7917) + - expat: add configure option --without-docbook to avoid docbook2X dependency (#7930) + - fix problems in MetaBAT easyconfig (#7931) + - also install ANTs scripts (and set $ANTSPATH as required by those scripts) (#7940) + - fix "source_urls" for mawk (#7960) + - fix LWM2, OTF2, OPARI2, and Score-P download URLs (#7994) + - rename arrow to Arrow for old easyconfig (#8007) + - MEME v5.0.4 - Fix missing Python and Perl dependencies (#8010) + - use https:// in homepage & source_urls for OpenMPI and hwloc easyconfigs (#8013, #8014, #8015 and #8016) + - add missing bokeh dependency for dask 1.0.0 (+ add dask-jobqueue) (#8029) + - fix checking of binutils build dep in easyconfig tests (#8038) + - remove MKLFFT from RELION v3.0.4 in foss-2017b (#8043) + - fix checksums for boot/nlme extensions in R easyconfigs (#8054) +- other changes: + - avoid use of .items() in R (bundle) easyconfigs (#7791) + - trim down test configuration: only test with Lmod 6.x with Tcl/Lua on Python 2.6/2.7 (#7795) + - use %(pyshortver)s template in (old) SIP easyconfigs (#7797) + - add PyTorch to whitelist for not having 'use_pip' enabled (#7844) + - don't use local variable 'pylibdir' in list comprehension in PyQt easyconfig, since that doesn't work in Python 3 (#7848) + - use pip instead of setup.py with h5py/2.7.1 and 2017b toolchains (#7864) + + v3.8.1 (January 29th 2019) -------------------------- From 12012da07c5570f7c92fdd6bd38f723f1610a243 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Apr 2019 11:31:42 +0200 Subject: [PATCH 1172/5331] minor tweaks to EasyBuild v3.9.0 release notes + bump version to 3.9.0 --- RELEASE_NOTES | 79 +++++++++++++++++++++------------------------------ setup.py | 2 +- 2 files changed, 34 insertions(+), 47 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index fab0ca023dc..cb53857dc3b 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,85 +3,72 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 10,358 easyconfig files, for 1,643 different software packages, +The latest version of easybuild-easyconfig provides 11,028 easyconfig files, for 1,711 different software packages, 31 different (compiler) toolchains, 13 software bundles and 1 meta-package. v3.9.0 (April 12th 2019) ------------------------ feature release +- added easyconfigs for new toolchains: intel/2019.02 (#7598), intel/2019.03 (#7846) - added example easyconfig files for 68 new software packages: - - arrow (#8007), ACT (#7928), aiohttp (#7728), at-spi2-atk and at-spi2-core (#7658), BCEL (#7937), Bader (#7804), - BlobTools (#7565), barrnap (#7738), biscuit (#5868), bitarray (#7772), bmtagger (#7890), bsddb3 (#7642), - CONCOCT (#7891), Cheetah (#7952), CheckM (#7712), cyvcf2 (#8031), DAS_Tool (#7741), ExaBayes (#7801), - FastANI (#7992), Flask (#7734), fastp (#7693), GRASS (#7489), GTDB-Tk (#7995), Giza (#7843), giflib (#7663), - glew (#7685), gpustat (#8025), HPCX (#7725), IntelPython (#7920), KNIME (#7554), KronaTools (#7721), + - ACT (#7928), aiohttp (#7728), at-spi2-atk and at-spi2-core (#7658), Bader (#7804), barrnap (#7738), BCEL (#7937), + biscuit (#5868), bitarray (#7772), BlobTools (#7565, #7583), bmtagger (#7890), bsddb3 (#7642), + CheckM (#7712), Cheetah (#7952), CONCOCT (#7891), cyvcf2 (#8031), DAS_Tool (#7741), ExaBayes (#7801), + FastANI (#7992), fastp (#7693), Flask (#7734), giflib (#7663), Giza (#7843), glew (#7685), gpustat (#8025), + GRASS (#7489), GTDB-Tk (#7995), HPCX (#7725), IntelPython (#7920), KNIME (#7554), KronaTools (#7721), KyotoCabinet (#7955), Leptonica (#7932), libepoxy (#7655), libpsl (#7666), MAGMA (#7829), MATLAB-Engine (#7758), - MaxBin (#7767), MetaBAT (#7746), MinPath (#7763), NGSadmix (#7524), NIMBLE (#7564), ncdu (#7505), PCAngsd (#7727), - Ploticus (#7545), POT (#8011), ProjectQ (#7576), PyRETIS (#8041), pizzly (#7724), pocl (#7681), pullseq (#7740), - pyBigWig (#7600), Pyke3 (#8034), RDKit (#7973), RNAIndel (#8009), SPLASH (#7843), SRPRISM (#7890), SciPy-bundle (#7922), - SqueezeMeta (#7771), scikit-optimize (#7613), sep (#8032), slidingwindow (#7909), TensorRT (#7584), Transrate (#5108), - taxator-tk (#7894), tesseract (#7932), VCF-kit (#7786), VV (#7297) + MaxBin (#7767), MetaBAT (#7746, #7931), MinPath (#7763), ncdu (#7505), NGSadmix (#7524), NIMBLE (#7564), + PCAngsd (#7727), pizzly (#7724), Ploticus (#7545), pocl (#7681), POT (#8011), ProjectQ (#7576), pullseq (#7740), + pyBigWig (#7600), Pyke3 (#8034), PyRETIS (#8041), RDKit (#7973), RNAIndel (#8009), scikit-optimize (#7613), + SciPy-bundle (#7922), sep (#8032), slidingwindow (#7909), SPLASH (#7843), SqueezeMeta (#7771), SRPRISM (#7890), + taxator-tk (#7894), TensorRT (#7584), tesseract (#7932), Transrate (#5108), VCF-kit (#7786, #7882), VV (#7297) - added additional easyconfigs for various supported software packages, including: - - ABySS 2.0.2, ABySS 2.0.3, ABySS 2.0.3, ACT 18.0.2, AFNI 19.0.01, AFNI 19.0.01, AMOS 3.1.0, ATK 2.28.1, AUGUSTUS 3.3.2, AUGUSTUS 3.3.2, AUGUSTUS 3.3.2, AUGUSTUS 3.3.2, Advisor 2019_update2.eb, Amber 16, Amber 16, Amber 16, Amber 16, Amber 16, Amber 16, Amber 16, Amber 18, Amber 18, Arrow 0.7.1, Autoconf 2.69, Automake 1.16.1, Autotools 20180311, aiohttp 3.5.4, angsd 0.925, ant 1.10.1, astropy 2.0.12, astropy 2.0.12, at spi2, at spi2, BCEL 5.2, BCFtools 1.6, BLAST+ 2.2.31.eb, BLAST+ 2.6.0, BLAST+ 2.7.1, BLAST+ 2.8.1, BLAST 2.8.1, BUSCO 3.0.2, Bader 1.02, Bader 1.03, BamTools 2.5.1, Bazel 0.20.0, Biopython 1.70, Biopython 1.70, Biopython 1.70, Bismark 0.20.1, Bison 3.3.2, Bison 3.3.2.eb, BlobTools 20180528, Boost.Python 1.65.1, Boost.Python 1.67.0, Bowtie2 2.3.4.2, barrnap 0.9, basemap 1.2.0, beagle lib, binutils 2.32, binutils 2.32.eb, biscuit 0.1.4, bitarray 0.8.3, bitarray 0.8.3, bmtagger 3.101, bokeh 1.0.4, bsddb3 6.2.6, buildenv default, bx python, CD HIT, CDO 1.9.5, CDO 1.9.5, CLAPACK 3.2.1, CLAPACK 3.2.1, CLHEP 2.3.4.3, CLHEP 2.4.1.0, CLHEP 2.4.1.0, CONCOCT 1.0.0, CUDA 10.1.105.eb, CellRanger 3.0.2.eb, CheckM 1.0.13, Clang 6.0.1, Clang 7.0.1, cftime 1.0.1, cuDNN 7.0.5.15, cuDNN 7.0.5.15, cuDNN 7.4.2.24, DAS_Tool 1.1.1, DBG2OLC 20180221, DBG2OLC 20180221, DBus 1.13.8, Doxygen 1.8.15, dask 0.19.4, dbus glib, EMBOSS 6.6.0, EasyBuild 3.8.1.eb, ExaBayes 1.5, Exonerate 2.4.0, Exonerate 2.4.0, ecCodes 2.9.2, ecCodes 2.9.2, expat 2.2.6, FFTW 3.3.6, FFmpeg 4.1, FLTK 1.3.4, FLTK 1.3.4, FLTK 1.3.4, FTGL 2.1.3, FUSE 3.4.1, Flask 1.0.2, FragGeneScan 1.31, FreeXL 1.0.5, FriBidi 1.0.5, fastp 0.19.7, flex 2.6.4, fontconfig 2.13.1, freetype 2.9.1, future 0.16.0, GATE 8.0, GATK 4.0.1.2, GATK 4.1.0.0, GCC 8.3.0, GCCcore 8.3.0.eb, GConf 3.2.6, GDB 8.0.1, GDB 8.0.1, GEOS 3.6.2, GLPK 4.65, GMP 6.1.2, GObject Introspection, GObject Introspection, GRASS 7.6.0, GROMACS 2018.4, GROMACS 2018.4, GST plugins, GStreamer 0.10.36, GStreamer 1.15.1, GTK+ 3.22.30, GTS 0.7.6, Gdk Pixbuf, Gdk Pixbuf, Geant4 10.03.p03, Geant4 10.5, Geant4 10.5, GffCompare 0.10.6, GitPython 2.1.11, Giza 1.1.0, Go 1.11.5.eb, Go 1.12.1, Go 1.12.eb, Guile 1.8.8, gc 7.6.10, gettext 0.19.8.1, gffread 0.10.6, gflags 2.2.1, giflib 5.1.4, git lfs, git 2.21.0, glew 2.1.0, glog 0.3.5, gnuplot 5.2.6, gperf 3.1, gzip 1.10, HDF5 1.10.1, HDF5 1.10.1, HDF5 1.10.5, HDF5 1.10.5, HISAT2 2.1.0, HISAT2 2.1.0, HISAT2 2.1.0, HMMER 3.1b2, HMMER 3.1b2, HPCX 2.3.0, HPL 2.3, HPL 2.3, HTSeq 0.11.2, HTSeq 0.9.1, HTSeq 0.9.1, HTSeq 0.9.1, HTSeq 0.9.1, HTSlib 1.6, HTSlib 1.9, HarfBuzz 1.9.0, HarfBuzz 2.2.0, h5py 2.7.1, h5py 2.7.1, h5py 2.7.1, h5py 2.8.0, help2man 1.47.8, hwloc 2.0.3, IGVTools 2.4.18, IPython 7.2.0, ImageJ 1.51a.eb, Inspector 2019_update2.eb, IntelPython 2.7.15, IntelPython 3.6.8, icc 2019.2.187, icc 2019.3.199, iccifort 2019.2.187, iccifort 2019.3.199, ifort 2019.2.187, ifort 2019.3.199, iimpi 2019.02.eb, iimpi 2019.03.eb, imbalanced learn, imkl 2019.2.187, imkl 2019.3.199, impi 2019.2.187, impi 2019.3.199, intel 2019.02.eb, intel 2019.03.eb, intltool 0.51.0, ispc 1.10.0.eb, itac 2019.2.026.eb, JUnit 4.12, JasPer 1.900.1, JasPer 2.0.14, Java 1.8.0_202.eb, Java 1.9.0.4.eb, Java 11.0.2.eb, Java 11.eb, Jellyfish 1.1.12, Jellyfish 1.1.12, KNIME 3.6.2.eb, Keras 2.2.0, Keras 2.2.0, Kraken 1.1, Kraken2 2.0.7, KronaTools 2.7, LIBSVM 3.23, LLVM 5.0.0, LLVM 5.0.0, LLVM 7.0.1, LZO 2.10, Leptonica 1.77.0, LibTIFF 4.0.10, LoFreq 2.1.3.1, LoFreq 2.1.3.1, LocARNA 1.9.2.2, lftp 4.8.4, libGLU 9.0.0, libGLU 9.0.0, libGLU 9.0.0, libcerf 1.11, libcerf 1.11, libdrm 2.4.97, libepoxy 1.5.3, libffi 3.2.1, libgcrypt 1.8.4, libgd 2.2.5, libgpg error, libgpuarray 0.7.5, libgpuarray 0.7.5, libgpuarray 0.7.5, libgpuarray 0.7.5, libharu 2.3.0, libidn 1.35, libjpeg turbo, libmatheval 1.1.11, libpciaccess 0.14, libpng 1.6.36, libpsl 0.20.2, libreadline 8.0, libspatialite 4.3.0a, libtasn1 4.13, libtool 2.4.6, libunistring 0.9.10, libunwind 1.2.1, libwebp 1.0.2, libxml2 2.9.9, libxslt 1.1.33, lpsolve 5.5.2.5, lpsolve 5.5.2.5, lpsolve 5.5.2.5, M4 1.4.18, MACS2 2.1.2.1, MACS2 2.1.2.1, MAGMA 1.07b, MATLAB Engine, MATLAB Engine, MATLAB Enginet 4.0.0, UCX 1.5.0rc1, UDUNITS 2.2. + - AFNI 19.0.01, Arrow 0.7.1, BLAST+ 2.8.1, CUDA 10.1.105, GCC(core) 8.3.0, GTK+ 3.22.30, Java (OpenJDK) 11(.0.2), + Meson 0.50.0, MultiQC 1.7, Nim 0.19.2, Ninja 1.9.0, netCDF 4.6.2, netCDF-Fortran 4.4.5, PCRE 8.43, Perl 5.28.1, + PGI 19.1, Python 3.7.2, RELION 3.0.4, Ruby 2.6.1, SCons 3.0.4, SQLite 3.27.2, SuiteSparse 5.4.0, TINKER 8.6.1, + TensorFlow 1.13.1, X11 20190311 - minor enhancements, including: - - Python: add ujson extension (#7517) - - add 'asnipe' as extension to R 3.5.1 easyconfigs (#7572) - - add liquidSVM extension to R 3.5.1 (#7597) - - add libunwind dependency to recent Mesa easyconfig when building with foss/GCC (#7629) - - add oddsratio/mltools/h2o extensions to R 3.5.1 easyconfigs (#7744) + - add various extensions to R 3.5.1 easyconfigs: asnipe (#7572), liquidSVM (#7597), oddsratio/mltools/h2o (#7744), + mlegp (#7814), bartMachine/lqa (#7865), PresenceAbsence/GUTS/GenSA (#7905), parsedate (#7935), circular (#7975) + - add ujson extension in recent Python easyconfigs (#7517) - run various checks on easyconfigs that are touched in pull requests and involve Python packages (#7754) - - add mlegp extension in R 3.5.1 easyconfigs (#7814) - - replace ncurses-devel OS dependency in CMake easyconfigs using dummy toolchain with proper ncurses dependency (#7834) - - add 'bartMachine' and 'lqa' extensions to R 3.5.1 (#7865) - - add cpan minus extension to recent perl easyconfigs (#7866) - - add PresenceAbsence, GUTS, GenSA extensions to R 3.5.1 easyconfigs (#7905) - - add parsedate extension to R 3.5.1 easyconfigs (#7935) - - prefer https:// over ftp:// for source_urls in recent GROMACS easyconfigs (#7948) - - add 'circular' extension to R 3.5.1 easyconfigs (#7975) + - add cpanminus extension to recent Perl easyconfigs (#7866) + - also install ANTs scripts (and set $ANTSPATH as required by those scripts) (#7940) - add missing configopts in GATE 8.1 easyconfig to enable Davis feature (#8000) - various bug fixes, including: - - Mesa-18.1.1: add patch to detect MIT-SHM (#7536) + - add patch for Mesa 18.1.1 to detect MIT-SHM (#7536) - add proper description to MINC-2.4.03 (#7551) - - Blobtools: pre-download taxdump (#7583) + - add libunwind dependency to recent Mesa easyconfig when building with foss/GCC (#7629) - add/reorder missing/misplaced extensions in Python 2.7.15 and 3.6.6 easyconfigs (#7696) - - add Python versionsuffix, follow up for pr #7702 (#7708) - fix Jellyfish dependency in easyconfig for Kraken 1.0 (Jellyfish 1.x is required) (#7743) - use https in most recent XZ easyconfigs (#7782) - add patch for OpenMPI 3.1.x to fix ib-query 'Invalid argument' error (#7789) - - restore checksums check for R-* easyconfigs (#7792) - - build OpenBLAS with -fno-tree-vectorize (asm constraint bugs for <0.3.6) + cleanup & SHA256 checksums (#7790 and #7793) - - fix Travis config to test with both Python 2.6 & 2.7 (#7798) + - build OpenBLAS with -fno-tree-vectorize (asm constraint bugs for <0.3.6) + cleanup & SHA256 checksums (#7790, #7793) - extra patch for TensorFlow 1.12.0 to remove -B/usr/bin from linker_bin_path_flag in cuda_configure.bzl (#7800) - - fix STAR-Fusion-1.5.0 (#7802) - - fix checksum for boot extension in R 3.5.1 easyconfigs (#7814) - - add add_ompi_datatype_attribute_to_release_ucp_datatype.patch to older OpenMPI-3.x versions (#7824) + - fix easyconfig for STAR-Fusion 1.5.0 (#7802) + - fix checksums for boot/nlme extensions in R easyconfigs (#7814, #8054) + - add patch for OpenMPI 3.x to fix UCX memory leak (#7535, #7824) + - replace ncurses-devel OS dependency in CMake easyconfigs using dummy toolchain with proper ncurses dependency (#7834) - use PythonBundle for snakemake-5.2.4-foss-2018b-Python-3.6.6.eb (+ fix moduleclass) (#7842) - use correct buildopts + add missing zlib dependency in StringTie 1.3.5 easyconfig (#7845) - - stick to intervaltree 2.1.0 as required extension for VCF-kit + fix stripping out of hardcoded versions for dependencies (#7882) - - fix typo in comment in pplacer easyconfig (#7885) - update GStreamer to not enable dw and fix some missing dependencies (#7889) - add missing XZ dependency to most recent Pysam easyconfigs (#7897) - - remove outdated 'typing' Python package from Python 3.7.2 easyconfig (#7917) - expat: add configure option --without-docbook to avoid docbook2X dependency (#7930) - - fix problems in MetaBAT easyconfig (#7931) - - also install ANTs scripts (and set $ANTSPATH as required by those scripts) (#7940) - - fix "source_urls" for mawk (#7960) + - fix source URLs for mawk (#7960) - fix LWM2, OTF2, OPARI2, and Score-P download URLs (#7994) - - rename arrow to Arrow for old easyconfig (#8007) - - MEME v5.0.4 - Fix missing Python and Perl dependencies (#8010) - use https:// in homepage & source_urls for OpenMPI and hwloc easyconfigs (#8013, #8014, #8015 and #8016) - add missing bokeh dependency for dask 1.0.0 (+ add dask-jobqueue) (#8029) - fix checking of binutils build dep in easyconfig tests (#8038) - - remove MKLFFT from RELION v3.0.4 in foss-2017b (#8043) - - fix checksums for boot/nlme extensions in R easyconfigs (#8054) - other changes: - - avoid use of .items() in R (bundle) easyconfigs (#7791) - - trim down test configuration: only test with Lmod 6.x with Tcl/Lua on Python 2.6/2.7 (#7795) + - avoid use of .items() in R (bundle) easyconfigs, to fix compatibility with EasyBuild running on top of Python 3 (#7791) + - trim down test configuration: only test with Lmod 6.x with Tcl/Lua on Python 2.6/2.7 (#7795, #7798) - use %(pyshortver)s template in (old) SIP easyconfigs (#7797) - add PyTorch to whitelist for not having 'use_pip' enabled (#7844) - don't use local variable 'pylibdir' in list comprehension in PyQt easyconfig, since that doesn't work in Python 3 (#7848) - use pip instead of setup.py with h5py/2.7.1 and 2017b toolchains (#7864) + - prefer https:// over ftp:// for source_urls in recent GROMACS easyconfigs (#7948) + - rename arrow to Arrow for old easyconfig (#8007) v3.8.1 (January 29th 2019) diff --git a/setup.py b/setup.py index 07428d587cf..a3cfff2eeaa 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.9.0.dev0' +VERSION = '3.9.0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) From bdf1c5787ba8ee37de6b15cdb0d79d5ed19cd264 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Apr 2019 13:18:35 +0200 Subject: [PATCH 1173/5331] bump version to 3.9.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index a3cfff2eeaa..ab6ac620876 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.9.0' +VERSION = '3.9.1.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) From 67cf2884d3b5003b6bfaba756fd8b60374470931 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Apr 2019 14:07:42 +0200 Subject: [PATCH 1174/5331] adding easyconfigs: EasyBuild-3.9.0.eb --- .../e/EasyBuild/EasyBuild-3.9.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.0.eb new file mode 100644 index 00000000000..6140b7de208 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.0.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.9.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://files.pythonhosted.org/packages/18/59/3274a58af6af84a87f7655735b452c06c769586ee73954f5ee15d303aa29/', + # vsc-base + 'https://files.pythonhosted.org/packages/48/aa/f05d350c358338d0e843835660e3993cc5eb28401f32c0c5b8bc9a9458d5/', + # easybuild-framework + 'https://files.pythonhosted.org/packages/96/58/79e6e5351a414a8ffe3acc1f0d15c9ffaafd26af98e87a8e06115ede3a2c/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/83/a3/8a3807671f28135ddca51a8e36d3ecbb15889f251ac77a429ef805f89076/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/dd/63/eb75c7afb17859941dbf0e2fb17a126ffbbaf3159872e46aa9e6e8a193f3/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.11.3.tar.gz', + 'vsc-base-2.8.4.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '8b102ba585863769d974ad117764039ac3cea21372a3baa5cdb6b93166673ad6', # vsc-install-0.11.3.tar.gz + 'a6d3ab52c9dec938d98e53860dce4aba79ca8ea4e81f6e07bf2c3787e764bc3e', # vsc-base-2.8.4.tar.gz + '8f00f22661451a8c15667ab377c6e6151b9e16138d3d3216f45aeff007115ed0', # easybuild-framework-3.9.0.tar.gz + '311ebb2ccc1876de150dad5d434f2eda09a0b69c4e77ceb5d2b499e0a9a321bb', # easybuild-easyblocks-3.9.0.tar.gz + '2f4a626bf201b942cd93b034157d920ed22d960d5a24131b61dbb76796ebea8c', # easybuild-easyconfigs-3.9.0.tar.gz +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' From aa72fe9dff7a5574197060b6d84ab05fde5b4d8d Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 12 Apr 2019 10:49:16 -0700 Subject: [PATCH 1175/5331] IGV 2.5 Java-11 --- .../easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb new file mode 100644 index 00000000000..7dfe862ecda --- /dev/null +++ b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb @@ -0,0 +1,35 @@ +# EasyBuild easyconfig +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'IGV' +version = '2.5.0' +versionsuffix = '-Java-11' + +homepage = 'http://www.broadinstitute.org/software/igv/' +description = """This package contains command line utilities for + preprocessing, computing feature count density (coverage), sorting, and + indexing data files.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/' + + '%(version_major)s.%(version_minor)s'] +sources = ['%(name)s_%(version)s.zip'] +checksums = ['44efdd0500dd6ace8e1c70dad0d758d9ab90492b391d2af4a416f03808fee471'] + +dependencies = [('Java', '11.0.2', '', True)] + +sanity_check_paths = { + 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 87bc780ed968ced46c37a1473bafbbf93b0fcf88 Mon Sep 17 00:00:00 2001 From: install Date: Fri, 12 Apr 2019 11:16:31 -0700 Subject: [PATCH 1176/5331] Fixed sources link and resolved issue that would prevent successful build without a system install of CUDA. --- ...stat-0.5.0-fosscuda-2018b-Python-2.7.15.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..7ff8e499d58 --- /dev/null +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'gpustat' +version = '0.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/wookayin/gpustat' +description = 'dstat-like utilization monitor for NVIDIA GPUs' + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +dependencies = [ + ('Python', '2.7.15'), +] + +use_pip = True + +exts_list = [ + ('psutil', '5.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], + 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], + }), + ('blessings', '1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blessings'], + 'checksums': ['98e5854d805f50a5b58ac2333411b0482516a8210f23f43308baeb58d77c157d'], + }), + ('nvidia-ml-py', '7.352.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nvidia-ml-py'], + 'checksums': ['b4a342ba52a51ff794af38279ce62f78b278ba5f50c13103af52c4f6113ff65e'], + 'modulename': 'pynvml', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gpustat'], + 'checksums': ['2f43421dbcd9ebd8caf179aeb5f78ac123786033fb9a4310ce0f8e18b25eb03e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gpustat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 6d54826171bcb016a913a2d9252c6be923204c03 Mon Sep 17 00:00:00 2001 From: adiemu5 <39637225+adiemu5@users.noreply.github.com> Date: Fri, 12 Apr 2019 13:19:48 -0500 Subject: [PATCH 1177/5331] Delete gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb Comitted the wrong file by mistake. Apologies. --- ...stat-0.5.0-fosscuda-2018b-Python-2.7.15.eb | 43 ------------------- 1 file changed, 43 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb deleted file mode 100644 index 7ff8e499d58..00000000000 --- a/easybuild/easyconfigs/g/gpustat/gpustat-0.5.0-fosscuda-2018b-Python-2.7.15.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'gpustat' -version = '0.5.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/wookayin/gpustat' -description = 'dstat-like utilization monitor for NVIDIA GPUs' - -toolchain = {'name': 'fosscuda', 'version': '2018b'} - -dependencies = [ - ('Python', '2.7.15'), -] - -use_pip = True - -exts_list = [ - ('psutil', '5.6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/psutil'], - 'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'], - }), - ('blessings', '1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/b/blessings'], - 'checksums': ['98e5854d805f50a5b58ac2333411b0482516a8210f23f43308baeb58d77c157d'], - }), - ('nvidia-ml-py', '7.352.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nvidia-ml-py'], - 'checksums': ['b4a342ba52a51ff794af38279ce62f78b278ba5f50c13103af52c4f6113ff65e'], - 'modulename': 'pynvml', - }), - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/g/gpustat'], - 'checksums': ['2f43421dbcd9ebd8caf179aeb5f78ac123786033fb9a4310ce0f8e18b25eb03e'], - }), -] - -sanity_check_paths = { - 'files': ['bin/gpustat'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' From 989cc15edfcece7f2313cb80d9e026c36867af13 Mon Sep 17 00:00:00 2001 From: install Date: Fri, 12 Apr 2019 11:20:22 -0700 Subject: [PATCH 1178/5331] Fixed sources link and resolved issue that would prevent successful build without a system install of CUDA. --- easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb index 2effe8d520c..0d14bfeac14 100644 --- a/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb @@ -9,9 +9,11 @@ description = 'htop-like GPU usage monitor' toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = ['https://github.com/Syllo/nvtop/archive/'] -sources = ['https://github.com/Syllo/nvtop/archive/%(version)s.tar.gz'] +sources = ['%(version)s.tar.gz'] checksums = ['de3d7b6a889f886f3bc28c15c3c34cfb6fcb7cb7ebc9a0cc36c3c77d837029b1'] +configopts = '-DNVML_INCLUDE_DIRS=$EBROOTCUDA/include -DNVML_LIBRARIES=$EBROOTCUDA/lib64/stubs/libnvidia-ml.so' + dependencies = [ ('ncurses', '6.1'), ] From e81bc6cc7d576dabb209f23b3d93f40706356ee1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 13 Apr 2019 14:47:58 +0200 Subject: [PATCH 1179/5331] adding easyconfigs: fosscuda-2019a.eb --- .../c/CUDA/CUDA-10.1.105-GCC-8.2.0-2.31.1.eb | 19 ++++++++ .../f/FFTW/FFTW-3.3.8-gompic-2019a.eb | 17 +++++++ .../easyconfigs/f/fosscuda/fosscuda-2019a.eb | 32 +++++++++++++ .../easyconfigs/g/gcccuda/gcccuda-2019a.eb | 21 +++++++++ .../easyconfigs/g/gompic/gompic-2019a.eb | 21 +++++++++ .../libevent/libevent-2.1.8-GCCcore-8.2.0.eb | 32 +++++++++++++ .../o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb | 39 +++++++++++++++ .../p/PMIx/PMIx-3.0.2-GCCcore-8.2.0.eb | 47 +++++++++++++++++++ ...APACK-2.0.2-gompic-2019a-OpenBLAS-0.3.5.eb | 22 +++++++++ .../u/UCX/UCX-1.5.1-GCCcore-8.2.0.eb | 42 +++++++++++++++++ 10 files changed, 292 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2019a.eb create mode 100644 easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb create mode 100644 easybuild/easyconfigs/g/gcccuda/gcccuda-2019a.eb create mode 100644 easybuild/easyconfigs/g/gompic/gompic-2019a.eb create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-3.0.2-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2019a-OpenBLAS-0.3.5.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.5.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..f56236e9ada --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,19 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'CUDA' +version = '10.1.105' +nv_version = '418.39' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] +sources = ['%%(namelower)s_%%(version)s_%s_linux.run' % nv_version] +checksums = ['33ac60685a3e29538db5094259ea85c15906cbd0f74368733f4111eab6187c8f'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2019a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2019a.eb new file mode 100644 index 00000000000..8821627edaa --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2019a.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompic', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb new file mode 100644 index 00000000000..dee5b918b37 --- /dev/null +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb @@ -0,0 +1,32 @@ +easyblock = 'Toolchain' + +name = 'fosscuda' +version = '2019a' + +homepage = '(none)' +description = """GCC based compiler toolchain __with CUDA support__, and including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '8.2.0-2.31.1' + +blaslib = 'OpenBLAS' +blasver = '0.3.5' +blas = '-%s-%s' % (blaslib, blasver) + +# toolchain used to build fosscuda dependencies +comp_mpi_tc_name = 'gompic' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain dependencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp_mpi_tc, + (blaslib, blasver, '', ('GCC', gccver)), + ('FFTW', '3.3.8', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2019a.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2019a.eb new file mode 100644 index 00000000000..31bb58d6d7c --- /dev/null +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2019a.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'gcccuda' +version = '2019a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'GCC' +comp_ver = '8.2.0-2.31.1' +comp = (comp_name, comp_ver) + +# compiler toolchain dependencies +dependencies = [ + comp, + ('CUDA', '10.1.105', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2019a.eb b/easybuild/easyconfigs/g/gompic/gompic-2019a.eb new file mode 100644 index 00000000000..c6d17476287 --- /dev/null +++ b/easybuild/easyconfigs/g/gompic/gompic-2019a.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'gompic' +version = '2019a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, + including OpenMPI for MPI support with CUDA features enabled.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '8.2.0-2.31.1' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # part of gcccuda + ('CUDA', '10.1.105', '', ('GCC', gccver)), # part of gcccuda + ('OpenMPI', '3.1.3', '', ('gcccuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..2c5fd0420c7 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.8' + +homepage = 'http://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['965cc5a8bb46ce4199a47e9b2c9e1cae3b137e8356ffdad6d94d3b9069b71dc2'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb new file mode 100644 index 00000000000..534a050f1be --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '3.1.3' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'gcccuda', 'version': '2019a'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d'] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '1.11.11') +] + +configopts = '--enable-shared --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.0.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.0.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..f0ce2e732ce --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.0.2-GCCcore-8.2.0.eb @@ -0,0 +1,47 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '3.0.2' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pmix/pmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['df68f35a3ed9517eeade80b13855cebad8fde2772b36a3f6be87559b6d430670'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('libevent', '2.1.8'), + ('zlib', '1.2.11'), + ('hwloc', '1.11.11'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB ' +configopts += ' --with-hwloc=$EBROOTHWLOC ' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2019a-OpenBLAS-0.3.5.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2019a-OpenBLAS-0.3.5.eb new file mode 100644 index 00000000000..3cb6b461cd4 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2019a-OpenBLAS-0.3.5.eb @@ -0,0 +1,22 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompic', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +checksums = ['0c74aeae690fe5ee4db7926f49c5d0bb69ce09eea75beb915e00bba07530395c'] + +blaslib = 'OpenBLAS' +blasver = '0.3.5' + +versionsuffix = "-%s-%s" % (blaslib, blasver) + +dependencies = [(blaslib, blasver)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.5.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..09bb17858a0 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.5.1-GCCcore-8.2.0.eb @@ -0,0 +1,42 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.5.1' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['567119cd80ad2ae6968ecaa4bd1d2a80afadd037ccc988740f668de10d2fdb7e'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +dependencies = [ + ('numactl', '2.0.12'), +] + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +moduleclass = 'lib' From fb9de938f245c7bb4ade019c479fd723e4e18e3b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 13 Apr 2019 23:18:09 +0200 Subject: [PATCH 1180/5331] fosscuda need GCC, CUDA and OpenMPI as explicit dependencies instead of gompic toolchain because of toolchain preperation functions. --- easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb index dee5b918b37..d5450aaae14 100644 --- a/easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb @@ -20,10 +20,12 @@ comp_mpi_tc_name = 'gompic' comp_mpi_tc = (comp_mpi_tc_name, version) # compiler toolchain dependencies -# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain -# because of toolchain preperation functions +# We need GCC, CUDA and OpenMPI as explicit dependencies instead of +# gompic toolchain because of toolchain preperation functions. dependencies = [ - comp_mpi_tc, + ('GCC', gccver), # part of gompic + ('CUDA', '10.1.105', '', ('GCC', gccver)), # part of gompic + ('OpenMPI', '3.1.3', '', ('gcccuda', version)), # part of gompic (blaslib, blasver, '', ('GCC', gccver)), ('FFTW', '3.3.8', '', comp_mpi_tc), ('ScaLAPACK', '2.0.2', blas, comp_mpi_tc), From c6a9d1c21bdd862ca41126e1cc97bdafa454c15c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 13 Apr 2019 23:21:18 +0200 Subject: [PATCH 1181/5331] adding easyconfigs: SciPy-bundle-2019.03-fosscuda-2019a.eb --- .../SciPy-bundle-2019.03-fosscuda-2019a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-fosscuda-2019a.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-fosscuda-2019a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-fosscuda-2019a.eb new file mode 100644 index 00000000000..deaf95d7624 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-fosscuda-2019a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2019.03' + +homepage = 'http://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} +toolchainopts = {'pic': True, 'lowopt': True} + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +use_pip = True + +# order is important! +# package versions updated Mar 15th 2019 +exts_list = [ + ('numpy', '1.16.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6c692e3879dde0b67a9dc78f9bfb6f61c666b4562fd8619632d7043fb5b691b0'], + }), + ('scipy', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + 'checksums': ['e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c'], + }), + ('mpi4py', '3.0.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'], + }), + ('pandas', '0.24.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], + }), + ('mpmath', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), +] + +moduleclass = 'lang' From 951192f56f456580a6f510374aa7bb8a96fb834b Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Sun, 14 Apr 2019 11:11:51 +0200 Subject: [PATCH 1182/5331] adding easyconfigs: Tkinter-2.7.15-GCCcore-8.2.0.eb, Tkinter-3.7.2-GCCcore-8.2.0.eb --- .../t/Tkinter/Tkinter-2.7.15-GCCcore-8.2.0.eb | 23 +++++++++++++++++++ .../t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.15-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.15-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.15-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..97bea5384e8 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.15-GCCcore-8.2.0.eb @@ -0,0 +1,23 @@ +name = 'Tkinter' +version = '2.7.15' + +homepage = 'http://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['18617d1f15a380a919d517630a9cd85ce17ea602f9bbdc58ddc672df4b0239db'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.9'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' + diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..61f292dfb10 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb @@ -0,0 +1,23 @@ +name = 'Tkinter' +version = '3.7.2' + +homepage = 'http://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['f09d83c773b9cc72421abba2c317e4e6e05d919f9bcf34468e192b6a6c8e328d'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.9'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' + From 2b173112b5e704bedffbb028bd1f74e5be2d01a5 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Sun, 14 Apr 2019 14:13:01 +0200 Subject: [PATCH 1183/5331] adding easyconfigs: x264-20190413-GCCcore-8.2.0.eb, LAME-3.100-GCCcore-8.2.0.eb, Yasm-1.3.0-GCCcore-8.2.0.eb, x265-3.0-GCCcore-8.2.0.eb, FFmpeg-4.1.3-GCCcore-8.2.0.eb --- .../f/FFmpeg/FFmpeg-4.1.3-GCCcore-8.2.0.eb | 43 +++++++++++++++++++ .../l/LAME/LAME-3.100-GCCcore-8.2.0.eb | 33 ++++++++++++++ .../x/x264/x264-20190413-GCCcore-8.2.0.eb | 37 ++++++++++++++++ .../x/x265/x265-3.0-GCCcore-8.2.0.eb | 36 ++++++++++++++++ .../y/Yasm/Yasm-1.3.0-GCCcore-8.2.0.eb | 35 +++++++++++++++ 5 files changed, 184 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1.3-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20190413-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/x/x265/x265-3.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1.3-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..f7a16e297d3 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1.3-GCCcore-8.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '4.1.3' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://ffmpeg.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2') +] + +dependencies = [ + ('NASM', '2.14.02'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('x264', '20190413'), + ('LAME', '3.100'), + ('x265', '3.0'), + ('X11', '20190311'), + ('freetype', '2.9.1'), + ('fontconfig', '2.13.1'), + ('FriBidi', '1.0.5'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..611fa61cef6 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Stephane Thiell +### + +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [('ncurses', '6.1')] + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/x264/x264-20190413-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20190413-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..a39c1f2aad4 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20190413-GCCcore-8.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20190413' + +homepage = 'http://www.videolan.org/developers/x264.html' + +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] +checksums = ['3d269a9cfb23a67fa63a47d09840c773a2e25e535036b3033d7065302b7d089c'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('NASM', '2.14.02'), +] + +configopts = " --enable-shared --enable-static" + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', + 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..153ee1d2c10 --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.0-GCCcore-8.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.0' + +homepage = 'http://x265.org/' + +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [ + 'http://ftp.videolan.org/pub/videolan/x265/', + 'http://download.videolan.org/pub/videolan/x265/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['c5b9fc260cabbc4a81561a448f4ce9cad7218272b4011feabc3a6b751b2f0662'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), + ('Yasm', '1.3.0'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..55cf6f77509 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.2.0.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' + +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' From 208a3dd0bb081823b451adf3358368b3a40eb692 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 14 Apr 2019 14:33:59 +0200 Subject: [PATCH 1184/5331] Use https instead of http when possible. --- .../easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb | 2 +- .../easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb | 4 ++-- .../ScaLAPACK/ScaLAPACK-2.0.2-gompic-2019a-OpenBLAS-0.3.5.eb | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb index 2c5fd0420c7..a8344880127 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libevent' version = '2.1.8' -homepage = 'http://libevent.org/' +homepage = 'https://libevent.org/' description = """ The libevent API provides a mechanism to execute a callback function when diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb index 534a050f1be..9090fca6b02 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'OpenMPI' version = '3.1.3' -homepage = 'http://www.open-mpi.org/' +homepage = 'https://www.open-mpi.org/' description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'gcccuda', 'version': '2019a'} -source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] checksums = ['0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d'] diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2019a-OpenBLAS-0.3.5.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2019a-OpenBLAS-0.3.5.eb index 3cb6b461cd4..68d496845d5 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2019a-OpenBLAS-0.3.5.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompic-2019a-OpenBLAS-0.3.5.eb @@ -1,7 +1,7 @@ name = 'ScaLAPACK' version = '2.0.2' -homepage = 'http://www.netlib.org/scalapack/' +homepage = 'https://www.netlib.org/scalapack/' description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.""" From 5f0e59f509aa9bb07916129311efc895d0255f5a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 14 Apr 2019 15:56:11 +0200 Subject: [PATCH 1185/5331] adding easyconfigs: intelcuda-2019a.eb --- ...05-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 19 ++++++++++ .../i/iccifortcuda/iccifortcuda-2019a.eb | 24 ++++++++++++ .../easyconfigs/i/iimpic/iimpic-2019a.eb | 25 +++++++++++++ .../i/imkl/imkl-2019.1.144-iimpic-2019a.eb | 37 +++++++++++++++++++ .../impi-2018.4.274-iccifortcuda-2019a.eb | 29 +++++++++++++++ .../i/intelcuda/intelcuda-2019a.eb | 28 ++++++++++++++ 6 files changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2019a.eb create mode 100644 easybuild/easyconfigs/i/iimpic/iimpic-2019a.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb create mode 100644 easybuild/easyconfigs/i/intelcuda/intelcuda-2019a.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..0c27541fe79 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,19 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'CUDA' +version = '10.1.105' +nv_version = '418.39' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} + +source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] +sources = ['%%(namelower)s_%%(version)s_%s_linux.run' % nv_version] +checksums = ['33ac60685a3e29538db5094259ea85c15906cbd0f74368733f4111eab6187c8f'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2019a.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2019a.eb new file mode 100644 index 00000000000..ea5817b53f9 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2019a.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +name = 'iccifortcuda' +version = '2019a' + +homepage = '(none)' +description = """Intel C, C++ & Fortran compilers with CUDA toolkit""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp_name = 'iccifort' +comp_ver = '2019.1.144' +gccver = '8.2.0' +binutilsver = '2.31.1' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +cudacomp = (comp_name, '%s%s' % (comp_ver, gccsuff)) + +dependencies = [ + ('icc', comp_ver, gccsuff), + ('ifort', comp_ver, gccsuff), + ('CUDA', '10.1.105', '', cudacomp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpic/iimpic-2019a.eb b/easybuild/easyconfigs/i/iimpic/iimpic-2019a.eb new file mode 100644 index 00000000000..cefe5a9e722 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpic/iimpic-2019a.eb @@ -0,0 +1,25 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ +easyblock = "Toolchain" + +name = 'iimpic' +version = '2019a' + +homepage = 'https://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2019.1.144' +gccver = '8.2.0' +binutilsver = '2.31.1' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +intelver = '%s%s' % (compver, gccsuff) + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('CUDA', '10.1.105', '', ('iccifort', intelver)), + ('impi', '2018.4.274', '', ('iccifortcuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb new file mode 100644 index 00000000000..90685df7e9f --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-iimpic-2019a.eb @@ -0,0 +1,37 @@ +name = 'imkl' +version = '2019.1.144' + +homepage = 'https://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpic', 'version': '2019a'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] + +dontcreateinstalldir = 'True' + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb new file mode 100644 index 00000000000..2559fcf0074 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2018.4.274-iccifortcuda-2019a.eb @@ -0,0 +1,29 @@ +name = 'impi' +version = '2018.4.274' + +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'iccifortcuda', 'version': '2019a'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13651/'] +sources = ['l_mpi_%(version)s.tgz'] +checksums = ['a1114b3eb4149c2f108964b83cad02150d619e50032059d119ac4ffc9d5dd8e0'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2019a.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2019a.eb new file mode 100644 index 00000000000..65125927922 --- /dev/null +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2019a.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'intelcuda' +version = '2019a' + +homepage = '(none)' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, + Intel MPI & Intel MKL, with CUDA toolkit""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2019.1.144' +gccver = '8.2.0' +binutilsver = '2.31.1' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +intelver = '%s%s' % (compver, gccsuff) + +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('CUDA', '10.1.105', '', ('iccifort', intelver)), + ('impi', '2018.4.274', '', ('iccifortcuda', version)), + ('imkl', compver, '', ('iimpic', version)), +] + +moduleclass = 'toolchain' From 69f4a54798370ead60d721736b41dc1d1f94cc42 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 15 Apr 2019 11:38:03 +0200 Subject: [PATCH 1186/5331] adding easyconfigs: LS-PrePost-4.6-centos6-03Apr2019.eb, LS-PrePost-4.6-centos7-03Apr2019.eb --- .../LS-PrePost-4.6-centos6-03Apr2019.eb | 23 +++++++++++++++++++ .../LS-PrePost-4.6-centos7-03Apr2019.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6-03Apr2019.eb create mode 100644 easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7-03Apr2019.eb diff --git a/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6-03Apr2019.eb b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6-03Apr2019.eb new file mode 100644 index 00000000000..401fde8f016 --- /dev/null +++ b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6-03Apr2019.eb @@ -0,0 +1,23 @@ +easyblock = "Tarball" + +name = 'LS-PrePost' +version = '4.6' +versionsuffix = '-centos6-03Apr2019' + +homepage = 'http://lstc.com/products/ls-prepost' +description = """LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ftp.lstc.com/anonymous/outgoing/lsprepost/%(version)s/linux64/'] +sources = ['lsprepost-%%(version)s_mesa%s.tgz' % versionsuffix] +checksums = ['b30ac871c9949d2449515033be5e978a873111be5bdf430326681735fa92e2a7'] + +modextrapaths = {'PATH': '.', 'LD_LIBRARY_PATH': 'lib'} + +sanity_check_paths = { + 'files': ['lsprepost'], + 'dirs': ['lib'] +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7-03Apr2019.eb b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7-03Apr2019.eb new file mode 100644 index 00000000000..327b67a45c7 --- /dev/null +++ b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7-03Apr2019.eb @@ -0,0 +1,23 @@ +easyblock = "Tarball" + +name = 'LS-PrePost' +version = '4.6' +versionsuffix = '-centos7-03Apr2019' + +homepage = 'http://lstc.com/products/ls-prepost' +description = """LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ftp.lstc.com/anonymous/outgoing/lsprepost/%(version)s/linux64/'] +sources = ['lsprepost-%%(version)s_mesa%s.tgz' % versionsuffix] +checksums = ['9a89e606054bb481bf73dc8526c5ce4107d242090d0f336a6dfd5c57d782d62e'] + +modextrapaths = {'PATH': '.', 'LD_LIBRARY_PATH': 'lib'} + +sanity_check_paths = { + 'files': ['lsprepost'], + 'dirs': ['lib'] +} + +moduleclass = 'cae' From e0d7b238b87b58d310e76aed00e49a53e1175aad Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 15 Apr 2019 14:47:11 +0200 Subject: [PATCH 1187/5331] adding easyconfigs: SciPy-bundle-2019.03-intelcuda-2019a.eb --- .../SciPy-bundle-2019.03-intelcuda-2019a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intelcuda-2019a.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intelcuda-2019a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intelcuda-2019a.eb new file mode 100644 index 00000000000..180c9ecebd3 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.03-intelcuda-2019a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2019.03' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intelcuda', 'version': '2019a'} +toolchainopts = {'pic': True} + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +use_pip = True + +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +# order is important! +# package versions updated Mar 15th 2019 +exts_list = [ + ('numpy', '1.16.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': [ + 'numpy-1.12.0-mkl.patch', + 'numpy-1.16.1_fix-ifort-V-stderr.patch', + ], + 'checksums': [ + '6c692e3879dde0b67a9dc78f9bfb6f61c666b4562fd8619632d7043fb5b691b0', # numpy-1.16.2.zip + 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch + 'fc7f0c4b910bf3706d43661b94696f07b6e317bfeac062c2c78b3926fde713a7', # numpy-1.16.1_fix-ifort-V-stderr.patch + ], + }), + ('scipy', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + 'checksums': ['e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c'], + }), + ('mpi4py', '3.0.1', { + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['6549a5b81931303baf6600fa2e3bc04d8bd1d5c82f3c21379d0d64a9abcca851'], + }), + ('pandas', '0.24.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], + }), + ('mpmath', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), +] + +moduleclass = 'lang' From 9ede7d963e56ac1d15625f27a24bae995e20a9eb Mon Sep 17 00:00:00 2001 From: Lykle Voort Date: Tue, 16 Apr 2019 10:40:28 +0200 Subject: [PATCH 1188/5331] added easyconfig for unixODBC --- .../u/unixODBC/unixODBC-2.3.7-foss-2018b.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.7-foss-2018b.eb diff --git a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.7-foss-2018b.eb b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.7-foss-2018b.eb new file mode 100644 index 00000000000..d3d37d241ba --- /dev/null +++ b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.7-foss-2018b.eb @@ -0,0 +1,20 @@ +# Easyconfig for unixODBC +# Author: Lykle Voort +# SURFsara, Amsterdam, The Netherlands + +easyblock = 'ConfigureMake' + +name = 'unixODBC' +version = '2.3.7' + +homepage = "https://www.unixodbc.org" +description ="""unixODBC provides a uniform interface between +application and database driver""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['ftp://ftp.unixodbc.org/pub/unixODBC'] +checksums = ['45f169ba1f454a72b8fcbb82abd832630a3bf93baa84731cf2949f449e1e3e77'] + +moduleclass = 'data' From eb03838771ef6166704fed165ac86a5ea600f82e Mon Sep 17 00:00:00 2001 From: Lykle Voort Date: Tue, 16 Apr 2019 11:16:45 +0200 Subject: [PATCH 1189/5331] Update unixODBC config for style --- easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.7-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.7-foss-2018b.eb b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.7-foss-2018b.eb index d3d37d241ba..c504eda5c7f 100644 --- a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.7-foss-2018b.eb +++ b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.7-foss-2018b.eb @@ -8,7 +8,7 @@ name = 'unixODBC' version = '2.3.7' homepage = "https://www.unixodbc.org" -description ="""unixODBC provides a uniform interface between +description = """unixODBC provides a uniform interface between application and database driver""" toolchain = {'name': 'foss', 'version': '2018b'} From a9aa11ae52150bc29e1830ba863aef4adec49b41 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 16 Apr 2019 06:51:38 -0700 Subject: [PATCH 1190/5331] Java/11 wrapper --- easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb index 7dfe862ecda..df5e6e64fb0 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb @@ -9,7 +9,7 @@ easyblock = 'Tarball' name = 'IGV' version = '2.5.0' -versionsuffix = '-Java-11' +versionsuffix = '-Java-%(javaver)s' homepage = 'http://www.broadinstitute.org/software/igv/' description = """This package contains command line utilities for @@ -23,7 +23,7 @@ source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/' + sources = ['%(name)s_%(version)s.zip'] checksums = ['44efdd0500dd6ace8e1c70dad0d758d9ab90492b391d2af4a416f03808fee471'] -dependencies = [('Java', '11.0.2', '', True)] +dependencies = [('Java', '11', '', True)] sanity_check_paths = { 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], From ef3896bf3cf221193978ac29a39fd2c99cb16b0c Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 16 Apr 2019 09:52:37 -0500 Subject: [PATCH 1191/5331] move the eb files from snap folder the SNAP folder --- .../s/{snap => SNAP}/snap-2013-11-29-GCC-6.4.0-2.28.eb | 0 .../snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 0 .../s/{snap => SNAP}/snap_2013-11-29_makefile_correction.patch | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/{snap => SNAP}/snap-2013-11-29-GCC-6.4.0-2.28.eb (100%) rename easybuild/easyconfigs/s/{snap => SNAP}/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb (100%) rename easybuild/easyconfigs/s/{snap => SNAP}/snap_2013-11-29_makefile_correction.patch (100%) diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/SNAP/snap-2013-11-29-GCC-6.4.0-2.28.eb similarity index 100% rename from easybuild/easyconfigs/s/snap/snap-2013-11-29-GCC-6.4.0-2.28.eb rename to easybuild/easyconfigs/s/SNAP/snap-2013-11-29-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/SNAP/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb similarity index 100% rename from easybuild/easyconfigs/s/snap/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb rename to easybuild/easyconfigs/s/SNAP/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/s/snap/snap_2013-11-29_makefile_correction.patch b/easybuild/easyconfigs/s/SNAP/snap_2013-11-29_makefile_correction.patch similarity index 100% rename from easybuild/easyconfigs/s/snap/snap_2013-11-29_makefile_correction.patch rename to easybuild/easyconfigs/s/SNAP/snap_2013-11-29_makefile_correction.patch From 7c9d57322f5c1940ec1d40ef7afc79e6704b7e71 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 16 Apr 2019 10:06:15 -0500 Subject: [PATCH 1192/5331] adding easyconfigs: PLINKSEQ-0.10-GCC-6.4.0-2.28.eb, PLINKSEQ-0.10-iccifort-2017.4.196-GCC-6.4.0-2.28.eb --- .../PLINKSEQ/PLINKSEQ-0.10-GCC-6.4.0-2.28.eb | 35 +++++++++++++++++++ ...0.10-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-GCC-6.4.0-2.28.eb create mode 100644 easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-iccifort-2017.4.196-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..dea5bfd7072 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-GCC-6.4.0-2.28.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'PLINKSEQ' +version = '0.10' + +homepage = 'https://atgu.mgh.harvard.edu/plinkseq/' +description = """ PLINK/SEQ is an open-source C/C++ library for working with human + genetic variation data. The specific focus is to provide a platform for analytic tool + development for variation data from large-scale resequencing and genotyping projects, + particularly whole-exome and whole-genome studies. It is independent of (but designed + to be complementary to) the existing PLINK package. """ + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = ['https://psychgen.u.hpc.mssm.edu/plinkseq_downloads/'] +sources = ['%(namelower)s-src-%(version)s.tgz'] +checksums = ['e9d4705acf8b22eddba0c48cf502e3bd4236f3b60b010f39f94deecf37e94b58'] + +dependencies = [ + ('protobuf', '3.4.0'), + ('zlib', '1.2.11'), +] + +parallel = 1 + +binary_files = ["behead", "browser", "gcol", "mm", "mongoose", "pdas", "pseq", "smp", "tab2vcf"] + +files_to_copy = [(["build/execs/%s" % x for x in binary_files], "bin")] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binary_files], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-iccifort-2017.4.196-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..f9748d494bf --- /dev/null +++ b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'PLINKSEQ' +version = '0.10' + +homepage = 'https://atgu.mgh.harvard.edu/plinkseq/' +description = """ PLINK/SEQ is an open-source C/C++ library for working with human + genetic variation data. The specific focus is to provide a platform for analytic tool + development for variation data from large-scale resequencing and genotyping projects, + particularly whole-exome and whole-genome studies. It is independent of (but designed + to be complementary to) the existing PLINK package. """ + +toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} + +source_urls = ['https://psychgen.u.hpc.mssm.edu/plinkseq_downloads/'] +sources = ['%(namelower)s-src-%(version)s.tgz'] +checksums = ['e9d4705acf8b22eddba0c48cf502e3bd4236f3b60b010f39f94deecf37e94b58'] + +dependencies = [ + ('protobuf', '3.4.0'), + ('zlib', '1.2.11'), +] + +parallel = 1 + +binary_files = ["behead", "browser", "gcol", "mm", "mongoose", "pdas", "pseq", "smp", "tab2vcf"] + +files_to_copy = [(["build/execs/%s" % x for x in binary_files], "bin")] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binary_files], + 'dirs': [], +} + +moduleclass = 'bio' From 55ddb6de677627dc9fe913cc3356fe95db8ce2d6 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 16 Apr 2019 08:56:12 -0700 Subject: [PATCH 1193/5331] Java/11 wrapper --- easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb index df5e6e64fb0..a658a7cd6b2 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb @@ -18,8 +18,7 @@ description = """This package contains command line utilities for toolchain = {'name': 'dummy', 'version': ''} -source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/' + - '%(version_major)s.%(version_minor)s'] +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s'] sources = ['%(name)s_%(version)s.zip'] checksums = ['44efdd0500dd6ace8e1c70dad0d758d9ab90492b391d2af4a416f03808fee471'] From a547ccdf3a657d99f679fa93d73499e4ef7d87d6 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 16 Apr 2019 11:21:03 -0500 Subject: [PATCH 1194/5331] adding easyconfigs: POV-Ray-3.7.0.7-foss-2017b.eb, POV-Ray-3.7.0.7-intel-2017b.eb --- .../p/POV-Ray/POV-Ray-3.7.0.7-foss-2017b.eb | 61 +++++++++++++++++++ .../p/POV-Ray/POV-Ray-3.7.0.7-intel-2017b.eb | 61 +++++++++++++++++++ 2 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.7-foss-2017b.eb create mode 100644 easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.7-intel-2017b.eb diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.7-foss-2017b.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.7-foss-2017b.eb new file mode 100644 index 00000000000..7eca2969097 --- /dev/null +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.7-foss-2017b.eb @@ -0,0 +1,61 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'POV-Ray' +version = '3.7.0.7' + +homepage = 'http://www.povray.org/' +description = """The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program + which generates images from a text-based scene description, and is available for a variety + of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning + three-dimensional graphics. The source code is available for those wanting to do their own ports.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/POV-Ray/povray/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['POV-Ray-%(version)s_dont-touch-home.patch'] +checksums = [ + '085746e891edbb2cfda22bb2a8b86043bd680a68ad9121bc568118c730ace7b9', # v3.7.0.7.tar.gz + '45103afca808e279dcdee80194c65e2a760c76d011d351392a46e817b0b655f7', # POV-Ray-3.7.0.7_dont-touch-home.patch +] + +builddependencies = [('Autotools', '20170619')] + +dependencies = [ + ('Boost', '1.65.1'), + ('zlib', '1.2.11'), + ('libpng', '1.6.32'), + ('libjpeg-turbo', '1.5.2'), + ('X11', '20171023'), + ('LibTIFF', '4.0.9'), + ('SDL2', '2.0.8'), +] + +preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " +preconfigopts += " ./prebuild.sh && cd .. && " +configopts = "COMPILED_BY='EasyBuild' " +configopts += "--with-boost=$EBROOTBOOST --with-zlib=$EBROOTZLIB --with-libpng=$EBROOTLIBPNG " +configopts += "--with-libtiff=$EBROOTLIBTIFF --with-libjpeg=$EBROOTLIBJPEGMINTURBO --with-libsdl=$EBROOTSDL2 " +# configopts += " --with-libmkl=DIR " ## upstream needs to fix this, still in BETA + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/povray'], + 'dirs': ['etc/povray/%(version_major_minor)s', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.7-intel-2017b.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.7-intel-2017b.eb new file mode 100644 index 00000000000..dbe44fe14b3 --- /dev/null +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.7-intel-2017b.eb @@ -0,0 +1,61 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'POV-Ray' +version = '3.7.0.7' + +homepage = 'http://www.povray.org/' +description = """The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program + which generates images from a text-based scene description, and is available for a variety + of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning + three-dimensional graphics. The source code is available for those wanting to do their own ports.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/POV-Ray/povray/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['POV-Ray-%(version)s_dont-touch-home.patch'] +checksums = [ + '085746e891edbb2cfda22bb2a8b86043bd680a68ad9121bc568118c730ace7b9', # v3.7.0.7.tar.gz + '45103afca808e279dcdee80194c65e2a760c76d011d351392a46e817b0b655f7', # POV-Ray-3.7.0.7_dont-touch-home.patch +] + +builddependencies = [('Autotools', '20170619')] + +dependencies = [ + ('Boost', '1.65.1'), + ('zlib', '1.2.11'), + ('libpng', '1.6.32'), + ('libjpeg-turbo', '1.5.2'), + ('X11', '20171023'), + ('LibTIFF', '4.0.9'), + ('SDL2', '2.0.8'), +] + +preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " +preconfigopts += " ./prebuild.sh && cd .. && " +configopts = "COMPILED_BY='EasyBuild' " +configopts += "--with-boost=$EBROOTBOOST --with-zlib=$EBROOTZLIB --with-libpng=$EBROOTLIBPNG " +configopts += "--with-libtiff=$EBROOTLIBTIFF --with-libjpeg=$EBROOTLIBJPEGMINTURBO --with-libsdl=$EBROOTSDL2 " +# configopts += " --with-libmkl=DIR " ## upstream needs to fix this, still in BETA + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/povray'], + 'dirs': ['etc/povray/%(version_major_minor)s', 'share'] +} + +moduleclass = 'vis' From 28ba7e8060195097b62bf59e65eb17beb7cd6360 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 16 Apr 2019 11:21:51 -0500 Subject: [PATCH 1195/5331] Add dependency --- .../s/SDL2/SDL2-2.0.8-foss-2017b.eb | 36 +++++++++++++++++++ .../s/SDL2/SDL2-2.0.8-intel-2017b.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-foss-2017b.eb create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-intel-2017b.eb diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-foss-2017b.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-foss-2017b.eb new file mode 100644 index 00000000000..83ce9561ca6 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-foss-2017b.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.8' + +homepage = 'http://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['edc77c57308661d576e843344d8638e025a7818bff73f8fbfab09c3c5fd092ec'] + +dependencies = [ + ('X11', '20171023'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-intel-2017b.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-intel-2017b.eb new file mode 100644 index 00000000000..46b7bec07bb --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-intel-2017b.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.8' + +homepage = 'http://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['edc77c57308661d576e843344d8638e025a7818bff73f8fbfab09c3c5fd092ec'] + +dependencies = [ + ('X11', '20171023'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From dabd2adfc1bf269fa51d11625e948987ce49e0b5 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 16 Apr 2019 18:22:07 +0200 Subject: [PATCH 1196/5331] Add libffi build dep to 3.7.2 --- .../easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb index 61f292dfb10..b84ecb2f96d 100644 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb @@ -11,7 +11,10 @@ source_urls = ['http://www.python.org/ftp/python/%(version)s/'] sources = ['Python-%(version)s.tgz'] checksums = ['f09d83c773b9cc72421abba2c317e4e6e05d919f9bcf34468e192b6a6c8e328d'] -builddependencies = [('binutils', '2.31.1')] +builddependencies = [ + ('binutils', '2.31.1'), + ('libffi', '3.2.1'), +] dependencies = [ ('Python', version), From 23db229dc8d82900027f7573261a75b7b481c9e4 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 16 Apr 2019 11:43:13 -0500 Subject: [PATCH 1197/5331] adding easyconfigs: cutadapt-1.16-foss-2017b-Python-2.7.14.eb, cutadapt-1.16-foss-2017b-Python-3.6.3.eb, cutadapt-1.16-intel-2017b-Python-2.7.14.eb, cutadapt-1.16-intel-2017b-Python-3.6.3.eb --- .../cutadapt-1.16-foss-2017b-Python-2.7.14.eb | 38 +++++++++++++++++++ .../cutadapt-1.16-foss-2017b-Python-3.6.3.eb | 38 +++++++++++++++++++ ...cutadapt-1.16-intel-2017b-Python-2.7.14.eb | 35 +++++++++++++++++ .../cutadapt-1.16-intel-2017b-Python-3.6.3.eb | 35 +++++++++++++++++ 4 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..71be1d43b8a --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modufied by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS + +easyblock = 'PythonPackage' + +name = 'cutadapt' +version = '1.16' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'] + +dependencies = [ + ('Python', '2.7.14'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..ecead400ac5 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modufied by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS + +easyblock = 'PythonPackage' + +name = 'cutadapt' +version = '1.16' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'] + +dependencies = [ + ('Python', '3.6.3'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..54d2f0b83cc --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman (The Francis Crick Institute), Kenneth Hoste (HPC-UGent) + +easyblock = 'PythonPackage' + +name = 'cutadapt' +version = '1.16' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'] + +dependencies = [ + ('Python', '2.7.14'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..22e388a1ff3 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman (The Francis Crick Institute), Kenneth Hoste (HPC-UGent) + +easyblock = 'PythonPackage' + +name = 'cutadapt' +version = '1.16' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'] + +dependencies = [ + ('Python', '3.6.3'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From baf303115c31d453afcdf23ff58b621af451532b Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 16 Apr 2019 19:05:53 +0200 Subject: [PATCH 1198/5331] adding easyconfigs: GLib-2.60.1-GCCcore-8.2.0.eb, GObject-Introspection-1.60.1-GCCcore-8.2.0-Python-3.7.2.eb, cairo-1.16.0-GCCcore-8.2.0.eb --- .../c/cairo/cairo-1.16.0-GCCcore-8.2.0.eb | 47 ++++++++++++++++ .../g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb | 44 +++++++++++++++ ...ction-1.60.1-GCCcore-8.2.0-Python-3.7.2.eb | 53 +++++++++++++++++++ 3 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.60.1-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..7915f93dfc2 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-8.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.16.0' + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5e7b29b3f113ef870d1e3ecf8adf21f923396401604bda16d44be45e66052331'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libpng', '1.6.36'), + ('freetype', '2.9.1'), + ('pixman', '0.38.0'), + ('expat', '2.2.6'), + ('GLib', '2.60.1'), + ('X11', '20190311'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..4d4f3b8d4b2 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.60.1' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['89f884f5d5c6126140ec868cef184c42ce72902c13cd08f36e660371779b5560'] + +builddependencies = [ + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), + ('binutils', '2.31.1'), + ('Python', '3.7.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libffi', '3.2.1'), + ('gettext', '0.19.8.1'), + ('libxml2', '2.9.8'), + ('PCRE', '8.43'), + ('util-linux', '2.33'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.60.1-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.60.1-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..def266fbeb7 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.60.1-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.60.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['d844d1499ecd36f3ec8a3573616186d36626ec0c9a7981939e99aa02e9c824b3'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Autotools', '20180311'), + ('flex', '2.6.4'), + ('Bison', '3.0.5'), + ('cairo', '1.16.0'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('GLib', '2.60.1'), + ('libffi', '3.2.1'), + ('util-linux', '2.33'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +# avoid using hard-coded path to 'python3' in shebang of scripts +preconfigopts += "PYTHON=python3 " +buildopts = "PYTHON=python3 " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' From 35eb3b5594565c1675b764b2dd8ea6781b5e549d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 16 Apr 2019 19:22:52 +0200 Subject: [PATCH 1199/5331] Add new configs for ATK and friends --- .../a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb | 41 ++++++++++++++++ .../at-spi2-atk-2.32.0-GCCcore-8.2.0.eb | 38 +++++++++++++++ .../at-spi2-core-2.32.0-GCCcore-8.2.0.eb | 48 +++++++++++++++++++ ...pi2-core-2.32.0_remove-subdir-prefix.patch | 16 +++++++ 4 files changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.32.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0_remove-subdir-prefix.patch diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..a363bb3b85e --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.32.0-GCCcore-8.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.32.0' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cb41feda7fe4ef0daa024471438ea0219592baf7c291347e5a858bb64e4091cc'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), +] +dependencies = [ + ('GLib', '2.60.1'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.32.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.32.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..51d06f41cca --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.32.0-GCCcore-8.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.32.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + AT-SPI 2 toolkit bridge +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0b51e6d339fa2bcca3a3e3159ccea574c67b107f1ac8b00047fa60e34ce7a45c'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), +] + +dependencies = [ + ('GLib', '2.60.1'), + ('DBus', '1.13.8'), + ('at-spi2-core', '2.32.0'), + ('libxml2', '2.9.8'), + ('ATK', '2.32.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..83feb8a0458 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.32.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +patches = ['%(name)s-%(version)s_remove-subdir-prefix.patch'] +checksums = [ + '43a435d213f8d4b55e8ac83a46ae976948dc511bb4a515b69637cb36cf0e7220', # at-spi2-core-2.32.0.tar.xz + # at-spi2-core-2.32.0_remove-subdir-prefix.patch + '99757ee8076c9618affb35ffe80cb87e2661e44fd98d5c4df598815d15cdbf6d', +] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), + ('gettext', '0.19.8.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.60.1'), + ('DBus', '1.13.8'), + ('X11', '20190311'), +] + +configopts = "--libdir lib " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0_remove-subdir-prefix.patch b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0_remove-subdir-prefix.patch new file mode 100644 index 00000000000..807caaff2cc --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0_remove-subdir-prefix.patch @@ -0,0 +1,16 @@ +# Fix incorrect use of subdir argument in meson build script +--- atspi/meson.build.orig 2019-04-15 19:58:19.827123833 +0200 ++++ atspi/meson.build 2019-04-15 19:59:53.813135403 +0200 +@@ -55,9 +55,10 @@ + 'atspi-value.h', + ] + +-atspi_includedir = join_paths(get_option('prefix'), get_option('includedir'), 'at-spi-2.0', 'atspi') ++atspi_includesubdir = join_paths('at-spi-2.0', 'atspi') ++atspi_includedir = join_paths(get_option('includedir'), atspi_includesubdir) + +-install_headers(atspi_headers, subdir: atspi_includedir) ++install_headers(atspi_headers, subdir: atspi_includesubdir) + + atspi_enums = gnome.mkenums('atspi-enum-types', + sources: [ 'atspi-constants.h', 'atspi-types.h' ], From 5e1ccdcf3fc8c78398d4b1ce75bfa70da66e14ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 16 Apr 2019 19:43:13 +0200 Subject: [PATCH 1200/5331] Add configs for GTK+3.24.8 and deps --- .../g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb | 39 +++++++++++++++ .../Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb | 49 +++++++++++++++++++ .../Gdk-Pixbuf-2.38.1-post-install-bin.patch | 27 ++++++++++ .../HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb | 39 +++++++++++++++ .../libepoxy/libepoxy-1.5.3-GCCcore-8.2.0.eb | 34 +++++++++++++ .../p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb | 39 +++++++++++++++ 6 files changed, 227 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-post-install-bin.patch create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..cc2b2f1f65c --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '3.24.8' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['666962de9b9768fe9ca785b0e2f42c8b9db3868a12fa9b356b167238d70ac799'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), + ('gettext', '0.19.8.1'), + ('pkg-config', '0.29.2'), + ('cairo', '1.16.0'), + ('Perl', '5.28.1'), +] + +dependencies = [ + ('ATK', '2.32.0'), + ('at-spi2-atk', '2.32.0'), + ('Gdk-Pixbuf', '2.38.1'), + ('Pango', '1.43.0'), + ('libepoxy', '1.5.3'), + ('X11', '20190311'), + ('FriBidi', '1.0.5'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +preconfigopts = "PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..72c0a2cb0fa --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.38.1' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +patches = ['Gdk-Pixbuf-%(version)s-post-install-bin.patch'] +checksums = [ + 'f19ff836ba991031610dcc53774e8ca436160f7d981867c8c3a37acfe493ab3a', # gdk-pixbuf-2.38.1.tar.xz + 'a7560a9582944a82c5b8a41db9831029f7867616ed2dd0af84edf299c6c7aaa0', # Gdk-Pixbuf-2.38.1-post-install-bin.patch +] + +builddependencies = [ + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), + ('binutils', '2.31.1'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), +] +dependencies = [ + ('GLib', '2.60.1'), + ('libjpeg-turbo', '2.0.2'), + ('libpng', '1.6.36'), + ('LibTIFF', '4.0.10'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dgir=true " + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-post-install-bin.patch b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-post-install-bin.patch new file mode 100644 index 00000000000..6656c72857d --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-post-install-bin.patch @@ -0,0 +1,27 @@ +--- meson.build.orig 2019-03-16 22:39:43.546535740 +0100 ++++ meson.build 2019-03-16 22:41:25.341826529 +0100 +@@ -415,6 +415,7 @@ + else + meson.add_install_script('build-aux/post-install.sh', + gdk_pixbuf_libdir, ++ gdk_pixbuf_bindir, + gdk_pixbuf_binary_version, + ) + endif +--- build-aux/post-install.sh.orig 2019-03-16 20:25:21.737362740 +0100 ++++ build-aux/post-install.sh 2019-03-16 22:37:52.524946556 +0100 +@@ -1,11 +1,12 @@ + #!/bin/sh + + libdir="$1" +-binary_version="$2" ++bindir="$2" ++binary_version="$3" + + if [ -z "$DESTDIR" ]; then + mkdir -p "$libdir/gdk-pixbuf-2.0/$binary_version" +- gdk-pixbuf-query-loaders > "$libdir/gdk-pixbuf-2.0/$binary_version/loaders.cache" ++ "$bindir/gdk-pixbuf-query-loaders" > "$libdir/gdk-pixbuf-2.0/$binary_version/loaders.cache" + else + echo "***" + echo "*** Warning: loaders.cache not built" diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..c6eb4a4fd8d --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '2.4.0' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b470eff9dd5b596edf078596b46a1f83c179449f051a469430afc15869db336f'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.60.1'), + ('cairo', '1.16.0'), + ('freetype', '2.9.1'), +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..931302d8586 --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.3-GCCcore-8.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.3' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/anholt/%(name)s/releases/download/%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['002958c5528321edd53440235d3c44e71b5b1e09b9177e8daf677450b6c4433d'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), +] + +dependencies = [ + ('X11', '20190311'), + ('Mesa', '19.0.1'), +] + +configopts = '-Degl=no --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..f6096d54de9 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.43.0' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['d2c0c253a5328a0eccb00cdd66ce2c8713fabd2c9836000b6e22a8b06ba3ddd2'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), + ('pkg-config', '0.29.2'), + ('FriBidi', '1.0.5'), +] + +dependencies = [ + ('X11', '20190311'), + ('GLib', '2.60.1'), + ('cairo', '1.16.0'), + ('HarfBuzz', '2.4.0'), +] + +configopts = "--buildtype=release --default-library=both " + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' From 4bb2d87160a420397fc56b910feb63f82b300b4b Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 16 Apr 2019 19:56:34 +0200 Subject: [PATCH 1201/5331] Remove leftovers --- easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb index 48da122e449..d1962b51c75 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb @@ -28,10 +28,8 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', ] sources = [SOURCELOWER_TAR_XZ] -#patches = ['Mesa-17.3.6_fix-strip-llvm-flags.patch'] checksums = [ '6884163c0ea9e4c98378ab8fecd72fe7b5f437713a14471beda378df247999d4', # mesa-19.0.1.tar.xz -# '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.3.6_fix-strip-llvm-flags.patch ] builddependencies = [ @@ -60,10 +58,6 @@ configopts = " --Dosmesa=gallium -Dglx=gallium-xlib --Ddri3=false" configopts += " --Dgbm=false --Dglx-direct=false --Dgallium-drivers='swrast,swr' -Degl=false" configopts += " --Dosmesa-bits=32 --Dllvm=true --Dshared-llvm=true" configopts += " --Dlibunwind=true" -# No equivalent to this: -#configopts += " --enable-texture-float " - -#buildopts = 'V=1' sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, From 46cd20449ae85849c65032e11621c030b8249420 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 16 Apr 2019 21:37:41 +0200 Subject: [PATCH 1202/5331] Add checksum --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1.3-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1.3-GCCcore-8.2.0.eb index f7a16e297d3..708cb328410 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1.3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.1.3-GCCcore-8.2.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['http://ffmpeg.org/releases/'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['29a679685bd7bc29158110f367edf67b31b451f2176f9d79d0f342b9e22d6a2a'] builddependencies = [ ('binutils', '2.31.1'), From b2f6a0ff23056d2e9cf4ff94ad8666873bbe3114 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 16 Apr 2019 15:48:24 -0500 Subject: [PATCH 1203/5331] rename the program from snap to SNAP --- ...-GCC-6.4.0-2.28.eb => SNAP-2013-11-29-GCC-6.4.0-2.28.eb} | 6 +++--- ...tion.patch => SNAP_2013-11-29_makefile_correction.patch} | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/s/SNAP/{snap-2013-11-29-GCC-6.4.0-2.28.eb => SNAP-2013-11-29-GCC-6.4.0-2.28.eb} (86%) rename easybuild/easyconfigs/s/SNAP/{snap_2013-11-29_makefile_correction.patch => SNAP_2013-11-29_makefile_correction.patch} (95%) diff --git a/easybuild/easyconfigs/s/SNAP/snap-2013-11-29-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/SNAP/SNAP-2013-11-29-GCC-6.4.0-2.28.eb similarity index 86% rename from easybuild/easyconfigs/s/SNAP/snap-2013-11-29-GCC-6.4.0-2.28.eb rename to easybuild/easyconfigs/s/SNAP/SNAP-2013-11-29-GCC-6.4.0-2.28.eb index 0ee58e0b052..965374b0774 100644 --- a/easybuild/easyconfigs/s/SNAP/snap-2013-11-29-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/SNAP/SNAP-2013-11-29-GCC-6.4.0-2.28.eb @@ -5,7 +5,7 @@ # easyblock = 'MakeCp' -name = 'snap' +name = 'SNAP' version = '2013-11-29' homepage = 'http://korflab.ucdavis.edu/software.html' @@ -15,11 +15,11 @@ SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.""" toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = ['http://korflab.ucdavis.edu/Software'] -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s_%(version)s_makefile_correction.patch'] checksums = [ 'e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a', # snap-2013-11-29.tar.gz - '02ea6dc6006ca5a5173dd2fc6a01b679a0910a68e0b51d00b7b9f732e4f79dcc', # snap_2013-11-29_makefile_correction.patch + '7855723413928bc52510816ee598969745b2ef4addf81e162173a53a3896794c', # SNAP_2013-11-29_makefile_correction.patch ] files_to_copy = [ diff --git a/easybuild/easyconfigs/s/SNAP/snap_2013-11-29_makefile_correction.patch b/easybuild/easyconfigs/s/SNAP/SNAP_2013-11-29_makefile_correction.patch similarity index 95% rename from easybuild/easyconfigs/s/SNAP/snap_2013-11-29_makefile_correction.patch rename to easybuild/easyconfigs/s/SNAP/SNAP_2013-11-29_makefile_correction.patch index 7e8a1b068c4..41a999285a2 100644 --- a/easybuild/easyconfigs/s/SNAP/snap_2013-11-29_makefile_correction.patch +++ b/easybuild/easyconfigs/s/SNAP/SNAP_2013-11-29_makefile_correction.patch @@ -1,4 +1,4 @@ -drop the hard coded "gcc", also remove the -Werror since there are warining with GCC +Drop the hard coded "gcc", also remove the -Werror since there are warnings with GCC author: fenglai liu (fenglai@accre.vanderbilt.edu) diff -Naur snap_ori/Makefile snap/Makefile From c3ae7db52494313859aebbf1f1f6644dc77574c2 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 16 Apr 2019 15:52:07 -0500 Subject: [PATCH 1204/5331] change the program name for toolchain iccifort --- ...> SNAP-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/s/SNAP/{snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb => SNAP-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb} (86%) diff --git a/easybuild/easyconfigs/s/SNAP/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/SNAP/SNAP-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb similarity index 86% rename from easybuild/easyconfigs/s/SNAP/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb rename to easybuild/easyconfigs/s/SNAP/SNAP-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index ffc5f1222ad..16b38002ca5 100644 --- a/easybuild/easyconfigs/s/SNAP/snap-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/SNAP/SNAP-2013-11-29-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -5,7 +5,7 @@ # easyblock = 'MakeCp' -name = 'snap' +name = 'SNAP' version = '2013-11-29' homepage = 'http://korflab.ucdavis.edu/software.html' @@ -15,11 +15,11 @@ SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.""" toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} source_urls = ['http://korflab.ucdavis.edu/Software'] -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s_%(version)s_makefile_correction.patch'] checksums = [ 'e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a', # snap-2013-11-29.tar.gz - '02ea6dc6006ca5a5173dd2fc6a01b679a0910a68e0b51d00b7b9f732e4f79dcc', # snap_2013-11-29_makefile_correction.patch + '7855723413928bc52510816ee598969745b2ef4addf81e162173a53a3896794c', # SNAP_2013-11-29_makefile_correction.patch ] files_to_copy = [ From c143af8bf456048d7c508b34baa9eded5d549590 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 17 Apr 2019 08:45:22 +0200 Subject: [PATCH 1205/5331] Remove unnecessary preconfigopts --- easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb index cc2b2f1f65c..201b6489441 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb @@ -34,6 +34,5 @@ dependencies = [ ] configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " -preconfigopts = "PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/" moduleclass = 'vis' From 80037b57b054f137c2c3713b329ec86995790ee3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 17 Apr 2019 08:53:13 +0200 Subject: [PATCH 1206/5331] Add name and date to patch --- .../at-spi2-core/at-spi2-core-2.32.0_remove-subdir-prefix.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0_remove-subdir-prefix.patch b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0_remove-subdir-prefix.patch index 807caaff2cc..de43aa3b2f1 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0_remove-subdir-prefix.patch +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0_remove-subdir-prefix.patch @@ -1,4 +1,5 @@ # Fix incorrect use of subdir argument in meson build script +# Mikael Öhman , 2019-04-16 --- atspi/meson.build.orig 2019-04-15 19:58:19.827123833 +0200 +++ atspi/meson.build 2019-04-15 19:59:53.813135403 +0200 @@ -55,9 +55,10 @@ From 0eb2ead632d2529ac5925da7882704c5ccc69ebd Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 17 Apr 2019 09:23:00 +0200 Subject: [PATCH 1207/5331] Fix some configuration issues. Still not working --- .../easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb index d1962b51c75..4d7566d7dd2 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb @@ -38,7 +38,6 @@ builddependencies = [ ('Ninja', '1.9.0'), ('flex', '2.6.4'), ('Bison', '3.0.5'), - ('Autotools', '20180311'), ('pkg-config', '0.29.2'), ('Mako', '1.0.8'), ('libxml2', '2.9.8'), @@ -54,10 +53,10 @@ dependencies = [ ('libunwind', '1.3.1'), ] -configopts = " --Dosmesa=gallium -Dglx=gallium-xlib --Ddri3=false" -configopts += " --Dgbm=false --Dglx-direct=false --Dgallium-drivers='swrast,swr' -Degl=false" -configopts += " --Dosmesa-bits=32 --Dllvm=true --Dshared-llvm=true" -configopts += " --Dlibunwind=true" +configopts = " -Dosmesa=gallium -Dglx=gallium-xlib -Ddri-drivers='' -Ddri3=false -Dvulkan-drivers=''" +configopts += " -Dgbm=false -Dglx-direct=false -Dgallium-drivers='swrast,swr' -Degl=false" +configopts += " -Dosmesa-bits=32 -Dllvm=true -Dshared-llvm=true" +configopts += " -Dlibunwind=true" sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, From 1b12f5dc8858c924f3906bbcf27325e0d7f58fc8 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 17 Apr 2019 09:32:43 +0200 Subject: [PATCH 1208/5331] New build options from @akesandgren --- easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb index 4d7566d7dd2..c169aa9070c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb @@ -53,10 +53,10 @@ dependencies = [ ('libunwind', '1.3.1'), ] -configopts = " -Dosmesa=gallium -Dglx=gallium-xlib -Ddri-drivers='' -Ddri3=false -Dvulkan-drivers=''" +configopts = " -Dplatforms=x11 -Dosmesa=gallium -Ddri3=false -Ddri-drivers='' -Dvulkan-drivers=''" configopts += " -Dgbm=false -Dglx-direct=false -Dgallium-drivers='swrast,swr' -Degl=false" -configopts += " -Dosmesa-bits=32 -Dllvm=true -Dshared-llvm=true" -configopts += " -Dlibunwind=true" +configopts += " -Dllvm=true -Dshared-llvm=true" +configopts += " -Dlibunwind=true -Dglx=xlib" sanity_check_paths = { 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, From b45d3fc7c782c65a233e1e11a703c4d24f455443 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 17 Apr 2019 10:27:04 +0200 Subject: [PATCH 1209/5331] Fix checksum for updated patch comment --- .../a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb index 83feb8a0458..9ed46381df1 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.32.0-GCCcore-8.2.0.eb @@ -16,7 +16,7 @@ patches = ['%(name)s-%(version)s_remove-subdir-prefix.patch'] checksums = [ '43a435d213f8d4b55e8ac83a46ae976948dc511bb4a515b69637cb36cf0e7220', # at-spi2-core-2.32.0.tar.xz # at-spi2-core-2.32.0_remove-subdir-prefix.patch - '99757ee8076c9618affb35ffe80cb87e2661e44fd98d5c4df598815d15cdbf6d', + '0c64246320906acd587127f12554f9f028e39a70c89c2c7622772e3b8518cd69', ] builddependencies = [ From d42b75ab927fd5a4cb9743113a1c0db5b4a37991 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 17 Apr 2019 11:11:01 +0200 Subject: [PATCH 1210/5331] Add description, author, date to patch --- .../easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb | 2 +- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-post-install-bin.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb index 72c0a2cb0fa..ef38d0386b3 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_XZ] patches = ['Gdk-Pixbuf-%(version)s-post-install-bin.patch'] checksums = [ 'f19ff836ba991031610dcc53774e8ca436160f7d981867c8c3a37acfe493ab3a', # gdk-pixbuf-2.38.1.tar.xz - 'a7560a9582944a82c5b8a41db9831029f7867616ed2dd0af84edf299c6c7aaa0', # Gdk-Pixbuf-2.38.1-post-install-bin.patch + '4fcbc1ca390405cba34830ef6a28d0de1f68a730aa6aa2b9cba3a9d3ce145350', # Gdk-Pixbuf-2.38.1-post-install-bin.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-post-install-bin.patch b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-post-install-bin.patch index 6656c72857d..3aee130cc70 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-post-install-bin.patch +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-post-install-bin.patch @@ -1,3 +1,5 @@ +# Fix postinstall bug where it assumes install prefix is in PATH +# Mikael Öhman , 2019-04-16 --- meson.build.orig 2019-03-16 22:39:43.546535740 +0100 +++ meson.build 2019-03-16 22:41:25.341826529 +0100 @@ -415,6 +415,7 @@ From 8abe4bbae3645095414e7a3c1dc78e6a149bdc56 Mon Sep 17 00:00:00 2001 From: Ruben Di Battista Date: Wed, 17 Apr 2019 12:33:19 +0200 Subject: [PATCH 1211/5331] patchelf: Bump version to 0.10 for GCCcore 7.2.0 --- .../p/patchelf/patchelf-0.10-GCCcore-7.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-7.2.0.eb diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-7.2.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-7.2.0.eb new file mode 100644 index 00000000000..2a2577c381e --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-7.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.10' + +homepage = 'http://nixos.org/patchelf.html' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b3cb6bdedcef5607ce34a350cf0b182eb979f8f7bc31eae55a93a70a3f020d13'] + +builddependencies = [ + ('binutils', '2.29'), + ('Autotools', '20180311'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +moduleclass = 'tools' From 561ed61b711c93aeb8a01ec1e8aa8b4d3a1b1c30 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 17 Apr 2019 16:16:46 -0500 Subject: [PATCH 1212/5331] adding easyconfigs: ANTs-2.3.0-foss-2017b-Python-2.7.14.eb, ANTs-2.3.0-intel-2017b-Python-2.7.14.eb --- .../ANTs-2.3.0-foss-2017b-Python-2.7.14.eb | 46 +++++++++++++++++++ .../ANTs-2.3.0-intel-2017b-Python-2.7.14.eb | 46 +++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-intel-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..d7d2d862a3a --- /dev/null +++ b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'ANTs' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://stnava.github.io/ANTs/' +description = """ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, + interpreting and visualizing multidimensional data.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stnava/ANTs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34bdeaa3bafc2e115e89acaae5733445e4b29f8fb98110067a187b036cb03057'] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '2.7.14'), + ('VTK', '8.0.1', versionsuffix), +] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release ' +configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON ' +configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF' + +skipsteps = ['install'] + +# need to ensure user has write permissions on all files, to avoid permission denied problems when copying +buildopts = ' && mkdir -p %(installdir)s && chmod -R u+w . && cp -a * %(installdir)s/' + +postinstallcmds = ["cp -a %(builddir)s/ANTs-%(version)s/Scripts/* %(installdir)s/bin/"] + +sanity_check_paths = { + 'files': ['bin/ANTS', 'bin/antsBrainExtraction.sh'], + 'dirs': ['lib'], +} + +modextravars = {'ANTSPATH': '%(installdir)s/bin'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..c6b61065738 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'ANTs' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://stnava.github.io/ANTs/' +description = """ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, + interpreting and visualizing multidimensional data.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True, 'vectorize': False} + +source_urls = ['https://github.com/stnava/ANTs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34bdeaa3bafc2e115e89acaae5733445e4b29f8fb98110067a187b036cb03057'] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '2.7.14'), + ('VTK', '8.0.1', versionsuffix), +] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release ' +configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON ' +configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF' + +skipsteps = ['install'] + +# need to ensure user has write permissions on all files, to avoid permission denied problems when copying +buildopts = ' && mkdir -p %(installdir)s && chmod -R u+w . && cp -a * %(installdir)s/' + +postinstallcmds = ["cp -a %(builddir)s/ANTs-%(version)s/Scripts/* %(installdir)s/bin/"] + +sanity_check_paths = { + 'files': ['bin/ANTS', 'bin/antsBrainExtraction.sh'], + 'dirs': ['lib'], +} + +modextravars = {'ANTSPATH': '%(installdir)s/bin'} + +moduleclass = 'data' From 62a0ea8eaa7c4dd3ed78eafabb1e1dc1e5344ffc Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 17 Apr 2019 16:38:47 -0500 Subject: [PATCH 1213/5331] adding easyconfigs: OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb, OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb, OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb --- .../OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb | 85 +++++++++++++++++++ .../OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb | 85 +++++++++++++++++++ .../OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb | 85 +++++++++++++++++++ 3 files changed, 255 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..32b20978cfc --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,85 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] +sources = [ + '%(version)s.zip', + {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '3546c3837f88177c898e4172942da7a3ca6c4e8e98a33d0cbccb2b499167c5ba', # 3.3.0.zip + '4333833e40afaa22c804169e44f9a63e357e21476b765a5683bcb3760107f0da', # ippicv_linux_20151201.tgz +] + +builddependencies = [('CMake', '3.10.2')] + +dependencies = [ + ('Python', '2.7.14'), + ('zlib', '1.2.11'), + ('FFmpeg', '3.4.1'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.32'), + ('LibTIFF', '4.0.9'), + ('JasPer', '2.0.14'), + ('Java', '1.8', '', True), + ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('GLib', '2.53.5'), + ('GTK+', '2.24.32'), +] + +separate_build_dir = True + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +# The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.%s ' % SHLIB_EXT +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +postinstallcmds = ["cp 3rdparty/ippicv/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT, 'lib/libippicv.a'] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'] +} +sanity_check_commands = ["python -c 'import cv2'"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..49be1beb7ab --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,85 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] +sources = [ + '%(version)s.zip', + {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '3546c3837f88177c898e4172942da7a3ca6c4e8e98a33d0cbccb2b499167c5ba', # 3.3.0.zip + '4333833e40afaa22c804169e44f9a63e357e21476b765a5683bcb3760107f0da', # ippicv_linux_20151201.tgz +] + +builddependencies = [('CMake', '3.10.2')] + +dependencies = [ + ('Python', '2.7.14'), + ('zlib', '1.2.11'), + ('FFmpeg', '3.4.1'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.32'), + ('LibTIFF', '4.0.9'), + ('JasPer', '2.0.14'), + ('Java', '1.8', '', True), + ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('GLib', '2.53.5'), + ('GTK+', '2.24.32'), +] + +separate_build_dir = True + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +# The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.%s ' % SHLIB_EXT +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +postinstallcmds = ["cp 3rdparty/ippicv/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT, 'lib/libippicv.a'] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'] +} +sanity_check_commands = ["python -c 'import cv2'"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..1da7ca700c5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb @@ -0,0 +1,85 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '3.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + # The Hash is version dependent! see 3rdparty/ippicv/downloader.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/81a676001ca8075ada498583e4166079e5744668/ippicv', +] +sources = [ + '%(version)s.zip', + {'filename': 'ippicv_linux_20151201.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '3546c3837f88177c898e4172942da7a3ca6c4e8e98a33d0cbccb2b499167c5ba', # 3.3.0.zip + '4333833e40afaa22c804169e44f9a63e357e21476b765a5683bcb3760107f0da', # ippicv_linux_20151201.tgz +] + +builddependencies = [('CMake', '3.10.2')] + +dependencies = [ + ('Python', '3.6.3'), + ('zlib', '1.2.11'), + ('FFmpeg', '3.4.1'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.32'), + ('LibTIFF', '4.0.9'), + ('JasPer', '2.0.14'), + ('Java', '1.8', '', True), + ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('GLib', '2.53.5'), + ('GTK+', '2.24.32'), +] + +separate_build_dir = True + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +# The destination directory is "linux-" see 3rdparty/ippicv/downloader.cmake +ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' +preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (ippicv_dir, ippicv_dir) + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.%s ' % SHLIB_EXT +configopts += '-DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' +configopts += '-DJASPER_LIBRARY=$EBROOTJASPER/lib/libjasper.a ' +configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +postinstallcmds = ["cp 3rdparty/ippicv/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT, 'lib/libippicv.a'] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'] +} +sanity_check_commands = ["python -c 'import cv2'"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' From 4b16bb8b07f25c8436d83e949bc3cea6297ef3b9 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 17 Apr 2019 16:39:27 -0500 Subject: [PATCH 1214/5331] Use Jave wrapper --- .../o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb index e799c5ef748..90c2a281e9c 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb @@ -36,7 +36,7 @@ dependencies = [ ('libpng', '1.6.32'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8.0_152', '', True), + ('Java', '1.8', '', True), ('ant', '1.10.1', '-Java-%(javaver)s', True), ('GLib', '2.53.5'), ('GTK+', '2.24.32'), From 53de9c4fa26fc9ae82227038d920651f06d19894 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 18 Apr 2019 09:45:16 -0500 Subject: [PATCH 1215/5331] Added attribution --- .../easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-GCC-6.4.0-2.28.eb | 5 +++++ .../PLINKSEQ-0.10-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-GCC-6.4.0-2.28.eb index dea5bfd7072..7a2dcdc7466 100644 --- a/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-GCC-6.4.0-2.28.eb @@ -1,3 +1,8 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + easyblock = 'MakeCp' name = 'PLINKSEQ' diff --git a/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index f9748d494bf..ea2add50ac2 100644 --- a/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -1,3 +1,8 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + easyblock = 'MakeCp' name = 'PLINKSEQ' From a8f4a69b66492becdf0bc98537ff1a8819a68598 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 18 Apr 2019 09:50:42 -0500 Subject: [PATCH 1216/5331] Fix typo --- .../c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb | 2 +- .../c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb index 71be1d43b8a..9c55f5133d2 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ # Biozentrum - University of Basel # Modified by: Adam Huffman # The Francis Crick Institute -# Modufied by: Albert Bogdanowicz +# Modified by: Albert Bogdanowicz # Institute of Biochemistry and Biophysics PAS easyblock = 'PythonPackage' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb index ecead400ac5..be5125cab5b 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ # Biozentrum - University of Basel # Modified by: Adam Huffman # The Francis Crick Institute -# Modufied by: Albert Bogdanowicz +# Modified by: Albert Bogdanowicz # Institute of Biochemistry and Biophysics PAS easyblock = 'PythonPackage' From 8c1d4febd82f095d4d0b63fa2b79e59e2c3bc126 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 18 Apr 2019 12:15:05 -0500 Subject: [PATCH 1217/5331] adding easyconfigs: GATE-8.2-foss-2017b-Python-2.7.14.eb, GATE-8.2-intel-2017b-Python-2.7.14.eb --- .../GATE/GATE-8.2-foss-2017b-Python-2.7.14.eb | 31 +++++++++++++++++++ .../GATE-8.2-intel-2017b-Python-2.7.14.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATE/GATE-8.2-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/g/GATE/GATE-8.2-intel-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/g/GATE/GATE-8.2-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GATE/GATE-8.2-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..f50740e963a --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-8.2-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,31 @@ +name = 'GATE' +version = '8.2' +versionsuffix = '-Python-2.7.14' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = ['http://www.opengatecollaboration.org/sites/default/files/'] +sources = ['Gate-%(version)s.tar.gz'] +patches = ['GATE-7.0_Makefile-prefix.patch'] +checksums = [ + 'edd8b1017310442bb6819a2815d61b63b1da1aef613fea2678aede134cbad741', # Gate-8.2.tar.gz + 'e72c230df1cdd05c07ac405b22bf26931abdcd3e5f7b942e9c88251ac24cc6af', # GATE-7.0_Makefile-prefix.patch +] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Geant4', '10.5'), + ('CLHEP', '2.4.1.0'), + ('ROOT', '6.10.08', versionsuffix), +] + +# enable extra capabilities (Davis requires Geant4 10.04 or newer) +configopts = "-DGATE_USE_OPTICAL=1 -DGATE_USE_DAVIS=1" + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATE/GATE-8.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/g/GATE/GATE-8.2-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..997478d0d63 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-8.2-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,31 @@ +name = 'GATE' +version = '8.2' +versionsuffix = '-Python-2.7.14' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['http://www.opengatecollaboration.org/sites/default/files/'] +sources = ['Gate-%(version)s.tar.gz'] +patches = ['GATE-7.0_Makefile-prefix.patch'] +checksums = [ + 'edd8b1017310442bb6819a2815d61b63b1da1aef613fea2678aede134cbad741', # Gate-8.2.tar.gz + 'e72c230df1cdd05c07ac405b22bf26931abdcd3e5f7b942e9c88251ac24cc6af', # GATE-7.0_Makefile-prefix.patch +] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Geant4', '10.5'), + ('CLHEP', '2.4.1.0'), + ('ROOT', '6.10.08', versionsuffix), +] + +# enable extra capabilities (Davis requires Geant4 10.04 or newer) +configopts = "-DGATE_USE_OPTICAL=1 -DGATE_USE_DAVIS=1" + +moduleclass = 'cae' From f635efe5f75585b5c5b541e3626b655ad62cafe4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 19 Apr 2019 08:53:30 +0200 Subject: [PATCH 1218/5331] GTK+ must set XDG_DATA_DIRS --- easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb index 201b6489441..11428031459 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb @@ -35,4 +35,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' From 7ed48605ba593e9c907374601bf0141b6f2982f3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 19 Apr 2019 15:24:23 +0200 Subject: [PATCH 1219/5331] adding easyconfigs: lz4-1.9.0-GCCcore-7.3.0.eb and patches: lz4-1.9.0_fix_test.patch --- .../l/lz4/lz4-1.9.0-GCCcore-7.3.0.eb | 33 +++++++++++++++++++ .../l/lz4/lz4-1.9.0_fix_test.patch | 14 ++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.0-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.0_fix_test.patch diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..e85bfc618b0 --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.0-GCCcore-7.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.0' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://github.com/lz4/lz4/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['lz4-1.9.0_fix_test.patch'] +checksums = [ + 'f8b6d5662fa534bd61227d313535721ae41a68c9d84058b7b7d86e143572dcfb', # v1.9.0.tar.gz + '848c500c2882e6af5763acfedf700c0282507d74973ca73845e5b00594283bc8', # lz4-1.9.0_fix_test.patch +] + +builddependencies = [('binutils', '2.30')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.0_fix_test.patch b/easybuild/easyconfigs/l/lz4/lz4-1.9.0_fix_test.patch new file mode 100644 index 00000000000..78fca5f2938 --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.0_fix_test.patch @@ -0,0 +1,14 @@ +Fix error in test +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ur lz4-1.9.0.orig/tests/Makefile lz4-1.9.0/tests/Makefile +--- lz4-1.9.0.orig/tests/Makefile 2019-04-16 22:55:28.000000000 +0200 ++++ lz4-1.9.0/tests/Makefile 2019-04-19 15:08:53.616562619 +0200 +@@ -315,7 +315,7 @@ + ! $(LZ4) -c --fast=-1 tmp-tlb-dg20K # lz4 should fail when fast=-1 + # Test for #596 + @echo "TEST" > tmp-tlb-test +- $(LZ4) tmp-tlb-test ++ $(LZ4) tmp-tlb-test tmp-tlb-test.lz4 + $(LZ4) tmp-tlb-test.lz4 tmp-tlb-test2 + $(DIFF) -q tmp-tlb-test tmp-tlb-test2 + @$(RM) tmp-tlb* From 270974120e72e1a6426984f26fb36ff4e51d8880 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 19 Apr 2019 16:32:20 +0200 Subject: [PATCH 1220/5331] adding easyconfigs: vt-0.57721-foss-2018b.eb --- .../easyconfigs/v/vt/vt-0.57721-foss-2018b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/v/vt/vt-0.57721-foss-2018b.eb diff --git a/easybuild/easyconfigs/v/vt/vt-0.57721-foss-2018b.eb b/easybuild/easyconfigs/v/vt/vt-0.57721-foss-2018b.eb new file mode 100644 index 00000000000..7569ec41155 --- /dev/null +++ b/easybuild/easyconfigs/v/vt/vt-0.57721-foss-2018b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'vt' +version = '0.57721' + +homepage = 'http://genome.sph.umich.edu/wiki/Vt' +description = """A tool set for short variant discovery in genetic sequence data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/atks/vt/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('cURL', '7.60.0'), +] + +runtest = 'test' + +files_to_copy = [(["vt"], "bin"), "README.md", "LICENSE"] + +sanity_check_paths = { + 'files': ["bin/vt"], + 'dirs': [], +} + +moduleclass = 'bio' From 3c3724602ec98814b47cde14fff75fdf8ae9ad6b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 19 Apr 2019 16:33:11 +0200 Subject: [PATCH 1221/5331] adding easyconfigs: bam-readcount-0.8.0-foss-2018b.eb --- .../bam-readcount-0.8.0-foss-2018b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-foss-2018b.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-foss-2018b.eb new file mode 100644 index 00000000000..e9419a4580c --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-foss-2018b.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'CMakeMake' + +name = 'bam-readcount' +version = '0.8.0' + +homepage = 'https://github.com/genome/bam-readcount' +description = """Count DNA sequence reads in BAM files""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/genome/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4f4dd558e3c6bfb24d6a57ec441568f7524be6639b24f13ea6f2bb350c7ea65f'] + +builddependencies = [ + ('CMake', '3.12.1'), +] + +dependencies = [ + ('SAMtools', '1.9'), + ('zlib', '1.2.11'), + ('ncurses', '6.1'), +] + +prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && " + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/bam-readcount"], + 'dirs': [] +} + +moduleclass = 'bio' From 43ce7196a4f789f0dbf2e526adaf7ddb0dc94f51 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 19 Apr 2019 16:38:38 +0200 Subject: [PATCH 1222/5331] adding easyconfigs: INTEGRATE-Neo-1.2.1-foss-2018b.eb, HLAminer-1.4-foss-2018b-Perl-5.28.0.eb, netMHC-4.0a.eb --- .../HLAminer-1.4-foss-2018b-Perl-5.28.0.eb | 44 +++++++++++++++++++ .../INTEGRATE-Neo-1.2.1-foss-2018b.eb | 40 +++++++++++++++++ easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb | 44 +++++++++++++++++++ 3 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/h/HLAminer/HLAminer-1.4-foss-2018b-Perl-5.28.0.eb create mode 100644 easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b.eb create mode 100644 easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb diff --git a/easybuild/easyconfigs/h/HLAminer/HLAminer-1.4-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/h/HLAminer/HLAminer-1.4-foss-2018b-Perl-5.28.0.eb new file mode 100644 index 00000000000..97dfa48ddc7 --- /dev/null +++ b/easybuild/easyconfigs/h/HLAminer/HLAminer-1.4-foss-2018b-Perl-5.28.0.eb @@ -0,0 +1,44 @@ +easyblock = 'Tarball' + +name = 'HLAminer' +version = '1.4' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/hlaminer' +description = """\ + HLAminer is a software for HLA predictions from next-generation shotgun (NGS) sequence read data and supports direct + read alignment and targeted de novo assembly of sequence reads. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +# HLAminer is proprietary software, but free for academcs +# see: http://www.bcgsc.ca/platform/bioinfo/software/hlaminer/releases/1.4 +source_urls = ['http://www.bcgsc.ca/platform/bioinfo/software/hlaminer/releases/1.4'] +sources = ['%(name)s_%(version_major)s-%(version_minor)s.tar.gz'] +checksums = ['786271bc1d69fd5ee3bceffde19b36262027b72bc7bafba5d4beaf0a2fdcccd8'] + +dependencies = [ + ('Perl', '5.28.0'), + ('BioPerl', '1.7.2', versionsuffix), + ('BWA', '0.7.17'), +] + +postinstallcmds = [ + 'mv %(installdir)s/HLAminer_v1.4/* %(installdir)s/', + ( + "cd %(installdir)s/bin && " + "sed -i '1 i#!/usr/bin/env perl' *.pl && " + "sed -i 's,\.\.\/bin/,,g' *.sh ncbiBlastConfig.txt && " + "sed -i 's,\.\./database,$EBROOTHLAMINER/database,g' *.sh && " + "sed -i 's,/home/pubseq/BioSw/bwa/bwa-0.5.9/bwa,bwa,g' *.sh" + ), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['bin/HLAminer.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b.eb b/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b.eb new file mode 100644 index 00000000000..7d3dcd215b3 --- /dev/null +++ b/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b.eb @@ -0,0 +1,40 @@ +easyblock = 'CmdCp' + +name = 'INTEGRATE-Neo' +# version = '20180220' +version = '1.2.1' +commit = '6b9f666' + +homepage = '' +description = """ INTEGRATE-Neo is a gene fusion neoantigen discovering tool using next-generation sequencing data. + It is written in C++ and Python. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/ChrisMaherLab/INTEGRATE-Neo/archive/'] +sources = [{'download_filename': '%s.tar.gz' % commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['0f5058b3bafd972098759ffc8f4edfa05ff3e1657293c543c82669356846f9d8'] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '3.6.6'), + ('BWA', '0.7.17'), + ('HLAminer', '1.4', '-Perl-5.28.0'), + ('netMHC', '4.0a', '', True), +] + +start_dir = '%(name)s-V-%(version)s' + +cmds_map = [('.*', './install.sh -o bin')] + +files_to_copy = ['bin'] + +postinstallcmds = ["sed -i '1 i#!/usr/bin/env python' bin/*.py"] + +sanity_check_paths = { + 'files': ['bin/integrate-neo.py', 'bin/fusionBedpeAnnotator', 'bin/fusionBedpeSubsetter'], + 'dirs': [''], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb b/easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb new file mode 100644 index 00000000000..6de3a9692db --- /dev/null +++ b/easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb @@ -0,0 +1,44 @@ +easyblock = 'Tarball' + +name = 'netMHC' +version = '4.0a' + +homepage = 'http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC' +description = """ NetMHC 4.0 software predicts binding of peptides to a number of different + HLA alleles using artificial neural networks (ANN). """ + +toolchain = {'name': 'dummy', 'version': ''} + +# netMHC is proprietary software, but free for academcs +# see: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC +source_urls = ['http://www.cbs.dtu.dk/services/NetMHC-4.0'] +sources = [ + { + 'filename': '%(name)s-%(version)s.Linux.tar.gz', + 'extract_cmd': 'tar --strip-components=1 -xzf %s', + }, + { + 'download_filename': 'data.tar.gz', + 'filename': '%(name)s-%(version)s-data.tar.gz', + }, +] +checksums = [ + 'd9938388c50bf49d748e5c1293435d7d9fae5d0a33303d795e767429508e368a', # netMHC-4.0a.Linux.tar.gz + 'f3fb6d77ec11bc51de963e96fd75a0622f5098a2d1e37d750afa3709d5b876d1', # netMHC-4.0a-data.tar.gz +] + +postinstallcmds = [ + 'sed -i -e "s|setenv[[:space:]]NMHOME.*|setenv NMHOME \$EBROOTNETMHC|" %(installdir)s/netMHC', + 'sed -i -e "s|setenv[[:space:]]TMPDIR.*|setenv TMPDIR /tmp|" %(installdir)s/netMHC', +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['netMHC', 'Linux_x86_64/bin/netMHC'], + 'dirs': [], +} + +sanity_check_commands = ['netMHC -h'] + +moduleclass = 'bio' From 0f1bfcb28edf4fc7774ba1324e663383699e7830 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 19 Apr 2019 16:44:17 +0200 Subject: [PATCH 1223/5331] adding easyconfigs: DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb --- ...rv-20180922-fosscuda-2018b-Python-3.6.6.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..6aba7c3a750 --- /dev/null +++ b/easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'DeepSurv' +# the latest stable release, DeepSurv-2.0.0 is not fully compatible with Python 3 +version = '20180922' +commit = '27883dc' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jaredleekatzman/DeepSurv' +description = """ DeepSurv is a deep learning approach to survival analysis. """ + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('Theano', '1.0.3', versionsuffix), + ('h5py', '2.8.0', versionsuffix), + ('protobuf-python', '3.6.0', versionsuffix), + ('Pillow', '5.3.0', versionsuffix), + ('matplotlib', '3.0.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('Bottleneck', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bottleneck/'], + 'checksums': ['6efcde5f830aed64feafca0359b51db0e184c72af8ba6675b4a99f263922eb36'], + }), + ('future', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future/'], + 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], + }), + ('autograd', '1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/a/autograd/'], + 'checksums': ['a08bfa6d539b7a56e7c9f4d0881044afbef5e75f324a394c2494de963ea4a47d'], + }), + ('lifelines', '0.20.4', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lifelines/'], + 'checksums': ['efdf109b2f383c4125ca30414c13f88a9386f5d61d986bcb458cc41242f429bd'], + }), + ('logger', '1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/l/logger/'], + 'checksums': ['4ecac57133c6376fa215f0fe6b4dc4d60e4d1ad8be005cab4e8a702df682f8b3'], + }), + ('Optunity', '1.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/o/optunity/'], + 'checksums': ['a83618dd37e014c5993e8877749e0ee17864d24783f19f5ebdeedb5525c0a65b'], + }), + ('tensorboard_logger', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard_logger/'], + 'checksums': ['614eaf9b68f7ca9e5db5972f241034a24ea593b938fc8a7e5544444099edeae5'], + }), + ('Lasagne', 'a61b76f', { + 'source_tmpl': 'a61b76f.tar.gz', + 'source_urls': ['https://github.com/Lasagne/Lasagne/archive/'], + 'checksums': ['d3167def99c63638e1956d335b197a812f5952349d691b638e62e0847979c11e'], + }), + (name, '27883dc', { + 'source_tmpl': '27883dc.tar.gz', + 'source_urls': ['https://github.com/jaredleekatzman/DeepSurv/archive/'], + 'checksums': ['f7ddd934763ddf47732285b9e078bb2ffc746aad81cb2ac044d7fb1d69bf3581'], + }), +] + +moduleclass = 'lib' From cafac7c885a3d3b160f3fc5f61ea29b0dbced439 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 19 Apr 2019 16:48:52 +0200 Subject: [PATCH 1224/5331] adding easyconfigs: NBO-7.0-intel-2017b.eb and patches: NBO-7.0_make.patch --- .../easyconfigs/n/NBO/NBO-7.0-intel-2017b.eb | 44 +++++++++++++++++++ .../easyconfigs/n/NBO/NBO-7.0_make.patch | 14 ++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/n/NBO/NBO-7.0-intel-2017b.eb create mode 100644 easybuild/easyconfigs/n/NBO/NBO-7.0_make.patch diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0-intel-2017b.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0-intel-2017b.eb new file mode 100644 index 00000000000..fb245f812df --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0-intel-2017b.eb @@ -0,0 +1,44 @@ +# this recipe is configured for use with Gaussian G16, revision A03 or later + +easyblock = 'MakeCp' + +name = 'NBO' +version = '7.0' + +homepage = 'http://nbo.chem.wisc.edu/' +description = """ The Natural Bond Orbital (NBO) program is a discovery tool +for chemical insights from complex wavefunctions. """ + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers + +# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +sources = ['nbo7.0-src.tar'] +patches = ['NBO-7.0_make.patch'] +checksums = [ + '45cc4b85c53f66328d0262b18150ec5557f252b244511148a858933469ecf88c', # nbo7.0-src.tar + '832e2f29f728d15e114b81978d3308ab7b1b7c73deccadd2a562a5ecfd7f27f4', # NBO-7.0_make.patch +] + +intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers + +buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' +buildopts += 'BLASLIB="$LDFLAGS $LIBBLAS" ' +buildopts += 'INT=%s ' % intlength + +parallel = 1 + +files_to_copy = ['bin', 'dox', 'man', 'tests'] + +postinstallcmds = [ + 'sed -i -e "s|setenv GAUNBO.*|setenv GAUNBO g16nbo|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv BINDIR.*|setenv BINDIR %(installdir)s/bin|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv INT.*|setenv INT %s|" %%(installdir)s/bin/gaunbo{6,7}' % intlength, +] + +sanity_check_paths = { + 'files': ['bin/%s.%s.exe' % (x, intlength) for x in ('gennbo', 'g09nbo', 'g16nbo', 'nbo7')], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0_make.patch b/easybuild/easyconfigs/n/NBO/NBO-7.0_make.patch new file mode 100644 index 00000000000..619bf030f1c --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0_make.patch @@ -0,0 +1,14 @@ +Don't reset CFLAGS and FFLAGS +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ur nbo7.orig/Make.config nbo7/Make.config +--- nbo7.orig/Make.config 2019-04-10 09:53:59.000000000 +0200 ++++ nbo7/Make.config 2019-04-16 11:27:27.714389238 +0200 +@@ -167,8 +167,6 @@ + + # ---------------------------------------------------------------------- + +-CFLAGS = +-FFLAGS = + LFLAGS = + PFLAGS = + From 956b209a93a5f0866132c22e9499bb36288ec2e6 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 19 Apr 2019 12:21:25 -0500 Subject: [PATCH 1225/5331] Do not install kernel at module load but point jupyter to install dir --- ...ernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb | 13 +++++++++---- ...rnel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb | 13 +++++++++---- 2 files changed, 18 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb index 7a2d0b648d9..68a5b87a247 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb @@ -46,12 +46,17 @@ exts_list = [ modextrapaths = {'R_LIBS': ''} -# The R kernel spec must be installed in order for Jupyter to see it -# This ensures that it is installed in the user local directory at module load -modluafooter = 'execute {cmd="R --slave -e \'library(IRkernel); IRkernel::installspec()\'", modeA={"load"}}' +# IPython notebook looks for the json kernel file in kernels/octave_kernels +kerneldir = '%(installdir)s/IRkernel' +postinstallcmds = [ + 'mkdir -p %s/kernels/ir' % kerneldir, + 'cp %s/kernelspec/* %s/kernels/ir' % (kerneldir, kerneldir) +] + +modextravars = {'JUPYTER_PATH': kerneldir} sanity_check_paths = { - 'files': [], + 'files': ['%s/kernels/ir/kernel.json' % kerneldir], 'dirs': [name], } diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb index 6d3d60c6168..b9fe7d46c25 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb @@ -46,12 +46,17 @@ exts_list = [ modextrapaths = {'R_LIBS': ''} -# The R kernel spec must be installed in order for Jupyter to see it -# This ensures that it is installed in the user local directory at module load -modluafooter = 'execute {cmd="R --slave -e \'library(IRkernel); IRkernel::installspec()\'", modeA={"load"}}' +# IPython notebook looks for the json kernel file in kernels/octave_kernels +kerneldir = '%(installdir)s/IRkernel' +postinstallcmds = [ + 'mkdir -p %s/kernels/ir' % kerneldir, + 'cp %s/kernelspec/* %s/kernels/ir' % (kerneldir, kerneldir) +] + +modextravars = {'JUPYTER_PATH': kerneldir} sanity_check_paths = { - 'files': [], + 'files': ['%s/kernels/ir/kernel.json' % kerneldir], 'dirs': [name], } From 4594b2b2de3a7befc8be462585221068056c15bb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Apr 2019 10:09:42 +0200 Subject: [PATCH 1226/5331] add Tkinter as exception for requiring -Python-* in versionsuffix --- test/easyconfigs/easyconfigs.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 8b06f97fc44..ad53184322d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -417,7 +417,8 @@ def check_python_packages(self, changed_ecs): failing_checks.append("'%s' set in exts_default_options in %s" % (key, ec_fn)) # if Python is a dependency, that should be reflected in the versionsuffix - if any(dep['name'] == 'Python' for dep in ec['dependencies']): + # Tkinter is an exception, since its version always matches the Python version anyway + if any(dep['name'] == 'Python' for dep in ec['dependencies']) and ec.name != 'Tkinter': if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): failing_checks.append("'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn) From 35c74b425191c7e9766f5f04323a1d63f8a63da5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Apr 2019 13:26:10 +0200 Subject: [PATCH 1227/5331] add check for custom sanity_check_paths in easyconfigs touched in PRs when generic easyblock is used --- test/easyconfigs/easyconfigs.py | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 8b06f97fc44..15d1ec2cb49 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -43,7 +43,8 @@ from easybuild.framework.easyblock import EasyBlock from easybuild.framework.easyconfig.default import DEFAULT_CONFIG from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS -from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for, resolve_template +from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, is_generic_easyblock, letter_dir_for +from easybuild.framework.easyconfig.easyconfig import resolve_template from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig from easybuild.framework.easyconfig.tools import check_sha256_checksums, dep_graph, get_paths_for, process_easyconfig from easybuild.tools import config @@ -423,6 +424,18 @@ def check_python_packages(self, changed_ecs): self.assertFalse(failing_checks, '\n'.join(failing_checks)) + def check_sanity_check_paths(self, changed_ecs): + """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" + + failing_checks = [] + + for ec in changed_ecs: + if is_generic_easyblock(ec.get('easyblock')) and not ec.get('sanity_check_paths'): + ec_fn = os.path.basename(ec.path) + failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) + + self.assertFalse(failing_checks, '\n'.join(failing_checks)) + def test_changed_files_pull_request(self): """Specific checks only done for the (easyconfig) files that were changed in a pull request.""" @@ -476,6 +489,7 @@ def test_changed_files_pull_request(self): # run checks on changed easyconfigs self.check_sha256_checksums(changed_ecs) self.check_python_packages(changed_ecs) + self.check_sanity_check_paths(changed_ecs) def test_zzz_cleanup(self): """Dummy test to clean up global temporary directory.""" From dd1d485b3b40ea43cbf17610c527ccf43aaa4a45 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 23 Apr 2019 14:37:41 +0200 Subject: [PATCH 1228/5331] Fix W391 --- easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.15-GCCcore-8.2.0.eb | 1 - easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.15-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.15-GCCcore-8.2.0.eb index 97bea5384e8..586e24c1e35 100644 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.15-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.15-GCCcore-8.2.0.eb @@ -20,4 +20,3 @@ dependencies = [ ] moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb index b84ecb2f96d..38aa86c7595 100644 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.7.2-GCCcore-8.2.0.eb @@ -23,4 +23,3 @@ dependencies = [ ] moduleclass = 'lang' - From 3713cbfb0e03b4f385ee2ebe949e715ca154e93e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Apr 2019 15:15:30 +0200 Subject: [PATCH 1229/5331] adding easyconfigs: OpenMPI-3.1.4-GCC-8.3.0-2.32.eb, hwloc-1.11.12-GCCcore-8.3.0.eb --- .../h/hwloc/hwloc-1.11.12-GCCcore-8.3.0.eb | 48 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb | 38 +++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..05ccfb01077 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-8.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.12' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +# need to build with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake +# cfr. https://github.com/open-mpi/hwloc/issues/315 +toolchainopts = {'vectorize': False} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f1d49433e605dd653a77e1478a78cee095787d554a94afe40d1376bca6708ca5'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('numactl', '2.0.12'), + ('libxml2', '2.9.9'), + ('libpciaccess', '0.14'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb new file mode 100644 index 00000000000..d9d03983158 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '3.1.4' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0-2.32'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a7c34ad052ea8201ed9e7389994069fe6996403beabdd2d711caf0532808156c'] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '1.11.12') +] + +configopts = '--enable-shared --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +moduleclass = 'mpi' From 647fc6b52b18619de5bf1d51811ead0323735197 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 23 Apr 2019 17:09:13 +0200 Subject: [PATCH 1230/5331] FriBidi is a runtime dep --- easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb index f6096d54de9..2bf5495d39d 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb @@ -20,7 +20,6 @@ builddependencies = [ ('Ninja', '1.9.0'), ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), ('pkg-config', '0.29.2'), - ('FriBidi', '1.0.5'), ] dependencies = [ @@ -28,6 +27,7 @@ dependencies = [ ('GLib', '2.60.1'), ('cairo', '1.16.0'), ('HarfBuzz', '2.4.0'), + ('FriBidi', '1.0.5'), ] configopts = "--buildtype=release --default-library=both " From 1c0f3624cfe43951e1fe460d06c669720d4f14de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Apr 2019 17:47:22 +0200 Subject: [PATCH 1231/5331] correctly register CMake as a build dependency in ARGoS easyconfig file --- .../a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b-Lua-5.2.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b-Lua-5.2.4.eb b/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b-Lua-5.2.4.eb index 4369a3eece2..91d5564119e 100644 --- a/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b-Lua-5.2.4.eb +++ b/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta53-foss-2018b-Lua-5.2.4.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/ilpincy/argos3/archive'] sources = ['%(version)s.tar.gz'] checksums = ['849ebb1af31d01519a1f3d9731064eaa8041b2ed140bb699096912de1272214c'] -dependencies = [('CMake', '3.12.1')] +builddependencies = [('CMake', '3.12.1')] dependencies = [ ('Lua', luaver), From f009894a03563ee67ded69efef839182ed4078dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Apr 2019 18:56:29 +0200 Subject: [PATCH 1232/5331] add pkg-config build dep for LUSCUS --- easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb index 55d6a0f1f2d..b896b140f17 100644 --- a/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb +++ b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb @@ -16,7 +16,10 @@ checksums = [ 'b4831c00ecb2311738ed236bbbe5307522d9fca90544967186cab342065b8fc7', # LUSCUS-0.8.6_fix-X11-link.patch ] -builddependencies = [('CMake', '3.12.1')] +builddependencies = [ + ('CMake', '3.12.1'), + ('pkg-config', '0.29.2'), +] dependencies = [ ('GTK+', '2.24.32'), From 107f0f8d3aed0378b5255f48f67cb67698ee4836 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Apr 2019 19:25:21 +0200 Subject: [PATCH 1233/5331] adding easyconfigs: LUSCUS-0.8.6-foss-2018b.eb --- .../l/LUSCUS/LUSCUS-0.8.6-foss-2018b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-foss-2018b.eb diff --git a/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-foss-2018b.eb b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-foss-2018b.eb new file mode 100644 index 00000000000..86bae2768d2 --- /dev/null +++ b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-foss-2018b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'LUSCUS' +version = '0.8.6' + +homepage = 'https://sourceforge.net/projects/luscus/' +description = "Luscus is the program for graphical display and editing of molecular systems." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['luscus_%(version)s.tar.gz'] +patches = ['LUSCUS-%(version)s_fix-X11-link.patch'] +checksums = [ + 'e1bf08de586b6e1c88c22b3d1d9b00a49c227fded7d6dc17023d3e9a84c573a3', # luscus_0.8.6.tar.gz + 'b4831c00ecb2311738ed236bbbe5307522d9fca90544967186cab342065b8fc7', # LUSCUS-0.8.6_fix-X11-link.patch +] + +builddependencies = [ + ('CMake', '3.12.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GTK+', '2.24.32'), + ('Mesa', '18.1.1'), + ('libGLU', '9.0.0'), +] + +sanity_check_paths = { + 'files': ['bin/luscus'], + 'dirs': [], +} + +moduleclass = 'vis' From c512adf3db7cc4f394f8bd17322065d08a651189 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Apr 2019 19:35:54 +0200 Subject: [PATCH 1234/5331] add (back) custom sanity_check_paths in recent Pango easyconfigs --- easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb | 6 ++++++ .../easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb | 6 ++++++ 7 files changed, 42 insertions(+) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb index d6e1571a8c3..fec5414da16 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb @@ -28,6 +28,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb index 9a731c0f6ab..fc8461d94e5 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb @@ -28,6 +28,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb index 169fa0b3ae7..e7d14c0cac6 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb @@ -29,6 +29,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb index 6595d0dfc14..6a945a99651 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb @@ -29,6 +29,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb index 1b4cd80e28f..90c6d08cc5a 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb @@ -29,6 +29,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb index c2745d70c20..f1ab48733b4 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb @@ -29,6 +29,12 @@ dependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb index f6096d54de9..0c4e95e1c0d 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb @@ -32,6 +32,12 @@ dependencies = [ configopts = "--buildtype=release --default-library=both " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } From 0d48b8f12f3d4e6afc603da6a592af4d853ca9e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 23 Apr 2019 19:50:46 +0200 Subject: [PATCH 1235/5331] Drop release date from suffix --- ...st-4.6-centos6-03Apr2019.eb => LS-PrePost-4.6-centos6.eb} | 5 +++-- ...st-4.6-centos7-03Apr2019.eb => LS-PrePost-4.6-centos7.eb} | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/l/LS-PrePost/{LS-PrePost-4.6-centos6-03Apr2019.eb => LS-PrePost-4.6-centos6.eb} (81%) rename easybuild/easyconfigs/l/LS-PrePost/{LS-PrePost-4.6-centos7-03Apr2019.eb => LS-PrePost-4.6-centos7.eb} (81%) diff --git a/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6-03Apr2019.eb b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6.eb similarity index 81% rename from easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6-03Apr2019.eb rename to easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6.eb index 401fde8f016..ac8a96481ef 100644 --- a/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6-03Apr2019.eb +++ b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6.eb @@ -2,7 +2,8 @@ easyblock = "Tarball" name = 'LS-PrePost' version = '4.6' -versionsuffix = '-centos6-03Apr2019' +release_date = '03Apr2019' +versionsuffix = '-centos6' homepage = 'http://lstc.com/products/ls-prepost' description = """LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA.""" @@ -10,7 +11,7 @@ description = """LS-PrePost is an advanced pre and post-processor that is delive toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ftp.lstc.com/anonymous/outgoing/lsprepost/%(version)s/linux64/'] -sources = ['lsprepost-%%(version)s_mesa%s.tgz' % versionsuffix] +sources = ['lsprepost-%%(version)s_mesa%s-%s.tgz' % (versionsuffix, release_date)] checksums = ['b30ac871c9949d2449515033be5e978a873111be5bdf430326681735fa92e2a7'] modextrapaths = {'PATH': '.', 'LD_LIBRARY_PATH': 'lib'} diff --git a/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7-03Apr2019.eb b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7.eb similarity index 81% rename from easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7-03Apr2019.eb rename to easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7.eb index 327b67a45c7..e746e93ebd9 100644 --- a/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7-03Apr2019.eb +++ b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7.eb @@ -2,7 +2,8 @@ easyblock = "Tarball" name = 'LS-PrePost' version = '4.6' -versionsuffix = '-centos7-03Apr2019' +release_date = '03Apr2019' +versionsuffix = '-centos7' homepage = 'http://lstc.com/products/ls-prepost' description = """LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA.""" @@ -10,7 +11,7 @@ description = """LS-PrePost is an advanced pre and post-processor that is delive toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://ftp.lstc.com/anonymous/outgoing/lsprepost/%(version)s/linux64/'] -sources = ['lsprepost-%%(version)s_mesa%s.tgz' % versionsuffix] +sources = ['lsprepost-%%(version)s_mesa%s-%s.tgz' % (versionsuffix, release_date)] checksums = ['9a89e606054bb481bf73dc8526c5ce4107d242090d0f336a6dfd5c57d782d62e'] modextrapaths = {'PATH': '.', 'LD_LIBRARY_PATH': 'lib'} From 101981078816b56eadfc43a9986ce48388a5b004 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 23 Apr 2019 21:23:43 +0200 Subject: [PATCH 1236/5331] adding easyconfigs: matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb, matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb, matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb, matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb --- ...atplotlib-3.0.3-foss-2019a-Python-3.7.2.eb | 65 +++++++++++++++++++ ...otlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb | 65 +++++++++++++++++++ ...tplotlib-3.0.3-intel-2019a-Python-3.7.2.eb | 65 +++++++++++++++++++ ...tlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb | 65 +++++++++++++++++++ 4 files changed, 260 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..8b2e3a6994d --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'check_ldshared': True, +} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('libpng', '1.6.36'), + ('freetype', '2.9.1'), + ('Tkinter', '%(pyver)s'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'check_ldshared': True, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +check_ldshared = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..8de598f8436 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'check_ldshared': True, +} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('libpng', '1.6.36'), + ('freetype', '2.9.1'), + ('Tkinter', '%(pyver)s'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'check_ldshared': True, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +check_ldshared = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..304d6f67310 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'check_ldshared': True, +} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('libpng', '1.6.36'), + ('freetype', '2.9.1'), + ('Tkinter', '%(pyver)s'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'check_ldshared': True, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +check_ldshared = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..20eea87599f --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intelcuda', 'version': '2019a'} + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'check_ldshared': True, +} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('libpng', '1.6.36'), + ('freetype', '2.9.1'), + ('Tkinter', '%(pyver)s'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'check_ldshared': True, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +check_ldshared = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From 29ca062d2b6f95a5cec620ee9fe4d6da2d4daa3a Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 23 Apr 2019 21:37:36 +0200 Subject: [PATCH 1237/5331] adding easyconfigs: UDUNITS-2.2.26-GCCcore-8.2.0.eb --- .../u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.2.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..9790180b300 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-GCCcore-8.2.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.26' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [('expat', '2.2.6')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From 803f2484d4601a4253b7decd6e2ddc7f7757de5f Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 23 Apr 2019 21:42:36 +0200 Subject: [PATCH 1238/5331] adding easyconfigs: ICU-64.2-GCCcore-8.2.0.eb --- .../i/ICU/ICU-64.2-GCCcore-8.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..7f33e1fdc47 --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '64.2' + +homepage = 'http://site.icu-project.org/home' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.icu-project.org/files/icu4c/%(version)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] + +builddependencies = [('binutils', '2.31.1')] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' From 3ec5cf61c881094cf0b1a24acc596c656e6ab870 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 23 Apr 2019 21:44:28 +0200 Subject: [PATCH 1239/5331] adding easyconfigs: PROJ-6.0.0-GCCcore-8.2.0.eb --- .../p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..1b220befbaf --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '6.0.0' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4510a2c1c8f9056374708a867c51b1192e8d6f9a5198dd320bf6a168e44a3657'] + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 5159b69543dda682fcadf705bf9cf89fbd73113a Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 24 Apr 2019 10:45:42 +0200 Subject: [PATCH 1240/5331] Add SQLite dep --- easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb index 1b220befbaf..d3ff2dd7a8d 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb @@ -24,6 +24,8 @@ checksums = ['4510a2c1c8f9056374708a867c51b1192e8d6f9a5198dd320bf6a168e44a3657'] builddependencies = [('binutils', '2.31.1')] +dependencies = [('SQLite', '3.27.2')] + sanity_check_paths = { 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], From e64a87395e74df84a90ae9eb7d0184bae3608d59 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 10:49:00 +0200 Subject: [PATCH 1241/5331] Update all old GTK+ easyconfigs with XDG_DATA_DIRS --- easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb | 4 ++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb | 4 ++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb | 4 ++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb | 4 ++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb | 4 ++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb | 4 ++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb | 4 ++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb | 4 ++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb | 4 ++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb | 4 ++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb | 4 ++++ 11 files changed, 44 insertions(+) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb index c29db47cc8e..6dabd0f4bcc 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb @@ -22,4 +22,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb index f8cd4f7bed7..42d00bdab27 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb @@ -22,4 +22,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb index 6dfeab05269..ef5a67efe0b 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb @@ -22,4 +22,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb index c33f283106b..8d3bcda5114 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb @@ -22,4 +22,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb index 78f4ad00b7a..4ef6887a80c 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb @@ -22,4 +22,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb index e9ae2112ba8..967a6b25ed2 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb @@ -25,4 +25,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb index 36ca4e79b81..3b8f4f86a1f 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb @@ -24,4 +24,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb index d827e3cb5d5..8a26eefdb3c 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb @@ -25,4 +25,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb index eb6263b536b..a583d5ce8cd 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb @@ -27,4 +27,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb index d35738f42de..dc6721786aa 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb @@ -24,4 +24,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb index 9bba0d51695..2664ebcd3ee 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb @@ -25,4 +25,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + moduleclass = 'vis' From e298da59b0a53ade886ea8d79853cfd4b9d39f12 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 11:08:47 +0200 Subject: [PATCH 1242/5331] adding easyconfigs: libgcrypt-1.8.4-GCCcore-8.2.0.eb --- .../libgcrypt-1.8.4-GCCcore-8.2.0.eb | 24 +++++++++++++++++++ .../libgpg-error-1.36-GCCcore-8.2.0.eb | 22 +++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.8.4-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.36-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.8.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.8.4-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..3d0b12fc87b --- /dev/null +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.8.4-GCCcore-8.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libgcrypt' +version = '1.8.4' + +homepage = 'https://gnupg.org/related_software/libgcrypt/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['f638143a0672628fde0cad745e9b14deb85dffb175709cacc1f4fe24b93f2227'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [('libgpg-error', '1.36')] + +sanity_check_paths = { + 'files': ['bin/libgcrypt-config', 'include/gcrypt.h', 'lib/libgcrypt.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.36-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.36-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..1efe63c47f3 --- /dev/null +++ b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.36-GCCcore-8.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libgpg-error' +version = '1.36' + +homepage = 'https://gnupg.org/related_software/libgpg-error/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['babd98437208c163175c29453f8681094bcaf92968a15cafb1a276076b33c97c'] + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ['bin/gpg-error-config', 'include/gpg-error.h', 'lib/libgpg-error.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From fd47401378bb47a32f1e1c1ca428b754650665ac Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 11:13:59 +0200 Subject: [PATCH 1243/5331] adding easyconfigs: libpsl-0.21.0-GCCcore-8.2.0.eb --- .../l/libpsl/libpsl-0.21.0-GCCcore-8.2.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpsl/libpsl-0.21.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..0b578b7c1ab --- /dev/null +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.0-GCCcore-8.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libpsl' +version = '0.21.0' + +homepage = 'https://rockdaboot.github.io/libpsl' +description = "C library for the Public Suffix List" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/rockdaboot/%(name)s/releases/download/%(name)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['41bd1c75a375b85c337b59783f5deb93dbb443fb0a52d257f403df7bd653ee12'] + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ['bin/psl', 'lib/libpsl.a'], + 'dirs': [] +} + +moduleclass = 'lib' From 24ca0d427ad1a1b786434b5e1969c9e07fd8737c Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 24 Apr 2019 11:14:59 +0200 Subject: [PATCH 1244/5331] Boegelbot is picky --- .../matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb | 8 ++------ .../matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb | 8 ++------ .../matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb | 9 +++------ .../matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb | 9 +++------ 4 files changed, 10 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb index 8b2e3a6994d..5607a2e2fee 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb @@ -11,12 +11,8 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'foss', 'version': '2019a'} -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, - 'check_ldshared': True, -} +download_dep_fail = True +use_pip = True builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb index 8de598f8436..9c769daa06e 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb @@ -11,12 +11,8 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'fosscuda', 'version': '2019a'} -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, - 'check_ldshared': True, -} +download_dep_fail = True +use_pip = True builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb index 304d6f67310..30bff8be078 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb @@ -11,12 +11,9 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'intel', 'version': '2019a'} -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, - 'check_ldshared': True, -} +download_dep_fail = True +use_pip = True +check_ldshared = True builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb index 20eea87599f..0ba7d08abfe 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb @@ -11,12 +11,9 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'intelcuda', 'version': '2019a'} -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, - 'check_ldshared': True, -} +download_dep_fail = True +use_pip = True +check_ldshared = True builddependencies = [ ('pkg-config', '0.29.2'), From e2680846724a3ed4cac66b564404df4b7f541aad Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 11:16:14 +0200 Subject: [PATCH 1245/5331] adding easyconfigs: libtasn1-4.13-GCCcore-8.2.0.eb --- .../l/libtasn1/libtasn1-4.13-GCCcore-8.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtasn1/libtasn1-4.13-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.13-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.13-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..aadaee15a1d --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.13-GCCcore-8.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.13' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU +Shishi and some other packages. It was written by Fabio Fiorina, and +has been shipped as part of GnuTLS for some time but is now a proper GNU +package.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['7e528e8c317ddd156230c4e31d082cd13e7ddeb7a54824be82632209550c8cca'] + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 9e864d72878a7472e03e70d2dec3cc5125fa33e1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 11:18:14 +0200 Subject: [PATCH 1246/5331] adding easyconfigs: libwebp-1.0.2-GCCcore-8.2.0.eb --- .../g/giflib/giflib-5.1.4-GCCcore-8.2.0.eb | 24 ++++++++++++++ .../l/libwebp/libwebp-1.0.2-GCCcore-8.2.0.eb | 32 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.1.4-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.1.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.1.4-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..64f1a0f2840 --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.1.4-GCCcore-8.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.1.4' + +homepage = 'http://libungif.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [('http://sourceforge.net/projects/giflib/files', 'download')] +sources = [SOURCE_TAR_BZ2] +checksums = ['df27ec3ff24671f80b29e6ab1c4971059c14ac3db95406884fc26574631ba8d5'] + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..d622ea4b212 --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.0.2-GCCcore-8.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.0.2' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3d47b48c40ed6476e8047b2ddb81d93835e0ca1b8d3e8c679afbb3004dd564b1'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('libjpeg-turbo', '2.0.2'), + ('libpng', '1.6.36'), + ('LibTIFF', '4.0.10'), + ('giflib', '5.1.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'lib'] +} + +moduleclass = 'lib' From ae7c439820452ac1bbc5f3ea8f9a914239896073 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 11:20:59 +0200 Subject: [PATCH 1247/5331] adding easyconfigs: LibSoup-2.66.1-GCCcore-8.2.0.eb --- .../l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..babebf7387b --- /dev/null +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'LibSoup' +version = '2.66.1' + +homepage = 'https://wiki.gnome.org/Projects/libsoup' +description = """libsoup is an HTTP client/server library for GNOME. It +uses GObjects and the glib main loop, to integrate well with GNOME +applications, and also has a synchronous API, for use in threaded +applications.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['4a2cb6c1174540af13661636035992c2b179dfcb39f4d3fa7bee3c7e355c43ff'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), +] + +dependencies = [ + ('libxml2', '2.9.8'), + ('SQLite', '3.27.2'), + ('GLib', '2.60.1'), + ('libpsl', '0.21.0'), + ('cURL', '7.63.0'), +] + +configopts = '--libdir lib -Dgssapi=false -Dvapi=false ' + +modextrapaths = { + 'XDG_DATA_DIRS': 'share', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'lib'] +} + +moduleclass = 'lib' From e35deff1a2d5f332a1a9e2c5fe84152092b16232 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 24 Apr 2019 11:24:52 +0200 Subject: [PATCH 1248/5331] Add missing checksum --- easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb index 7f33e1fdc47..bef1fee09c6 100644 --- a/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/i/ICU/ICU-64.2-GCCcore-8.2.0.eb @@ -12,6 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['http://download.icu-project.org/files/icu4c/%(version)s'] sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['627d5d8478e6d96fc8c90fed4851239079a561a6a8b9e48b0892f24e82d31d6c'] builddependencies = [('binutils', '2.31.1')] From a10d59de52555bbbba0ef92772dd4f17751e05ae Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 11:26:54 +0200 Subject: [PATCH 1249/5331] Add missing checksums. --- easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb | 1 + 5 files changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb index 6dabd0f4bcc..3098397ed1d 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['b2c6441e98bc5232e5f9bba6965075dcf580a8726398f7374d39f90b88ed4656'] dependencies = [ ('ATK', '2.18.0'), diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb index 42d00bdab27..1f0208e1ee0 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['0d15cec3b6d55c60eac205b1f3ba81a1ed4eadd9d0f8e7c508bc7065d0c4ca50'] dependencies = [ ('ATK', '2.20.0'), diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb index ef5a67efe0b..4d2d9727f67 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['0d15cec3b6d55c60eac205b1f3ba81a1ed4eadd9d0f8e7c508bc7065d0c4ca50'] dependencies = [ ('ATK', '2.20.0'), diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb index 8d3bcda5114..fa2599d5d55 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['68c1922732c7efc08df4656a5366dcc3afdc8791513400dac276009b40954658'] dependencies = [ ('ATK', '2.22.0'), diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb index 4ef6887a80c..e8e91ac0591 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['68c1922732c7efc08df4656a5366dcc3afdc8791513400dac276009b40954658'] dependencies = [ ('ATK', '2.22.0'), From 41b3e839de6d8a9fd900bcb38217dba20f091958 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 11:30:03 +0200 Subject: [PATCH 1250/5331] adding easyconfigs: OpenJPEG-2.3.1-GCCcore-8.2.0.eb --- .../OpenJPEG/OpenJPEG-2.3.1-GCCcore-8.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.3.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.3.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.3.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..22ba84f859a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.3.1-GCCcore-8.2.0.eb @@ -0,0 +1,48 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchenson Cancer Research Center Seattle WA +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.3.1' + +homepage = 'http://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/openjpeg/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['63f5a4713ecafc86de51bfad89cc07bb788e9bba24ebbf0c4ca637621aadb6a9'] + +separate_build_dir = True + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3') +] + +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.36'), + ('LibTIFF', '4.0.10') +] + +sanity_check_paths = { + 'files': ['bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' From a123b7b0664d6f58bea927545cfc12f970116264 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 11:34:15 +0200 Subject: [PATCH 1251/5331] adding easyconfigs: WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb and patches: WebKitGTK+-2.24.1_turn_off_various_problematic_features.patch --- .../WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb | 54 ++++++++++++++++ ...urn_off_various_problematic_features.patch | 62 +++++++++++++++++++ 2 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1_turn_off_various_problematic_features.patch diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..a6938230eb6 --- /dev/null +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,54 @@ +easyblock = 'CMakeMake' + +name = 'WebKitGTK+' +version = '2.24.1' + +homepage = 'https://webkitgtk.org/' +description = """WebKitGTK+ is a full-featured port of the WebKit +rendering engine, suitable for projects requiring any kind of web +integration, from hybrid HTML/CSS applications to full-fledged web +browsers. It offers WebKit’s full functionality and is useful in a wide +range of systems from desktop computers to embedded systems like phones, +tablets, and televisions.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['https://webkitgtk.org/releases'] +sources = ['webkitgtk-%(version)s.tar.xz'] +patches = ['%(name)s-%(version)s_turn_off_various_problematic_features.patch'] +checksums = [ + '53cb8eaad2ca4caaae663d68331b83fd27d5bd5f6c5388d6ea3c455e338f396d', # webkitgtk-2.24.1.tar.xz + # WebKitGTK+-2.24.1_turn_off_various_problematic_features.patch + 'e555454ca07a88442acafd6b71e35e99f9ed2049d8f80b39e48b2b04b3d43ae0', +] + +osdependencies = [ + # Would be better to use the system package due to security reasons + # But we need at least libgcrypt 1.7.0 and Ubuntu 16.04 and RH 7.5 + # are both using a too old version. + # ('libgcrypt-dev', 'libgcrypt20-dev', 'libgcrypt-devel'), + ('libsecret-1-dev', 'libsecret-devel'), +] + +builddependencies = [ + ('CMake', '3.13.3'), + ('Perl', '5.28.1'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), +] +dependencies = [ + ('gperf', '3.1'), + ('cairo', '1.16.0'), + ('GTK+', '3.24.8'), + ('LibSoup', '2.66.1'), + ('ATK', '2.32.0'), + ('libgcrypt', '1.8.4'), + ('libwebp', '1.0.2'), + ('libxslt', '1.1.33'), + ('libtasn1', '4.13'), + ('GStreamer', '1.14.4'), + ('OpenJPEG', '2.3.1'), +] + +configopts = "-DPORT=GTK " + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1_turn_off_various_problematic_features.patch b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1_turn_off_various_problematic_features.patch new file mode 100644 index 00000000000..abbf1627d12 --- /dev/null +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1_turn_off_various_problematic_features.patch @@ -0,0 +1,62 @@ +Turning off some features that we either don't need or are somewhat complicated to handle the dependencies for. + +Åke Sandgren, 20190418 +diff -ru webkitgtk-2.22.5.orig/Source/cmake/GStreamerDefinitions.cmake webkitgtk-2.22.5/Source/cmake/GStreamerDefinitions.cmake +--- webkitgtk-2.22.5.orig/Source/cmake/GStreamerDefinitions.cmake 2018-11-05 16:22:07.000000000 +0100 ++++ webkitgtk-2.22.5/Source/cmake/GStreamerDefinitions.cmake 2019-02-08 13:05:24.130109573 +0100 +@@ -1,5 +1,5 @@ +-WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_VIDEO PUBLIC ON) +-WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_WEB_AUDIO PUBLIC ON) ++WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_VIDEO PUBLIC OFF) ++WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_WEB_AUDIO PUBLIC OFF) + + WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_MEDIA_SOURCE PUBLIC ON) + +diff -ru webkitgtk-2.24.1.orig/Source/cmake/OptionsGTK.cmake webkitgtk-2.24.1/Source/cmake/OptionsGTK.cmake +--- webkitgtk-2.24.1.orig/Source/cmake/OptionsGTK.cmake 2019-04-09 10:00:35.000000000 +0200 ++++ webkitgtk-2.24.1/Source/cmake/OptionsGTK.cmake 2019-04-18 21:13:08.407728621 +0200 +@@ -76,15 +76,15 @@ + WEBKIT_OPTION_DEFINE(ENABLE_GTKDOC "Whether or not to use generate gtkdoc." PUBLIC OFF) + WEBKIT_OPTION_DEFINE(ENABLE_INTROSPECTION "Whether to enable GObject introspection." PUBLIC ON) + WEBKIT_OPTION_DEFINE(ENABLE_OPENGL "Whether to use OpenGL." PUBLIC ON) +-WEBKIT_OPTION_DEFINE(ENABLE_PLUGIN_PROCESS_GTK2 "Whether to build WebKitPluginProcess2 to load GTK2 based plugins." PUBLIC ON) ++WEBKIT_OPTION_DEFINE(ENABLE_PLUGIN_PROCESS_GTK2 "Whether to build WebKitPluginProcess2 to load GTK2 based plugins." PUBLIC OFF) + WEBKIT_OPTION_DEFINE(ENABLE_QUARTZ_TARGET "Whether to enable support for the Quartz windowing target." PUBLIC ${GTK3_SUPPORTS_QUARTZ}) + WEBKIT_OPTION_DEFINE(ENABLE_X11_TARGET "Whether to enable support for the X11 windowing target." PUBLIC ${GTK3_SUPPORTS_X11}) + WEBKIT_OPTION_DEFINE(ENABLE_WAYLAND_TARGET "Whether to enable support for the Wayland windowing target." PUBLIC ${GTK3_SUPPORTS_WAYLAND}) +-WEBKIT_OPTION_DEFINE(USE_LIBNOTIFY "Whether to enable the default web notification implementation." PUBLIC ON) +-WEBKIT_OPTION_DEFINE(USE_LIBHYPHEN "Whether to enable the default automatic hyphenation implementation." PUBLIC ON) +-WEBKIT_OPTION_DEFINE(USE_LIBSECRET "Whether to enable the persistent credential storage using libsecret." PUBLIC ON) ++WEBKIT_OPTION_DEFINE(USE_LIBNOTIFY "Whether to enable the default web notification implementation." PUBLIC OFF) ++WEBKIT_OPTION_DEFINE(USE_LIBHYPHEN "Whether to enable the default automatic hyphenation implementation." PUBLIC OFF) ++WEBKIT_OPTION_DEFINE(USE_LIBSECRET "Whether to enable the persistent credential storage using libsecret." PUBLIC OFF) + WEBKIT_OPTION_DEFINE(USE_OPENJPEG "Whether to enable support for JPEG2000 images." PUBLIC ON) +-WEBKIT_OPTION_DEFINE(USE_WOFF2 "Whether to enable support for WOFF2 Web Fonts." PUBLIC ON) ++WEBKIT_OPTION_DEFINE(USE_WOFF2 "Whether to enable support for WOFF2 Web Fonts." PUBLIC OFF) + + # Private options specific to the GTK+ port. Changing these options is + # completely unsupported. They are intended for use only by WebKit developers. +@@ -134,9 +134,9 @@ + WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_ACCELERATED_2D_CANVAS PUBLIC OFF) + WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_ASYNC_SCROLLING PRIVATE ON) + WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_DRAG_SUPPORT PUBLIC ON) +-WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_GEOLOCATION PUBLIC ON) ++WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_GEOLOCATION PUBLIC OFF) + WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_ICONDATABASE PUBLIC ON) +-WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_SPELLCHECK PUBLIC ON) ++WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_SPELLCHECK PUBLIC OFF) + WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_TOUCH_EVENTS PUBLIC ON) + WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_WEB_CRYPTO PUBLIC ON) + WEBKIT_OPTION_DEFAULT_PORT_VALUE(ENABLE_WEBDRIVER PUBLIC ON) +diff -ru webkitgtk-2.24.1.orig/Source/cmake/WebKitFeatures.cmake webkitgtk-2.24.1/Source/cmake/WebKitFeatures.cmake +--- webkitgtk-2.24.1.orig/Source/cmake/WebKitFeatures.cmake 2019-02-14 12:09:09.000000000 +0100 ++++ webkitgtk-2.24.1/Source/cmake/WebKitFeatures.cmake 2019-04-18 21:14:10.051113569 +0200 +@@ -215,7 +215,7 @@ + WEBKIT_OPTION_DEFINE(ENABLE_WEBGL2 "Toggle WebGL2 support" PRIVATE OFF) + WEBKIT_OPTION_DEFINE(ENABLE_WEBGPU "Toggle WebGPU support" PRIVATE OFF) + WEBKIT_OPTION_DEFINE(ENABLE_WEBMETAL "Toggle WebMetal support" PRIVATE OFF) +- WEBKIT_OPTION_DEFINE(ENABLE_WEB_AUDIO "Toggle Web Audio support" PRIVATE ON) ++ WEBKIT_OPTION_DEFINE(ENABLE_WEB_AUDIO "Toggle Web Audio support" PRIVATE OFF) + WEBKIT_OPTION_DEFINE(ENABLE_WEB_AUTHN "Toggle Web AuthN support" PRIVATE OFF) + WEBKIT_OPTION_DEFINE(ENABLE_WEB_CRYPTO "Toggle WebCrypto Subtle-Crypto support" PRIVATE ON) + WEBKIT_OPTION_DEFINE(ENABLE_WEB_RTC "Toggle WebRTC support" PRIVATE OFF) From b9484b0138c076f28f278bc4ad870da8cf6f28b2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 13:07:22 +0200 Subject: [PATCH 1252/5331] Add missing sanity_check --- .../w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb index a6938230eb6..3f693911839 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb @@ -51,4 +51,9 @@ dependencies = [ configopts = "-DPORT=GTK " +sanity_check_paths = { + 'files': ['bin/WebKitWebDriver', 'lib/libwebkit2gtk-4.0.%s' % SHLIB_EXT], + 'dirs': ['include/webkitgtk-4.0/webkit2', 'libexec/webkit2gtk-4.0'], +} + moduleclass = 'lib' From 83633ebba812abb923d01cfcb4b546f42d34af77 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 13:23:01 +0200 Subject: [PATCH 1253/5331] Add missin sanity_check_paths --- easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb | 5 +++++ easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb | 5 +++++ 13 files changed, 65 insertions(+) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb index 3098397ed1d..01b9324df53 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb @@ -23,6 +23,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb index 1f0208e1ee0..c2a9dc97ec0 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb @@ -23,6 +23,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb index 4d2d9727f67..903aa877564 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb @@ -23,6 +23,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb index fa2599d5d55..20478335c2f 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb @@ -23,6 +23,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb index e8e91ac0591..c4dfb4aa1f2 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb @@ -23,6 +23,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb index 967a6b25ed2..da29a06a743 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb @@ -25,6 +25,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb index 3b8f4f86a1f..7c78377569b 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb @@ -24,6 +24,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb index 8a26eefdb3c..522c274bd99 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb @@ -25,6 +25,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb index a583d5ce8cd..790f906aa10 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb @@ -27,6 +27,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb index dc6721786aa..4fdea8f3c39 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb @@ -24,6 +24,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb index 2664ebcd3ee..2998eb97abf 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb @@ -25,6 +25,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb index 98410764762..e80efa1f6da 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb @@ -34,6 +34,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-3.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-3.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb index 11428031459..f9c74eb4060 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb @@ -35,6 +35,11 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-3.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-3.0'], +} + modextrapaths = { 'XDG_DATA_DIRS': 'share', } From 4c41afcc7bab929e99429e7fcd003c5e9832f775 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Apr 2019 13:28:27 +0200 Subject: [PATCH 1254/5331] adding easyconfigs: RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb --- ...RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..dc9c93177cf --- /dev/null +++ b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'RNAIndel' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/stjude/RNAIndel' +description = """RNAIndel calls coding indels and classifies them into somatic, germline, + and artifact from tumor RNA-Seq data.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cb47b4506d704362e471c8ca3757498636d40598c112df216bd56d2e42f7e45f'] + +dependencies = [ + ('Python', '3.6.6'), + ('Pysam', '0.15.1', versionsuffix), + ('scikit-learn', '0.20.0', versionsuffix), + ('Java', '1.8', '', True), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/rnaindel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["rnaindel --help"] + +moduleclass = 'bio' From fff150407e184c2e611636020d986264f933bc80 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 13:35:36 +0200 Subject: [PATCH 1255/5331] Make gtk+v3 sanity_check_paths more generic. --- easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb | 4 ++-- easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb index e80efa1f6da..797e04d0dbd 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb @@ -35,8 +35,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " sanity_check_paths = { - 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-3.%s' % SHLIB_EXT], - 'dirs': ['include/gtk-3.0'], + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-%%(version_major)s.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-%(version_major)s.0'], } modextrapaths = { diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb index f9c74eb4060..c1776bac900 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb @@ -36,8 +36,8 @@ dependencies = [ configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " sanity_check_paths = { - 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-3.%s' % SHLIB_EXT], - 'dirs': ['include/gtk-3.0'], + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-%%(version_major)s.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-%(version_major)s.0'], } modextrapaths = { From 3c9723a9b69f296fcabd4e6669da875c8eddce94 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 14:27:48 +0200 Subject: [PATCH 1256/5331] adding easyconfigs: SDL2-2.0.9-GCCcore-8.2.0.eb --- .../s/SDL2/SDL2-2.0.9-GCCcore-8.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.9-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.9-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.9-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..65889ebcb83 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.9-GCCcore-8.2.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.9' + +homepage = 'http://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['255186dc676ecd0c1dbf10ec8a2cc5d6869b5079d8a38194c2aecdff54b324b1'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [('X11', '20190311')] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 5fc2193bd6c1c6f9d87816f9dcac5d1cbab7baa8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Apr 2019 14:43:40 +0200 Subject: [PATCH 1257/5331] {data}[GCCcore/8.2.0] openpyxl v2.6.2 (+ lxml v4.3.3, Pillow v6.0.0) for Python 2.7.15 & 3.7.2 --- .../l/lxml/lxml-4.3.3-GCCcore-8.2.0.eb | 32 ++++++++++++++++ .../openpyxl/openpyxl-2.6.2-GCCcore-8.2.0.eb | 37 ++++++++++++++++++ .../p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb | 38 +++++++++++++++++++ 3 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/l/lxml/lxml-4.3.3-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-2.6.2-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.3.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.3.3-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..e260a43337d --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-4.3.3-GCCcore-8.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '4.3.3' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] +checksums = ['4a03dd682f8e35a10234904e0b9508d705ff98cf962c5851ed052e9340df3d90'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('libxml2', '2.9.8'), + ('libxslt', '1.1.33'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-2.6.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-2.6.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..982a8b75714 --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-2.6.2-GCCcore-8.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '2.6.2' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('lxml', '4.3.3'), + ('Pillow', '6.0.0'), +] + +use_pip = True + +exts_list = [ + ('et_xmlfile', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/e/et_xmlfile'], + 'checksums': ['614d9722d572f6246302c4491846d2c393c199cfa4edc9af593437691683335b'], + }), + ('jdcal', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/e/j/jdcal'], + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/o/openpyxl'], + 'checksums': ['1d2af392cef8c8227bd2ac3ebe3a28b25aba74fd4fa473ce106065f0b73bfe2e'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..243c594905c --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '6.0.0' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['809c0a2ce9032cbcd7b5313f71af4bdc5c8c771cb86eb7559afd954cab82ebb5'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('libjpeg-turbo', '2.0.2'), + ('libpng', '1.6.36'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.10'), + ('freetype', '2.9.1') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' From 347b760dd65c7d634c7cdeb6cea62cb03d6ed694 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Wed, 24 Apr 2019 14:58:21 +0200 Subject: [PATCH 1258/5331] Boegelbot is really really picky --- .../m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb | 1 - .../m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb | 1 - .../m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb | 1 - .../matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb | 1 - 4 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb index 5607a2e2fee..c3055d9ac50 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb @@ -11,7 +11,6 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'foss', 'version': '2019a'} -download_dep_fail = True use_pip = True builddependencies = [ diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb index 9c769daa06e..bcde5d12ec5 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb @@ -11,7 +11,6 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'fosscuda', 'version': '2019a'} -download_dep_fail = True use_pip = True builddependencies = [ diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb index 30bff8be078..d4c946b7d88 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb @@ -11,7 +11,6 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'intel', 'version': '2019a'} -download_dep_fail = True use_pip = True check_ldshared = True diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb index 0ba7d08abfe..bf83aa2a5f0 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb @@ -11,7 +11,6 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'intelcuda', 'version': '2019a'} -download_dep_fail = True use_pip = True check_ldshared = True From 711b14c1f6e7034225aa51cb5da7d62df48bf141 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 15:11:30 +0200 Subject: [PATCH 1259/5331] adding easyconfigs: GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb --- .../GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..4e59c323248 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '1.16.0' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0e8e2f7118be437cba879353970cf83c2acced825ecb9275ba05d9186ef07c00'] + +builddependencies = [ + ('Bison', '3.0.5'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), + ('gettext', '0.19.8.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.60.1'), + ('zlib', '1.2.11'), + ('libunwind', '1.3.1'), +] + +configopts = '--with-dw=no ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' From d9bc1e9fdb49e686bf3238c1f1f7b4607fe7134e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 15:14:00 +0200 Subject: [PATCH 1260/5331] Update to use GStreamer 1.16.0 --- .../w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb index 3f693911839..79efbd5f30a 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb @@ -45,7 +45,7 @@ dependencies = [ ('libwebp', '1.0.2'), ('libxslt', '1.1.33'), ('libtasn1', '4.13'), - ('GStreamer', '1.14.4'), + ('GStreamer', '1.16.0'), ('OpenJPEG', '2.3.1'), ] From 4b4a83936eff7e720115c5a0ee1e5df4ea9f569f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Apr 2019 15:29:07 +0200 Subject: [PATCH 1261/5331] PythonBundle already has a decent customised sanity_check_paths for bundles of Python packages --- test/easyconfigs/easyconfigs.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index ff52df696f8..53033c8c7ff 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -428,10 +428,16 @@ def check_python_packages(self, changed_ecs): def check_sanity_check_paths(self, changed_ecs): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" + # PythonBundle already has a decent customised sanity_check_paths for bundles of Python packages + whitelist = ['PythonBundle'] + failing_checks = [] for ec in changed_ecs: - if is_generic_easyblock(ec.get('easyblock')) and not ec.get('sanity_check_paths'): + + easyblock = ec.get('easyblock') + + if is_generic_easyblock(easyblock) and easyblock not in whitelist and not ec.get('sanity_check_paths'): ec_fn = os.path.basename(ec.path) failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) From c00272f38416f981ae387ea7695390c1340fd9bc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 15:32:40 +0200 Subject: [PATCH 1262/5331] adding easyconfigs: GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb --- ...ST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..abd483fb871 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '1.16.0' + +homepage = 'http://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] + +builddependencies = [ + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), + ('Bison', '3.0.5'), +] + +dependencies = [ + ('GStreamer', '1.16.0'), + ('gettext', '0.19.8.1'), + ('Mesa', '19.0.1'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' From 430028800f11bb21b22a7d6e8c0e54bbc8db1a4e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Apr 2019 15:44:14 +0200 Subject: [PATCH 1263/5331] adding easyconfigs: wxWidgets-3.0.4-GCC-8.2.0-2.31.1.eb --- .../wxWidgets-3.0.4-GCC-8.2.0-2.31.1.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.0.4-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.0.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.0.4-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..4c0ce3cd20f --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.0.4-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.0.4' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/wxWidgets/wxWidgets/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e176e339d4475d7f1e24b1e479959e58fac64516189d4ba2df3f2fb9e4719c84'] + +builddependencies = [ + ('gettext', '0.19.8.1'), +] + +dependencies = [ + ('libpng', '1.6.36'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.2'), + ('LibTIFF', '4.0.10'), + ('expat', '2.2.6'), + ('GTK+', '3.24.8'), + ('Mesa', '19.0.1'), + ('libGLU', '9.0.0'), + ('SDL2', '2.0.9'), + ('GST-plugins-base', '1.16.0'), + ('GLib', '2.60.1'), + ('WebKitGTK+', '2.24.1'), +] + +preconfigopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' + +prebuildopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major)s.0/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From a8184ae4c6d3d0bbca75a9e80a2f444ca1b9e61f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Apr 2019 15:49:21 +0200 Subject: [PATCH 1264/5331] PythonPackage also has a decent custom sanity_check_paths already --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 53033c8c7ff..5da46a777cc 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -428,8 +428,8 @@ def check_python_packages(self, changed_ecs): def check_sanity_check_paths(self, changed_ecs): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" - # PythonBundle already has a decent customised sanity_check_paths for bundles of Python packages - whitelist = ['PythonBundle'] + # PythonBundle & PythonPackage already have a decent customised sanity_check_paths + whitelist = ['PythonBundle', 'PythonPackage'] failing_checks = [] From 656a70a2bdb15aa6f2e2a84d6e2866cb816d258c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 24 Apr 2019 09:24:46 -0500 Subject: [PATCH 1265/5331] adding easyconfigs: Anaconda2-2019.03.eb, Anaconda3-2019.03.eb --- .../a/Anaconda2/Anaconda2-2019.03.eb | 21 ++++++++++++++++++ .../a/Anaconda3/Anaconda3-2019.03.eb | 22 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.03.eb create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.03.eb diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.03.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.03.eb new file mode 100644 index 00000000000..7f36c2c856a --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.03.eb @@ -0,0 +1,21 @@ +# author: Jillian Rowe +# config upgrade to v5.0.1, v5.1.0, v5.3.0, v2018.12 by Joachim Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda2' +version = '2019.03' + +homepage = 'https://www.continuum.io/anaconda-overview' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://repo.continuum.io/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['cedfee5b5a3f62fcdac0a1d2d12396d0f232d2213d24d6dc893df5d8e64b8773'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.03.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.03.eb new file mode 100644 index 00000000000..ad7d7c70a14 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.03.eb @@ -0,0 +1,22 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12 by Joachim Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2019.03' + +homepage = 'https://www.continuum.io/anaconda-overview' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://repo.continuum.io/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['45c851b7497cc14d5ca060064394569f724b67d9b5f98a926ed49b834a6bb73a'] + +moduleclass = 'lang' From b5b334324945cf27ec28167724987c04e86f786a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Apr 2019 16:33:17 +0200 Subject: [PATCH 1266/5331] update to metaWRAP 1.2 --- ...n-2.7.15.eb => metaWRAP-1.2-foss-2018b-Python-2.7.15.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/m/metaWRAP/{metaWRAP-1.1.5-foss-2018b-Python-2.7.15.eb => metaWRAP-1.2-foss-2018b-Python-2.7.15.eb} (93%) diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.1.5-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb similarity index 93% rename from easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.1.5-foss-2018b-Python-2.7.15.eb rename to easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb index 3c5a2be60ce..3bca1951011 100644 --- a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.1.5-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb @@ -1,8 +1,8 @@ easyblock = 'Tarball' name = 'metaWRAP' -commit = '689cb92' -version = '1.1.5' +commit = '16a1135' +version = '1.2' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/bxlab/metaWRAP' @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/bxlab/metaWRAP/archive/'] sources = [{'download_filename': '%s.tar.gz' % commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['4aee033cd4af0b59525dffb792c074c6948c8bfc0552645f3639a975ac78e3b7'] +checksums = ['31688b02bf74871973569ce685985687277a9466078a3786b64f5504917ebc17'] # see https://github.com/bxlab/metaWRAP/blob/master/installation/dependancies.md dependencies = [ From 00089ef026440eb5e4b0333db18c91c8dc5f61fb Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 24 Apr 2019 16:25:15 -0500 Subject: [PATCH 1267/5331] Added required dependency packages --- .../cutadapt-1.16-foss-2017b-Python-2.7.14.eb | 22 ++++++++++++++----- .../cutadapt-1.16-foss-2017b-Python-3.6.3.eb | 22 ++++++++++++++----- ...cutadapt-1.16-intel-2017b-Python-2.7.14.eb | 22 ++++++++++++++----- .../cutadapt-1.16-intel-2017b-Python-3.6.3.eb | 22 ++++++++++++++----- 4 files changed, 64 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb index 9c55f5133d2..9f8d094d4ad 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-2.7.14.eb @@ -7,7 +7,7 @@ # Modified by: Albert Bogdanowicz # Institute of Biochemistry and Biophysics PAS -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'cutadapt' version = '1.16' @@ -19,16 +19,26 @@ description = """Cutadapt finds and removes adapter sequences, primers, poly-A t toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'] - dependencies = [ ('Python', '2.7.14'), ] use_pip = True -download_dep_fail = True + +exts_list = [ + ('bz2file', '0.98', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('xopen', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], + 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], + 'checksums': ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'], + }), +] sanity_check_paths = { 'files': ['bin/cutadapt'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb index be5125cab5b..8784bad6041 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb @@ -7,7 +7,7 @@ # Modified by: Albert Bogdanowicz # Institute of Biochemistry and Biophysics PAS -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'cutadapt' version = '1.16' @@ -19,16 +19,26 @@ description = """Cutadapt finds and removes adapter sequences, primers, poly-A t toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'] - dependencies = [ ('Python', '3.6.3'), ] use_pip = True -download_dep_fail = True + +exts_list = [ + ('bz2file', '0.98', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('xopen', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], + 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], + 'checksums': ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'], + }), +] sanity_check_paths = { 'files': ['bin/cutadapt'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb index 54d2f0b83cc..3ddabadd1a7 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-2.7.14.eb @@ -4,7 +4,7 @@ # Biozentrum - University of Basel # Modified by: Adam Huffman (The Francis Crick Institute), Kenneth Hoste (HPC-UGent) -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'cutadapt' version = '1.16' @@ -16,16 +16,26 @@ description = """Cutadapt finds and removes adapter sequences, primers, poly-A t toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'] - dependencies = [ ('Python', '2.7.14'), ] use_pip = True -download_dep_fail = True + +exts_list = [ + ('bz2file', '0.98', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('xopen', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], + 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], + 'checksums': ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'], + }), +] sanity_check_paths = { 'files': ['bin/cutadapt'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb index 22e388a1ff3..ffd35630e41 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb @@ -4,7 +4,7 @@ # Biozentrum - University of Basel # Modified by: Adam Huffman (The Francis Crick Institute), Kenneth Hoste (HPC-UGent) -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'cutadapt' version = '1.16' @@ -16,16 +16,26 @@ description = """Cutadapt finds and removes adapter sequences, primers, poly-A t toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'] - dependencies = [ ('Python', '3.6.3'), ] use_pip = True -download_dep_fail = True + +exts_list = [ + ('bz2file', '0.98', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('xopen', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], + 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], + 'checksums': ['9432045dcf59802ef9bb2d1f7232e8a015eb9b984e7c7ff35a6c8a57681e7a79'], + }), +] sanity_check_paths = { 'files': ['bin/cutadapt'], From c23f8f15c9b3271edf5613788547954184e70517 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 25 Apr 2019 07:08:46 +0200 Subject: [PATCH 1268/5331] fix conflict with easybuild/system curl --- easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-foss-2018b.eb | 1 + 1 file changed, 1 insertion(+) mode change 100755 => 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-foss-2018b.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-foss-2018b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-foss-2018b.eb old mode 100755 new mode 100644 index 4c83b857565..6e48cfa7fbb --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-foss-2018b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-foss-2018b.eb @@ -33,6 +33,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.4'), + ('cURL', '7.60.0'), ] moduleclass = 'bio' From 1f90e275c39206e9c1f9bf43f4bba3cf289e8f0f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 07:47:06 +0200 Subject: [PATCH 1269/5331] adding easyconfigs: wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb, wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb and patches: wxPython-4.0.4_use_bang_env_python.patch, wxPython-4.0.4_fix_install_path.patch --- ...on-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb | 47 +++++++++++++++++++ ...hon-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb | 47 +++++++++++++++++++ .../wxPython-4.0.4_fix_install_path.patch | 19 ++++++++ .../wxPython-4.0.4_use_bang_env_python.patch | 40 ++++++++++++++++ 4 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-4.0.4_fix_install_path.patch create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-4.0.4_use_bang_env_python.patch diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb new file mode 100644 index 00000000000..acb423f97f0 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb @@ -0,0 +1,47 @@ +name = 'wxPython' +version = '4.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.wxpython.org' +description = """wxPython is a GUI toolkit for the Python programming language. + It allows Python programmers to create programs with a robust, + highly functional graphical user interface, simply and easily. + It is implemented as a Python extension module (native code) + that wraps the popular wxWidgets cross platform GUI library, + which is written in C++.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = [PYPI_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fix_install_path.patch', + '%(name)s-%(version)s_use_bang_env_python.patch', +] +checksums = [ + '0d9ef4260cb2f3e23ed9dcf6baa905ba585ac7d631613cddc299c4c83463ae29', # wxPython-4.0.4.tar.gz + 'dff61add598072f1816cf91f51fa57da191389f5cc52c3b53bf902c547d13af0', # wxPython-4.0.4_fix_install_path.patch + 'c355c60a8cce3018fc0c30ffc78623efd2481e9baf33673e22a57863e1a3ac87', # wxPython-4.0.4_use_bang_env_python.patch +] + +dependencies = [ + ('Python', '2.7.15'), + ('libpng', '1.6.36'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.2'), + ('LibTIFF', '4.0.10'), + ('expat', '2.2.6'), + ('GTK+', '3.24.8'), + ('GLib', '2.60.1'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '1.16.0'), + ('Mesa', '19.0.1'), + ('libGLU', '9.0.0'), + ('LibSoup', '2.66.1'), + ('WebKitGTK+', '2.24.1'), + ('wxWidgets', '3.0.4'), +] + +preinstallopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb new file mode 100644 index 00000000000..075fdd92430 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb @@ -0,0 +1,47 @@ +name = 'wxPython' +version = '4.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.wxpython.org' +description = """wxPython is a GUI toolkit for the Python programming language. + It allows Python programmers to create programs with a robust, + highly functional graphical user interface, simply and easily. + It is implemented as a Python extension module (native code) + that wraps the popular wxWidgets cross platform GUI library, + which is written in C++.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = [PYPI_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fix_install_path.patch', + '%(name)s-%(version)s_use_bang_env_python.patch', +] +checksums = [ + '0d9ef4260cb2f3e23ed9dcf6baa905ba585ac7d631613cddc299c4c83463ae29', # wxPython-4.0.4.tar.gz + 'dff61add598072f1816cf91f51fa57da191389f5cc52c3b53bf902c547d13af0', # wxPython-4.0.4_fix_install_path.patch + 'c355c60a8cce3018fc0c30ffc78623efd2481e9baf33673e22a57863e1a3ac87', # wxPython-4.0.4_use_bang_env_python.patch +] + +dependencies = [ + ('Python', '3.7.2'), + ('libpng', '1.6.36'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.2'), + ('LibTIFF', '4.0.10'), + ('expat', '2.2.6'), + ('GTK+', '3.24.8'), + ('GLib', '2.60.1'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '1.16.0'), + ('Mesa', '19.0.1'), + ('libGLU', '9.0.0'), + ('LibSoup', '2.66.1'), + ('WebKitGTK+', '2.24.1'), + ('wxWidgets', '3.0.4'), +] + +preinstallopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4_fix_install_path.patch b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4_fix_install_path.patch new file mode 100644 index 00000000000..eee014c81b2 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4_fix_install_path.patch @@ -0,0 +1,19 @@ +build.py calls setup.py without a prefix, this fixes that. + +Åke Sandgren, 20190201 +diff -ru wxPython-4.0.4.orig/build.py wxPython-4.0.4/build.py +--- wxPython-4.0.4.orig/build.py 2019-01-05 20:48:40.000000000 +0100 ++++ wxPython-4.0.4/build.py 2019-02-01 10:23:21.170098819 +0100 +@@ -1577,9 +1577,10 @@ + def cmd_install_py(options, args): + cmdTimer = CommandTimer('install_py') + DESTDIR = '' if not options.destdir else '--root=' + options.destdir ++ PREFIX = '' if not options.prefix else '--prefix=' + options.prefix + VERBOSE = '--verbose' if options.verbose else '' +- cmd = '"%s" setup.py install --skip-build %s %s %s' % ( +- PYTHON, DESTDIR, VERBOSE, options.extra_setup) ++ cmd = '"%s" setup.py install --skip-build %s %s %s %s' % ( ++ PYTHON, DESTDIR, PREFIX, VERBOSE, options.extra_setup) + runcmd(cmd) + + diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4_use_bang_env_python.patch b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4_use_bang_env_python.patch new file mode 100644 index 00000000000..387d18f2da6 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4_use_bang_env_python.patch @@ -0,0 +1,40 @@ +Don't use system python. +This is perhaps not needed but doesn't hurt. + +Åke Sandgren, 20190425 +diff -ru wxPython-4.0.4.orig/build.py wxPython-4.0.4/build.py +--- wxPython-4.0.4.orig/build.py 2019-01-05 20:48:40.000000000 +0100 ++++ wxPython-4.0.4/build.py 2019-04-24 21:37:32.296782206 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + #---------------------------------------------------------------------- + # Name: build.py + # Purpose: Master build controller script. +diff -ru wxPython-4.0.4.orig/ext/wxWidgets/build/osx/fix_xcode_ids.py wxPython-4.0.4/ext/wxWidgets/build/osx/fix_xcode_ids.py +--- wxPython-4.0.4.orig/ext/wxWidgets/build/osx/fix_xcode_ids.py 2019-01-03 00:48:23.000000000 +0100 ++++ wxPython-4.0.4/ext/wxWidgets/build/osx/fix_xcode_ids.py 2019-04-24 21:37:37.508731582 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + ############################################################################### + # Name: build/osx/fix_xcode_ids.py +diff -ru wxPython-4.0.4.orig/ext/wxWidgets/misc/scripts/png2c.py wxPython-4.0.4/ext/wxWidgets/misc/scripts/png2c.py +--- wxPython-4.0.4.orig/ext/wxWidgets/misc/scripts/png2c.py 2019-01-03 00:48:23.000000000 +0100 ++++ wxPython-4.0.4/ext/wxWidgets/misc/scripts/png2c.py 2019-04-24 21:37:35.300753028 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # This script is a slightly modified version of the original found at + # +diff -ru wxPython-4.0.4.orig/wscript wxPython-4.0.4/wscript +--- wxPython-4.0.4.orig/wscript 2019-01-05 20:48:40.000000000 +0100 ++++ wxPython-4.0.4/wscript 2019-04-24 21:37:40.556701977 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + #----------------------------------------------------------------------------- + # WAF script for building and installing the wxPython extension modules. + # From a3c2a7ac251042ef700abf857797af00e386d369 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 08:40:24 +0200 Subject: [PATCH 1270/5331] adding easyconfigs: pkgconfig-1.5.1-GCCcore-8.2.0.eb --- .../pkgconfig-1.5.1-GCCcore-8.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..fdea69e249c --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'pkgconfig' +version = '1.5.1' + +homepage = 'http://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [('pkg-config', '0.29.2')] + +exts_list = [ + ('poetry', '0.12.12', { + 'source_urls': ['https://pypi.python.org/packages/source/p/poetry/'], + 'checksums': ['726420e7519e069d9245ebac3f1c367b7ef9aca420c6911a9261772c7c814a2d'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/p/pkgconfig/'], + 'checksums': ['97bfe3d981bab675d5ea3ef259045d7919c93897db7d3b59d4e8593cba8d354f'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'devel' From 3b11567ea41ffd576d8f6737d47078a5ecce37e0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 08:43:06 +0200 Subject: [PATCH 1271/5331] adding easyconfigs: HDF5-1.10.5-gompic-2019a.eb, HDF5-1.10.5-iimpic-2019a.eb --- .../h/HDF5/HDF5-1.10.5-gompic-2019a.eb | 21 +++++++++++++++++++ .../h/HDF5/HDF5-1.10.5-iimpic-2019a.eb | 21 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-gompic-2019a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpic-2019a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-gompic-2019a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-gompic-2019a.eb new file mode 100644 index 00000000000..40bd6365d90 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-gompic-2019a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.5' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompic', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpic-2019a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpic-2019a.eb new file mode 100644 index 00000000000..9e31a37e081 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-iimpic-2019a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.5' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpic', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From c3c03f7306d21a8ada588fa9f3770e98232cba0a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 09:17:23 +0200 Subject: [PATCH 1272/5331] This version of pkgconfig cant use pip. --- .../easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb index fdea69e249c..4e7799f3499 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb @@ -14,6 +14,8 @@ builddependencies = [('binutils', '2.31.1')] dependencies = [('pkg-config', '0.29.2')] +use_pip = False + exts_list = [ ('poetry', '0.12.12', { 'source_urls': ['https://pypi.python.org/packages/source/p/poetry/'], From 067d19706a7f33f73d78900270dfcc13df2cafa4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 10:15:44 +0200 Subject: [PATCH 1273/5331] adding easyconfigs: h5py-2.9.0-foss-2019a-Python-2.7.15.eb, h5py-2.9.0-foss-2019a-Python-3.7.2.eb, h5py-2.9.0-fosscuda-2019a-Python-2.7.15.eb, h5py-2.9.0-fosscuda-2019a-Python-3.7.2.eb, h5py-2.9.0-intel-2019a-Python-2.7.15.eb, h5py-2.9.0-intel-2019a-Python-3.7.2.eb, h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb, h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb --- .../h5py-2.9.0-foss-2019a-Python-2.7.15.eb | 34 +++++++++++++++++++ .../h5py-2.9.0-foss-2019a-Python-3.7.2.eb | 34 +++++++++++++++++++ ...h5py-2.9.0-fosscuda-2019a-Python-2.7.15.eb | 34 +++++++++++++++++++ .../h5py-2.9.0-fosscuda-2019a-Python-3.7.2.eb | 34 +++++++++++++++++++ .../h5py-2.9.0-intel-2019a-Python-2.7.15.eb | 34 +++++++++++++++++++ .../h5py-2.9.0-intel-2019a-Python-3.7.2.eb | 34 +++++++++++++++++++ ...5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb | 34 +++++++++++++++++++ ...h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb | 34 +++++++++++++++++++ 8 files changed, 272 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..d9d0d5fff25 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-2.7.15.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.15'), + ('SciPy-bundle', '2019.03'), + ('pkgconfig', '1.5.1'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..b14f692498d --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('pkgconfig', '1.5.1'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..84789a878ce --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-2.7.15.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.15'), + ('SciPy-bundle', '2019.03'), + ('pkgconfig', '1.5.1'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..e348a8a8a21 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-3.7.2.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('pkgconfig', '1.5.1'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..e1f25e81c70 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.15'), + ('SciPy-bundle', '2019.03'), + ('pkgconfig', '1.5.1'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..ba35a7cbd79 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('pkgconfig', '1.5.1'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..37d8ec82c96 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intelcuda', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.15'), + ('SciPy-bundle', '2019.03'), + ('pkgconfig', '1.5.1'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..1211d63d0c0 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intelcuda', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('pkgconfig', '1.5.1'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' From 906c68f79faaa3ece32436acfaaec3a94e8609d9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 25 Apr 2019 11:20:30 +0200 Subject: [PATCH 1274/5331] use ANTLR without Python dep --- .../a/ANTLR/ANTLR-2.7.7-foss-2018b.eb | 31 +++++++++++++++++++ .../easyconfigs/n/NCO/NCO-4.7.9-foss-2018b.eb | 2 +- 2 files changed, 32 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb new file mode 100644 index 00000000000..867b9d56beb --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' + +homepage = 'http://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['http://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +dependencies = [('Java', '1.8', '', True)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.7.9-foss-2018b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.7.9-foss-2018b.eb index b6458c27e17..14059b63174 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-4.7.9-foss-2018b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-4.7.9-foss-2018b.eb @@ -20,7 +20,7 @@ builddependencies = [ dependencies = [ ('UDUNITS', '2.2.26'), ('expat', '2.2.5'), - ('ANTLR', '2.7.7', '-Python-3.6.6'), + ('ANTLR', '2.7.7'), ('libdap', '3.20.3'), ('GSL', '2.5'), ('netCDF', '4.6.1'), From 4b51044ba3c3007b5ec7e4c2b722e488386c7860 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Thu, 25 Apr 2019 11:12:42 +0100 Subject: [PATCH 1275/5331] Use the correct CUDA for fosscuda depending on the architecture --- .../c/CUDA/CUDA-9.2.88-1-ppc64le.eb | 46 +++++++++++++++++++ .../easyconfigs/f/fosscuda/fosscuda-2018b.eb | 4 +- 2 files changed, 49 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-1-ppc64le.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-1-ppc64le.eb b/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-1-ppc64le.eb new file mode 100644 index 00000000000..005ab9d430d --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-1-ppc64le.eb @@ -0,0 +1,46 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham +easyblock = 'Tarball' +name = 'CUDA' +version = '9.2.88-1' +versionsuffix = '-ppc64le' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Manually create the source tarball like this: +# Install CUDA 9.2.88 on a ppc64le machine (via the RPMS) +# for x in $(rpm -qa |grep cuda); do echo "$x "; done > cuda_rpms +# rpm -ql $(cuda_rpms) > cuda_files +# tar cvzf cuda-9.2.88-1.ppc64le.tar.gz $(cuda_files) +sources = ['cuda-%(version)s.ppc64le.tar.gz'] +checksums = ['4a220b07919162c891c0e1b6327057d9775d74b9ba89c995a05600ab9d326d78'] + +postinstallcmds = [ + # We don't want the nccl libraries that may have been bundled with CUDA. They cause conflicts in PyTorch. + 'cd %(installdir)s && find . -name *nccl* -delete', + 'cd %(installdir)s && mv usr/local/cuda-9.2/* . ', + 'cd %(installdir)s && mv usr/lib64/pkgconfig . ', + 'cd %(installdir)s && rmdir usr/local/cuda-9.2 && rmdir usr/local && rmdir usr/lib64 && rmdir usr', +] + +modextrapaths = { + 'LD_LIBRARY_PATH': ('targets/ppc64le-linux/lib', 'extras/CUPTI/lib64'), + 'LIBRARY_PATH': 'lib64' +} + +modextravars = { + 'CUDA_HOME': '', + 'CUDA_ROOT': '', +} + +sanity_check_paths = { + 'files': ['bin/nvcc', 'bin/ptxas'], + 'dirs': ['include', 'pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb index 1de9a43aa60..844664be610 100644 --- a/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb @@ -24,7 +24,9 @@ comp_mpi_tc = (comp_mpi_tc_name, version) # because of toolchain preperation functions dependencies = [ ('GCC', gccver), # part of gompic - ('CUDA', '9.2.88', '', ('GCC', gccver)), # part of gompic + {'name': 'CUDA', 'version': '9.2.88', 'toolchain': ('GCC', gccver), 'arch': True}, + {'name': 'CUDA', 'version': '9.2.88-1', 'toolchain': ('dummy', 'dummy'), + 'versionsuffix': '-ppc64le', 'arch': 'POWER'}, ('OpenMPI', '3.1.1', '', ('gcccuda', version)), # part of gompic (blaslib, blasver, '', ('GCC', gccver)), ('FFTW', '3.3.8', '', comp_mpi_tc), From 9ca4fea97f9488bb7e6c6221f72bc1f8c9fe5fff Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Thu, 25 Apr 2019 11:40:48 +0100 Subject: [PATCH 1276/5331] Corresponding changes to gcccuda and gompic to match fosscuda --- easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb | 4 +++- easybuild/easyconfigs/g/gompic/gompic-2018b.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb index 2f9c39e59c3..b32f0d87c3f 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb @@ -15,7 +15,9 @@ comp = (comp_name, comp_ver) # compiler toolchain dependencies dependencies = [ comp, - ('CUDA', '9.2.88', '', comp), + {'name': 'CUDA', 'version': '9.2.88', 'toolchain': comp, 'arch': True}, + {'name': 'CUDA', 'version': '9.2.88-1', 'toolchain': ('dummy', 'dummy'), + 'versionsuffix': '-ppc64le', 'arch': 'POWER'}, ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2018b.eb b/easybuild/easyconfigs/g/gompic/gompic-2018b.eb index d855fd56301..65c213f9842 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2018b.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2018b.eb @@ -16,7 +16,9 @@ comp = (comp_name, comp_ver) # compiler toolchain dependencies dependencies = [ comp, # part of gcccuda - ('CUDA', '9.2.88', '', comp), # part of gcccuda + {'name': 'CUDA', 'version': '9.2.88', 'toolchain': comp, 'arch': True}, # part of gcccuda + {'name': 'CUDA', 'version': '9.2.88-1', 'toolchain': ('dummy', 'dummy'), + 'versionsuffix': '-ppc64le', 'arch': 'POWER'}, # part of gcccuda ('OpenMPI', '3.1.1', '', ('gcccuda', version)), ] From 9e6dbc6909972d1e88b3d7a46165d26b64c02ace Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Thu, 25 Apr 2019 11:42:05 +0100 Subject: [PATCH 1277/5331] Use the dedicated OpenBLAS easyblock to support POWER builds --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb index a6985ac7ae7..4665e38da8f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'OpenBLAS' version = '0.3.1' From ff543b586b3460087bae2b84c83fad0cb7cc0f2e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 13:00:33 +0200 Subject: [PATCH 1278/5331] Intel builds need check_ldshared. --- .../easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb | 3 +++ .../easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb | 3 +++ .../h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb | 3 +++ .../h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb | 3 +++ 4 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb index e1f25e81c70..3618c9fa54c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb @@ -16,6 +16,9 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb index ba35a7cbd79..e61d541a2cb 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb @@ -16,6 +16,9 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb index 37d8ec82c96..947d1b971ec 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb @@ -16,6 +16,9 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb index 1211d63d0c0..34cbf7f5e64 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb @@ -16,6 +16,9 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + # to really use mpi enabled hdf5 we now seem to need a configure step prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' From c31d9b89ea97cd4689925bd4e1932947b42a2e2f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 25 Apr 2019 13:31:14 +0200 Subject: [PATCH 1279/5331] adding easyconfigs: Arb-2.16.0-GCCcore-7.3.0.eb, FLINT-2.5.2-GCCcore-7.3.0.eb --- .../a/Arb/Arb-2.16.0-GCCcore-7.3.0.eb | 38 +++++++++++++++++++ .../f/FLINT/FLINT-2.5.2-GCCcore-7.3.0.eb | 37 ++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..723f110c18b --- /dev/null +++ b/easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCCcore-7.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Arb' +version = '2.16.0' + +homepage = 'http://%(namelower)slib.org' + +description = """Arb is a C library for arbitrary-precision interval arithmetic. + It has full support for both real and complex numbers. The library is thread-safe, + portable, and extensively tested.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +github_account = 'fredrik-johansson' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['77464be4d34a511bb004457f862fec857ff934b0ed58d56d6f52d76ebadd4daf'] + +builddependencies = [ + ('binutils', '2.30'), +] + +dependencies = [ + ('FLINT', '2.5.2'), + ('GMP', '6.1.2'), + ('MPFR', '4.0.1'), +] + +configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpir=$EBROOTMPIR' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..e90fcf75ff1 --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCCcore-7.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'FLINT' +version = '2.5.2' + +homepage = 'http://www.%(namelower)slib.org' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://www.%(namelower)slib.org'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cbf1fe0034533c53c5c41761017065f85207a1b770483e98b2392315f6575e87'] + +builddependencies = [ + ('binutils', '2.30'), +] + +dependencies = [ + ('GMP', '6.1.2'), + ('MPFR', '4.0.1'), +] + +configopts = '--with-gmp=$EBROOTGMP --with-mpir=$EBROOTMPIR' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' From e62d8c6e83dc97cb4d1b8d16c51249e783224b0f Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Thu, 25 Apr 2019 14:03:34 +0200 Subject: [PATCH 1280/5331] adding easyconfig for vtune2019u3, +download URL for vtune2018u3 --- .../easyconfigs/v/VTune/VTune-2018_update3.eb | 1 + .../easyconfigs/v/VTune/VTune-2019_update3.eb | 14 ++++++++++++++ 2 files changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb index 0bedbd3bc2b..eaf62006e25 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb @@ -7,6 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo toolchain = {'name': 'dummy', 'version': 'dummy'} +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13079/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['a47e3b304b993bc28190d7efaac29dcb4a9b533837f2fe4cd9d5617c537f568a'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb new file mode 100644 index 00000000000..8ca6b50437e --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb @@ -0,0 +1,14 @@ +name = 'VTune' +version = '2019_update3' + +homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15214/'] +sources = ['vtune_amplifier_%(version)s.tar.gz'] +checksums = ['d873abd0e98b477056030f3520fc8dfb1521dbb4dfaa6d20d830af02ec12a12d'] + +moduleclass = 'tools' From dc28d38674e62ea52f476dead73e4c6e8131dd1e Mon Sep 17 00:00:00 2001 From: jose_d Date: Thu, 25 Apr 2019 14:06:54 +0200 Subject: [PATCH 1281/5331] vtune: updated homepage URL --- easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb index 8ca6b50437e..e1d77dcfea1 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb @@ -1,7 +1,7 @@ name = 'VTune' version = '2019_update3' -homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' +homepage = 'https://software.intel.com/en-us/vtune' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" From 37a29b577034f7a50f51a9860b800f289551a025 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 25 Apr 2019 14:33:40 +0200 Subject: [PATCH 1282/5331] Delete ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb --- .../ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb deleted file mode 100644 index c39ebbf2028..00000000000 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ANTLR' -version = '2.7.7' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.antlr2.org/' -description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) - is a language tool that provides a framework for constructing recognizers, - compilers, and translators from grammatical descriptions containing - Java, C#, C++, or Python actions.""" - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = ['http://www.antlr2.org/download/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_includes.patch'] -checksums = [ - '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz - 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch -] - -dependencies = [ - ('Java', '1.8', '', True), - ('Python', '3.6.6'), -] - -configopts = '--disable-examples --disable-csharp ' - -sanity_check_paths = { - 'files': ['bin/antlr', 'bin/antlr-config'], - 'dirs': ['include'], -} - -moduleclass = 'tools' From 407a298e65aeead6af09567d3d260f9a8ee36033 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Thu, 25 Apr 2019 14:57:47 +0200 Subject: [PATCH 1283/5331] adding easyconfig for advisor2019u3, +download URL for advisor2019u2 --- .../a/Advisor/Advisor-2019_update2.eb | 1 + .../a/Advisor/Advisor-2019_update3.eb | 19 +++++++++++++++++++ 2 files changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb index c32ef0a445f..423480bc2c7 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb @@ -10,6 +10,7 @@ description = """Vectorization Optimization and Thread Prototyping toolchain = {'name': 'dummy', 'version': 'dummy'} +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15084/'] sources = ['advisor_%(version)s.tar.gz'] checksums = ['b63e11b0601013ad21789869ad76be5a836da566ee47c125dcda19ff8277de77'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb new file mode 100644 index 00000000000..0df139ad774 --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb @@ -0,0 +1,19 @@ +name = 'Advisor' +version = '2019_update3' + +homepage = 'https://software.intel.com/intel-advisor-xe' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15206/'] +sources = ['advisor_%(version)s.tar.gz'] +checksums = ['6597f165dee3c6444eb0f38a9069327d10584b09555f5d2c4ed86b8f84d980bb'] + +dontcreateinstalldir = 'True' + +moduleclass = 'perf' From b20c194fe58a36ab311225416156cd552e3c78dd Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 16:34:35 +0200 Subject: [PATCH 1284/5331] adding easyconfigs: GSL-2.5-GCC-8.2.0-2.31.1.eb --- .../g/GSL/GSL-2.5-GCC-8.2.0-2.31.1.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.5-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GSL/GSL-2.5-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..1018d5599aa --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.5-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.5' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0460ad7c2542caaddc6729762952d345374784100223995eb14d614861f2258d'] + +moduleclass = 'numlib' From aedac79de8445283963df508c702d92631e90557 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 25 Apr 2019 16:59:01 +0200 Subject: [PATCH 1285/5331] adding easyconfigs: scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb, Boost.Python-1.67.0-foss-2018b-Python-3.6.6.eb, cairomm-1.12.2-GCCcore-7.3.0.eb, CGAL-4.11.1-foss-2018b-Python-3.6.6.eb, graph-tool-2.27-foss-2018b-Python-3.6.6.eb --- ...t.Python-1.67.0-foss-2018b-Python-3.6.6.eb | 29 +++++++++++ .../CGAL-4.11.1-foss-2018b-Python-3.6.6.eb | 37 ++++++++++++++ .../c/cairomm/cairomm-1.12.2-GCCcore-7.3.0.eb | 26 ++++++++++ ...graph-tool-2.27-foss-2018b-Python-3.6.6.eb | 48 +++++++++++++++++++ ...ultilearn-0.2.0-foss-2018b-Python-3.6.6.eb | 47 ++++++++++++++++++ 5 files changed, 187 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/c/cairomm/cairomm-1.12.2-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/g/graph-tool/graph-tool-2.27-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..55670c329c7 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.67.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.67.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.sourceforge.net/boost/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.65.1_fix-Python3.patch'] +checksums = [ + '8aa4e330c870ef50a896634c931adf468b21f8a69b77007e45c444151229f665', # boost_1_67_0.tar.gz + '5585f98fb67425ec465dcbe2878af046ccd2729a8cdb802acf5d71cfa4022c26', # Boost-1.65.1_fix-Python3.patch +] + +dependencies = [ + ('Python', '3.6.6'), + ('Boost', version), +] + +only_python_bindings = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..dc1d8abbeca --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,37 @@ +name = 'CGAL' +version = '4.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['fb152fc30f007e5911922913f8dc38e0bb969b534373ca0fbe85b4d872300e8b'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.6.6'), + ('Boost', '1.67.0'), + ('MPFR', '4.0.1'), + ('GMP', '6.1.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.10.1'), +] + +builddependencies = [ + ('CMake', '3.11.4'), + ('Eigen', '3.3.4', '', True), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.12.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.12.2-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..6bd26d96c22 --- /dev/null +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.12.2-GCCcore-7.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'cairomm' +version = '1.12.2' + +homepage = 'http://cairographics.org' +description = "The Cairomm package provides a C++ interface to Cairo." + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['45c47fd4d0aa77464a75cdca011143fea3ef795c4753f6e860057da5fb8bd599'] + +builddependencies = [('binutils', '2.30')] +dependencies = [ + ('cairo', '1.14.12'), + ('libsigc++', '2.10.1'), +] + +sanity_check_paths = { + 'files': ['lib/libcairomm-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.27-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.27-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..2b09ecd8dd4 --- /dev/null +++ b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.27-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'graph-tool' +version = '2.27' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://graph-tool.skewed.de/' +description = """Graph-tool is an efficient Python module for manipulation and + statistical analysis of graphs (a.k.a. networks). Contrary to + most other python modules with similar functionality, the core + data structures and algorithms are implemented in C++, making + extensive use of template metaprogramming, based heavily on + the Boost Graph Library. This confers it a level of + performance that is comparable (both in memory usage and + computation time) to that of a pure C/C++ library.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'cstd': 'c++14'} + +source_urls = ['https://downloads.skewed.de/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['4740c69720dfbebf8fb3e77057b3e6a257ccf0432cdaf7345f873247390e4313'] + +dependencies = [ + ('Python', '3.6.6'), + ('Boost.Python', '1.67.0', versionsuffix), + ('expat', '2.2.5'), + ('CGAL', '4.11.1', versionsuffix), + ('sparsehash', '2.0.3'), + ('matplotlib', '3.0.0', versionsuffix), + ('PyCairo', '1.18.0', versionsuffix), + ('cairomm', '1.12.2'), +] + +configopts = '--enable-openmp --with-boost=$EBROOTBOOST --with-cairo=$EBROOTCAIRO --with-expat=$EBROOTEXPAT ' +configopts += '--with-boost-python=boost_python36 ' +configopts += '--with-python-module-path=%(installdir)s/lib/python%(pyshortver)s/site-packages' + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/graph_tool/all.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/graph_tool/include'], +} + +sanity_check_commands = ["python -c 'from graph_tool.all import graph_draw'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..e71d7eaaf7b --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scikit-multilearn' +version = '0.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit.ml' +description = """Scikit-multilearn is a BSD-licensed library for multi-label classification that +is built on top of the well-known scikit-learn ecosystem.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('scikit-learn', '0.20.2', versionsuffix), + ('networkx', '2.2', versionsuffix), + ('Keras', '2.2.4', versionsuffix), + ('python-igraph', '0.7.1.post6', versionsuffix), + ('graph-tool', '2.27', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('future', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future'], + 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], + }), + ('liac-arff', '2.4.0', { + 'modulename': 'arff', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff'], + 'checksums': ['47afcd1fd248b2892f66075987422d0576fc2c2fd0811d0cbd32f2135b065df5'], + }), + ('python-louvain', '0.13', { + 'modulename': 'community', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-louvain'], + 'checksums': ['b4938f20063bc53e68d5b182dcea0634dfb63a0e3489f929d4083c24a920b2fe'], + }), + (name, version, { + 'modulename': 'skmultilearn', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/scikit-multilearn/scikit-multilearn/archive'], + 'checksums': ['6ac89d25206c72a175369caaaceebb47ec992e588fb3552139832123ae4801de'], + }), +] + +moduleclass = 'data' From 90a8ebb6d565c0c80e5b5986549cb22da890110f Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Thu, 25 Apr 2019 16:25:20 +0100 Subject: [PATCH 1286/5331] Further things moved from OpenBLAS easyconfig to easyblock --- .../o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb index 4665e38da8f..c041c171982 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb @@ -25,19 +25,10 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] -skipsteps = ['configure'] - buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' -sanity_check_paths = { - 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', - 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', - 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], - 'dirs': [], -} - moduleclass = 'numlib' From 20ed812299e5401f15f31a51eeaf5d07408bb7ef Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 25 Apr 2019 17:40:25 +0200 Subject: [PATCH 1287/5331] use scikit-learn-0.20.0 --- .../scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb index e71d7eaaf7b..db2ac3007b9 100644 --- a/easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/scikit-multilearn/scikit-multilearn-0.2.0-foss-2018b-Python-3.6.6.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [ ('Python', '3.6.6'), - ('scikit-learn', '0.20.2', versionsuffix), + ('scikit-learn', '0.20.0', versionsuffix), ('networkx', '2.2', versionsuffix), ('Keras', '2.2.4', versionsuffix), ('python-igraph', '0.7.1.post6', versionsuffix), From a2f833001540ffc2d663ebe2bbba1d9ddc0d931c Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 25 Apr 2019 17:54:13 +0200 Subject: [PATCH 1288/5331] adding easyconfigs: libsndfile-1.0.28-GCCcore-8.2.0.eb --- .../libsndfile-1.0.28-GCCcore-8.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..4f86b9033dd --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.28-GCCcore-8.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libsndfile' +version = '1.0.28' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://www.mega-nerd.com/libsndfile/files/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1ff33929f042fa333aed1e8923aa628c3ee9e1eb85512686c55092d1e5a9dfa9'] + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'lib' From 23cff969a549ff8637daaca5ddb1822b4b666eb3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 18:03:02 +0200 Subject: [PATCH 1289/5331] Use multi_deps for Python versions instead. --- .../h/h5py/h5py-2.9.0-foss-2019a.eb | 35 +++++++++++++++++ .../h/h5py/h5py-2.9.0-fosscuda-2019a.eb | 35 +++++++++++++++++ .../h/h5py/h5py-2.9.0-intel-2019a.eb | 38 +++++++++++++++++++ .../h/h5py/h5py-2.9.0-intelcuda-2019a.eb | 38 +++++++++++++++++++ 4 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb new file mode 100644 index 00000000000..9e09dae9f90 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +builddependencies = [('pkgconfig', '1.5.1')] + +dependencies = [ + ('SciPy-bundle', '2019.03'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb new file mode 100644 index 00000000000..fcd64ca5199 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +builddependencies = [('pkgconfig', '1.5.1')] + +dependencies = [ + ('SciPy-bundle', '2019.03'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb new file mode 100644 index 00000000000..43d10148372 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +builddependencies = [('pkgconfig', '1.5.1')] + +dependencies = [ + ('SciPy-bundle', '2019.03'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb new file mode 100644 index 00000000000..111ed630ddd --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.9.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intelcuda', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] + +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +builddependencies = [('pkgconfig', '1.5.1')] + +dependencies = [ + ('SciPy-bundle', '2019.03'), + ('HDF5', '1.10.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' From b1d6ef10548836412dee5feadaa0dce45a30236c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 18:07:50 +0200 Subject: [PATCH 1290/5331] Delete easyconfigs with specific Python-version. --- .../h5py-2.9.0-foss-2019a-Python-2.7.15.eb | 34 ----------------- .../h5py-2.9.0-foss-2019a-Python-3.7.2.eb | 34 ----------------- ...h5py-2.9.0-fosscuda-2019a-Python-2.7.15.eb | 34 ----------------- .../h5py-2.9.0-fosscuda-2019a-Python-3.7.2.eb | 34 ----------------- .../h5py-2.9.0-intel-2019a-Python-2.7.15.eb | 37 ------------------- .../h5py-2.9.0-intel-2019a-Python-3.7.2.eb | 37 ------------------- ...5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb | 37 ------------------- ...h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb | 37 ------------------- 8 files changed, 284 deletions(-) delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-2.7.15.eb delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-3.7.2.eb delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-2.7.15.eb delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-3.7.2.eb delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-2.7.15.eb deleted file mode 100644 index d9d0d5fff25..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-2.7.15.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.9.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'foss', 'version': '2019a'} -toolchainopts = {'usempi': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] - -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - -dependencies = [ - ('Python', '2.7.15'), - ('SciPy-bundle', '2019.03'), - ('pkgconfig', '1.5.1'), - ('HDF5', '1.10.5'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-3.7.2.eb deleted file mode 100644 index b14f692498d..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a-Python-3.7.2.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.9.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'foss', 'version': '2019a'} -toolchainopts = {'usempi': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] - -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - -dependencies = [ - ('Python', '3.7.2'), - ('SciPy-bundle', '2019.03'), - ('pkgconfig', '1.5.1'), - ('HDF5', '1.10.5'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-2.7.15.eb deleted file mode 100644 index 84789a878ce..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-2.7.15.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.9.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'fosscuda', 'version': '2019a'} -toolchainopts = {'usempi': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] - -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - -dependencies = [ - ('Python', '2.7.15'), - ('SciPy-bundle', '2019.03'), - ('pkgconfig', '1.5.1'), - ('HDF5', '1.10.5'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-3.7.2.eb deleted file mode 100644 index e348a8a8a21..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a-Python-3.7.2.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.9.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'fosscuda', 'version': '2019a'} -toolchainopts = {'usempi': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] - -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - -dependencies = [ - ('Python', '3.7.2'), - ('SciPy-bundle', '2019.03'), - ('pkgconfig', '1.5.1'), - ('HDF5', '1.10.5'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb deleted file mode 100644 index 3618c9fa54c..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-2.7.15.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.9.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'intel', 'version': '2019a'} -toolchainopts = {'usempi': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] - -# required because we're building Python packages using Intel compilers on top of Python built with GCC -check_ldshared = True - -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - -dependencies = [ - ('Python', '2.7.15'), - ('SciPy-bundle', '2019.03'), - ('pkgconfig', '1.5.1'), - ('HDF5', '1.10.5'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb deleted file mode 100644 index e61d541a2cb..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a-Python-3.7.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.9.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'intel', 'version': '2019a'} -toolchainopts = {'usempi': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] - -# required because we're building Python packages using Intel compilers on top of Python built with GCC -check_ldshared = True - -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - -dependencies = [ - ('Python', '3.7.2'), - ('SciPy-bundle', '2019.03'), - ('pkgconfig', '1.5.1'), - ('HDF5', '1.10.5'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb deleted file mode 100644 index 947d1b971ec..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-2.7.15.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.9.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'intelcuda', 'version': '2019a'} -toolchainopts = {'usempi': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] - -# required because we're building Python packages using Intel compilers on top of Python built with GCC -check_ldshared = True - -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - -dependencies = [ - ('Python', '2.7.15'), - ('SciPy-bundle', '2019.03'), - ('pkgconfig', '1.5.1'), - ('HDF5', '1.10.5'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb deleted file mode 100644 index 34cbf7f5e64..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a-Python-3.7.2.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.9.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'intelcuda', 'version': '2019a'} -toolchainopts = {'usempi': True} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] - -# required because we're building Python packages using Intel compilers on top of Python built with GCC -check_ldshared = True - -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - -dependencies = [ - ('Python', '3.7.2'), - ('SciPy-bundle', '2019.03'), - ('pkgconfig', '1.5.1'), - ('HDF5', '1.10.5'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -moduleclass = 'data' From 96f9063997629769ffe0a46b9ce2e5f074a54380 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 25 Apr 2019 18:12:33 +0200 Subject: [PATCH 1291/5331] boegel is also picky --- ...atplotlib-3.0.3-foss-2019a-Python-3.7.2.eb | 18 +++++------------ ...otlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb | 18 +++++------------ ...tplotlib-3.0.3-intel-2019a-Python-3.7.2.eb | 20 ++++++------------- ...tlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb | 20 ++++++------------- 4 files changed, 22 insertions(+), 54 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb index c3055d9ac50..2b139175607 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-foss-2019a-Python-3.7.2.eb @@ -11,8 +11,6 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'foss', 'version': '2019a'} -use_pip = True - builddependencies = [ ('pkg-config', '0.29.2'), ] @@ -25,6 +23,8 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ] +use_pip = True + exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', @@ -32,26 +32,18 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), - ('kiwisolver', '1.0.1', { + ('kiwisolver', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], - 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], + 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'check_ldshared': True, 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], }), ] -check_ldshared = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -# sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] +sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] # use non-interactive plotting backend as default # see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb index bcde5d12ec5..fc6c98b0145 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-fosscuda-2019a-Python-3.7.2.eb @@ -11,8 +11,6 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'fosscuda', 'version': '2019a'} -use_pip = True - builddependencies = [ ('pkg-config', '0.29.2'), ] @@ -25,6 +23,8 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ] +use_pip = True + exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', @@ -32,26 +32,18 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), - ('kiwisolver', '1.0.1', { + ('kiwisolver', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], - 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], + 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'check_ldshared': True, 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], }), ] -check_ldshared = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -# sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] +sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] # use non-interactive plotting backend as default # see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb index d4c946b7d88..f391e849811 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intel-2019a-Python-3.7.2.eb @@ -11,9 +11,6 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'intel', 'version': '2019a'} -use_pip = True -check_ldshared = True - builddependencies = [ ('pkg-config', '0.29.2'), ] @@ -26,6 +23,9 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ] +use_pip = True +check_ldshared = True + exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', @@ -33,26 +33,18 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), - ('kiwisolver', '1.0.1', { + ('kiwisolver', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], - 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], + 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'check_ldshared': True, 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], }), ] -check_ldshared = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -# sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] +sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] # use non-interactive plotting backend as default # see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb index bf83aa2a5f0..693b92f22a5 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.0.3-intelcuda-2019a-Python-3.7.2.eb @@ -11,9 +11,6 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'intelcuda', 'version': '2019a'} -use_pip = True -check_ldshared = True - builddependencies = [ ('pkg-config', '0.29.2'), ] @@ -26,6 +23,9 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ] +use_pip = True +check_ldshared = True + exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', @@ -33,26 +33,18 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], }), - ('kiwisolver', '1.0.1', { + ('kiwisolver', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], - 'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'], + 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], }), (name, version, { 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'check_ldshared': True, 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], }), ] -check_ldshared = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -# sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] +sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """] # use non-interactive plotting backend as default # see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend From e61271dea46052437c4bd3cb9b2bd02c72b53218 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 18:50:53 +0200 Subject: [PATCH 1292/5331] Set download_dep_fail=True and use_pip=False for h5py. --- easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb | 3 +++ easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb | 3 +++ easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb | 3 +++ easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb | 3 +++ 4 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb index 9e09dae9f90..6c8e0052524 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb @@ -27,6 +27,9 @@ dependencies = [ ('HDF5', '1.10.5'), ] +use_pip = False +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb index fcd64ca5199..57596bed860 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb @@ -27,6 +27,9 @@ dependencies = [ ('HDF5', '1.10.5'), ] +use_pip = False +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb index 43d10148372..cffe3725772 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb @@ -30,6 +30,9 @@ dependencies = [ ('HDF5', '1.10.5'), ] +use_pip = False +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb index 111ed630ddd..d542a413e23 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb @@ -30,6 +30,9 @@ dependencies = [ ('HDF5', '1.10.5'), ] +use_pip = False +download_dep_fail = True + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages/'], From ae885f2334369c6adf11c673a788059f63a124b2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 19:20:20 +0200 Subject: [PATCH 1293/5331] Add missing sanity_check_paths. --- easybuild/easyconfigs/g/GSL/GSL-2.5-GCC-8.2.0-2.31.1.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GSL/GSL-2.5-GCC-8.2.0-2.31.1.eb index 1018d5599aa..340b6ec7d7e 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.5-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.5-GCC-8.2.0-2.31.1.eb @@ -15,4 +15,11 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['0460ad7c2542caaddc6729762952d345374784100223995eb14d614861f2258d'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + moduleclass = 'numlib' From 090afed5914c54615b3637b33e4ab258fb027a52 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 20:18:35 +0200 Subject: [PATCH 1294/5331] adding easyconfigs: ctffind-4.1.13-foss-2019a.eb, ctffind-4.1.13-fosscuda-2019a.eb and patches: ctffind-4.1.13_remove_bogus_include_lines.patch --- .../c/ctffind/ctffind-4.1.13-foss-2019a.eb | 47 +++++++++++++++++++ .../ctffind/ctffind-4.1.13-fosscuda-2019a.eb | 47 +++++++++++++++++++ ...nd-4.1.13_remove_bogus_include_lines.patch | 15 ++++++ 3 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.13_remove_bogus_include_lines.patch diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb new file mode 100644 index 00000000000..dc89a712855 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.13' + +homepage = 'http://grigoriefflab.janelia.org/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ctffind-4.1.13_remove_bogus_include_lines.patch'] +checksums = [ + '48231f8511b222176ea39b80c58ae8fb8a6bac5e0da247c54f5a84b52c8750cf', # ctffind-4.1.13.tar.gz + # ctffind-4.1.13_remove_bogus_include_lines.patch + 'ae218a61a24cec2e35fa4a7ddd497c0d1bb997957bfeb8866d941442afe26365', +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.2'), + ('LibTIFF', '4.0.10'), + ('GSL', '2.5'), + ('wxWidgets', '3.0.4'), +] + +separate_build_dir = True + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb new file mode 100644 index 00000000000..c1cc350084f --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.13' + +homepage = 'http://grigoriefflab.janelia.org/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ctffind-4.1.13_remove_bogus_include_lines.patch'] +checksums = [ + '48231f8511b222176ea39b80c58ae8fb8a6bac5e0da247c54f5a84b52c8750cf', # ctffind-4.1.13.tar.gz + # ctffind-4.1.13_remove_bogus_include_lines.patch + 'ae218a61a24cec2e35fa4a7ddd497c0d1bb997957bfeb8866d941442afe26365', +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.2'), + ('LibTIFF', '4.0.10'), + ('GSL', '2.5'), + ('wxWidgets', '3.0.4'), +] + +separate_build_dir = True + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13_remove_bogus_include_lines.patch b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13_remove_bogus_include_lines.patch new file mode 100644 index 00000000000..c1a6e0795e6 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13_remove_bogus_include_lines.patch @@ -0,0 +1,15 @@ +Remove include lines for files that doesn't exist. + +Åke Sandgren, 20190425 +diff -ru ctffind-4.1.13.orig/src/core/core_headers.h ctffind-4.1.13/src/core/core_headers.h +--- ctffind-4.1.13.orig/src/core/core_headers.h 2019-01-02 18:07:53.000000000 +0100 ++++ ctffind-4.1.13/src/core/core_headers.h 2019-04-25 19:53:37.110806262 +0200 +@@ -95,8 +95,6 @@ + #include "myapp.h" + #include "rle3d.h" + #include "local_resolution_estimator.h" +-#include "pdb.h" +-#include "water.h" + + + #ifdef MKL From 778fedfc8013081414feb967804cf74a62b090d1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Apr 2019 22:46:50 +0200 Subject: [PATCH 1295/5331] adding easyconfigs: FLTK-1.3.5-GCC-8.2.0-2.31.1.eb --- .../f/FLTK/FLTK-1.3.5-GCC-8.2.0-2.31.1.eb | 38 +++++++++++++++++++ .../x/xprop/xprop-1.2.4-GCCcore-8.2.0.eb | 32 ++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..7459a703626 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,38 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.5' + +homepage = 'http://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-1.3.4_fix-LDFLAGS.patch'] +checksums = ['8729b2a055f38c1636ba20f749de0853384c1d3e9d1a6b8d4d1305143e115702'] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '19.0.1'), + ('libGLU', '9.0.0'), + ('libpng', '1.6.36'), + ('libjpeg-turbo', '2.0.2'), + ('xprop', '1.2.4'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..5749f58da6b --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-8.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.4' + +homepage = "http://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://ftp.x.org/archive/individual/app/'] +sources = [SOURCE_TAR_GZ] +checksums = ['dddb6e208ffa515e68f001c22077a465f1365a4bcf91d9b37f336a6c0d15400d'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20190311'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' From 1f2898ef8d5d6f4f50ee38734136c039ace845c8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 26 Apr 2019 07:40:24 +0200 Subject: [PATCH 1296/5331] Add missing checksum --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.2.0-2.31.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.2.0-2.31.1.eb index 7459a703626..f82d2ddb13a 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-8.2.0-2.31.1.eb @@ -17,7 +17,10 @@ toolchainopts = {'pic': True} source_urls = ['http://fltk.org/pub/%(namelower)s/%(version)s/'] sources = ['%(namelower)s-%(version)s-source.tar.gz'] patches = ['FLTK-1.3.4_fix-LDFLAGS.patch'] -checksums = ['8729b2a055f38c1636ba20f749de0853384c1d3e9d1a6b8d4d1305143e115702'] +checksums = [ + '8729b2a055f38c1636ba20f749de0853384c1d3e9d1a6b8d4d1305143e115702', # fltk-1.3.5-source.tar.gz + 'b9d39f6dce92fdb34a149f686a5d56e72912f94fd09c4958f3bb12770603da7d', # FLTK-1.3.4_fix-LDFLAGS.patch +] configopts = '--enable-shared --enable-threads --enable-xft' From fc8f0db8b87ae2167c81ab5991fb8bf8ae43e475 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Fri, 26 Apr 2019 11:28:17 +0100 Subject: [PATCH 1297/5331] adding easyconfigs: Porechop-0.2.4-foss-2018b-Python-3.5.2.eb --- .../Porechop-0.2.4-foss-2018b-Python-3.5.2.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.5.2.eb diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.5.2.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.5.2.eb new file mode 100644 index 00000000000..4356f1b35b7 --- /dev/null +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.5.2.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'Porechop' +version = '0.2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/rrwick/Porechop' +description = """Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. + Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, + it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments + to effectively find adapters, even at low sequence identity""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/rrwick/Porechop/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'] + +dependencies = [ + ('Python', '3.5.2'), +] + +sanity_check_paths = { + 'files': ['bin/porechop', 'lib/python%(pyshortver)s/site-packages/porechop/porechop.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'] +} + +moduleclass = 'bio' From 23c3679ad92baa38c2e775d882cc0f9e6fca12d9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 26 Apr 2019 17:05:53 +0200 Subject: [PATCH 1298/5331] adding easyconfigs: Bazel-0.20.0-GCCcore-8.2.0.eb --- .../b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..91b63b0e361 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb @@ -0,0 +1,21 @@ +name = 'Bazel' +version = '0.20.0' + +homepage = 'http://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = ['Bazel-0.18.0_remove_define_DATE.patch'] +checksums = [ + '1945afa84fd8858b0a3c68c09915a4bc81065c61df2591387b2985e2297d30bd', # bazel-0.20.0-dist.zip + '55fd52c512a578dc8242fbf204cf42f28aa93611910a5a791e0dda4c3a1c7d60', # Bazel-0.18.0_remove_define_DATE.patch +] + +builddependencies = [('binutils', '2.31.1')] +dependencies = [('Java', '1.8', '', True)] + +moduleclass = 'devel' From d61d1d044069412a92b874f676bfd03d9c3f0c0d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 26 Apr 2019 17:08:49 +0200 Subject: [PATCH 1299/5331] adding easyconfigs: NCCL-2.4.2-gcccuda-2019a.eb --- .../n/NCCL/NCCL-2.4.2-gcccuda-2019a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.4.2-gcccuda-2019a.eb diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.4.2-gcccuda-2019a.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.4.2-gcccuda-2019a.eb new file mode 100644 index 00000000000..9efc27a9769 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.4.2-gcccuda-2019a.eb @@ -0,0 +1,28 @@ +easyblock = "MakeCp" + +name = 'NCCL' +version = '2.4.2' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +# gcccuda/2019a uses CUDA 10.1 +toolchain = {'name': 'gcccuda', 'version': '2019a'} + +cuda_version = '10.1' + +# Download from https://developer.nvidia.com/nccl/nccl-download (after log in) +sources = ['%%(namelower)s_%%(version)s-1+cuda%s_x86_64.txz' % cuda_version] +checksums = ['f714ef17ce9616eec1f125c44b6542fdf6f92bd82248064ea60dfe33b3d986d8'] + +skipsteps = ['build'] + +files_to_copy = ['lib', 'include'] + +sanity_check_paths = { + 'files': ['lib/libnccl.%s' % SHLIB_EXT, 'lib/libnccl_static.a', 'include/nccl.h'], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 42ac67bca5408b914e299670092ffb0243041a62 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 26 Apr 2019 17:17:12 +0200 Subject: [PATCH 1300/5331] Update checksum --- easybuild/easyconfigs/n/NCCL/NCCL-2.4.2-gcccuda-2019a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.4.2-gcccuda-2019a.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.4.2-gcccuda-2019a.eb index 9efc27a9769..4e220cd8970 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.4.2-gcccuda-2019a.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.4.2-gcccuda-2019a.eb @@ -14,7 +14,7 @@ cuda_version = '10.1' # Download from https://developer.nvidia.com/nccl/nccl-download (after log in) sources = ['%%(namelower)s_%%(version)s-1+cuda%s_x86_64.txz' % cuda_version] -checksums = ['f714ef17ce9616eec1f125c44b6542fdf6f92bd82248064ea60dfe33b3d986d8'] +checksums = ['27dad0e9495d2382e34d2701472a702007be65275b22f782e74613af08e0a39b'] skipsteps = ['build'] From 2daffb5545de91384edc4cbc27d26a714483c9cb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 26 Apr 2019 17:18:57 +0200 Subject: [PATCH 1301/5331] adding easyconfigs: protobuf-3.7.1-GCCcore-8.2.0.eb --- .../protobuf/protobuf-3.7.1-GCCcore-8.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.7.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.7.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.7.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..69b0d0e7ee6 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.7.1-GCCcore-8.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.7.1' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f1748989842b46fa208b2a6e4e2785133cfcc3e4d43c17fecb023733f0f5443f'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Autotools', '20180311'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From 24e8822c134cf365f3b4a8a21a83a19a2bbf784e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 26 Apr 2019 17:21:34 +0200 Subject: [PATCH 1302/5331] adding easyconfigs: TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb --- ...Flow-1.13.1-fosscuda-2019a-Python-3.7.2.eb | 108 ++++++++++++++++++ 1 file changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..73239118815 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb @@ -0,0 +1,108 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '1.13.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} +toolchainopts = {'usempi': True} + +builddependencies = [ + # must be Bazel <= 0.21, and Bazel 0.21.0 fails to install... + ('Bazel', '0.20.0'), + ('protobuf', '3.7.1'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('h5py', '2.9.0', versionsuffix), + ('cuDNN', '7.4.2.24'), + ('NCCL', '2.4.2'), +] + +use_pip = True + +exts_list = [ + ('protobuf-python', '3.7.1', { + 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', + 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], + 'use_pip': False, + 'start_dir': 'python', + 'modulename': 'google.protobuf', + }), + ('absl-py', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], + 'checksums': ['8718189e4bd6013bf79910b9d1cb0a76aecad8ce664f78e1144980fabdd2cd23'], + 'modulename': 'absl', + }), + ('astor', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], + 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], + }), + ('gast', '0.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], + 'checksums': ['fe939df4583692f0512161ec1c880e0a10e71e6a232da045ab8edd3756fbadf0'], + }), + ('grpcio', '1.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], + 'checksums': ['2ddbca16c2e7b3f2ffc6e34c7cfa6886fb01de9f156ad3f77b72ad652d632097'], + 'modulename': 'grpc', + }), + ('Markdown', '3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], + 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], + }), + ('tensorboard', '1.13.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'checksums': ['82c9c711b76949b7b3794fc319dc3d3b0fad25f7c0c5260ec4a8371b02d23da6'], + 'unpack_sources': False, + }), + ('termcolor', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('Werkzeug', '0.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], + 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], + }), + ('Keras-Applications', '1.0.7', { + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', + 'checksums': ['60607b2b98868983e5153bf1cc6aa468ba73adc93bc977a90edaa4bc595e69fa'], + 'modulename': 'keras_applications', + }), + ('Keras-Preprocessing', '1.0.9', { + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['5e3700117981c2db762e512ed6586638124fac5842170701628088a11aeb51ac'], + 'modulename': 'keras_preprocessing', + }), + ('tensorflow-estimator', '1.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow-estimator'], + 'source_tmpl': 'tensorflow_estimator-1.13.0-py2.py3-none-any.whl', + 'unpack_sources': False, + }), + (name, version, { + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'patches': [ + 'TensorFlow-1.11.0_swig-env.patch', + 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', + 'TensorFlow-1.13.1_lrt-flag.patch', + ], + 'checksums': [ + '7cd19978e6bc7edc2c847bce19f95515a742b34ea5e28e4389dade35348f58ed', # v1.13.1.tar.gz + 'aa53c7f6d42b4a9e91e0ba639d79f69a7db3c0a88c3b8e43d332479b6368391a', # TensorFlow-1.11.0_swig-env.patch + # TensorFlow-1.11.0_remove-msse-hardcoding.patch + 'a0f00ee4d03bb4fd3a645ee06045cedaf97d0b85675ec35187e9dd7e479d7bb6', + 'b388be35f2581786bcd533b1bfa375165d7f35e38a3aab74570019312816bf1b', # TensorFlow-1.13.1_lrt-flag.patch + ], + }), +] + +moduleclass = 'lib' From 15a4e379f5671c21d0bccdf9f7b3df49e4947c92 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Apr 2019 18:13:55 +0200 Subject: [PATCH 1303/5331] add singledispatch extension to Python 2.7.15 easyconfig using GCCcore/8.2.0 --- easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb index 48a50a65bf9..4ee0c7395d6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb @@ -320,6 +320,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/f/future'], 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), ] moduleclass = 'lang' From 42c8d362c78b08f3d8efe919cccc2fdd912a9ad8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Apr 2019 19:00:28 +0200 Subject: [PATCH 1304/5331] {lang}[intel/2019a] numba v0.43.1 for Python 3.7.2 + 2.7.15 --- .../n/numba/numba-0.43.1-intel-2019a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/numba-0.43.1-intel-2019a.eb diff --git a/easybuild/easyconfigs/n/numba/numba-0.43.1-intel-2019a.eb b/easybuild/easyconfigs/n/numba/numba-0.43.1-intel-2019a.eb new file mode 100644 index 00000000000..ee011f39d6a --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.43.1-intel-2019a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.43.1' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True} + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [ + ('SciPy-bundle', '2019.03'), + ('LLVM', '7.0.1'), +] + +use_pip = True + +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +exts_list = [ + ('llvmlite', '0.28.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'patches': ['llvmlite-0.26.0_fix-ffi-Makefile.patch'], + 'checksums': [ + 'a189c0cd8a80e8bbd002a1e422b1efcc2bceab2cb63b961f2d03ab711c3ba45b', # llvmlite-0.28.0.tar.gz + # llvmlite-0.26.0_fix-ffi-Makefile.patch + '40e6fe6de48709b45daebf8082f65ac26f73a4afdf58fc1e8099b97c575fecae', + ], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + 'checksums': ['e7789d473f332a17e40166d2960826d821edd75d148b4ed340a893a334b46fae'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' From ab420da6b46dc92bf5538a60dda86099bcd28f88 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Sat, 27 Apr 2019 21:30:46 +0200 Subject: [PATCH 1305/5331] adding easyconfigs: Vim-8.1.1209-GCCcore-8.2.0-Python-3.7.2.eb --- ...Vim-8.1.1209-GCCcore-8.2.0-Python-3.7.2.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vim/Vim-8.1.1209-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/v/Vim/Vim-8.1.1209-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/v/Vim/Vim-8.1.1209-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..b3d40728df5 --- /dev/null +++ b/easybuild/easyconfigs/v/Vim/Vim-8.1.1209-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'Vim' +version = '8.1.1209' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vim.org' +description = """ Vim is an advanced text editor that seeks to provide the power + of the de-facto Unix editor 'Vi', with a more complete feature set. """ + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/vim/vim/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2620209f517241eec1b1e58576568156caa9f3838be86ec1dcf6e2e1feefbe3c'] + +# this dependencies are required for --enable-pythoninterp=yes and --enable-perlinterp=yes to work +# check enabled features running "vim --version" after compilation + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('Python', '3.7.2'), + ('Perl', '5.28.1'), + ('PCRE', '8.43') +] + +configopts = '--with-features=huge --enable-python3interp=yes --enable-perlinterp=yes' + +sanity_check_paths = { + 'files': ['bin/vim', 'bin/vimdiff'], + 'dirs': [], +} + +moduleclass = 'tools' From 5c6368c8df64b021dbc75ec60a729e51d3f8b8ba Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Sat, 27 Apr 2019 23:20:37 +0200 Subject: [PATCH 1306/5331] adding easyconfigs: utf8proc-2.3.0-GCCcore-8.2.0.eb --- .../utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..e34f81c79d2 --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.3.0' +#versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +#sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'lib' From f993fd4f3bbe7f0624b2a6cc2ec6901542b86442 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Sat, 27 Apr 2019 23:21:42 +0200 Subject: [PATCH 1307/5331] adding easyconfigs: lz4-1.9.1-GCCcore-8.2.0.eb --- .../l/lz4/lz4-1.9.1-GCCcore-8.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..d52b30a5142 --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.1-GCCcore-8.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.1' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/lz4/lz4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f8377c89dad5c9f266edc0be9b73595296ecafd5bfa1000de148096c50052dc4'] + +builddependencies = [('binutils', '2.31.1')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From ba5c81e2218256e7628abf4942fcf5660ad2248a Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Sat, 27 Apr 2019 23:27:53 +0200 Subject: [PATCH 1308/5331] adding easyconfigs: Serf-1.3.9-GCCcore-8.2.0.eb, APR-util-1.6.1-GCCcore-8.2.0.eb, APR-1.7.0-GCCcore-8.2.0.eb, Subversion-1.12.0-GCCcore-8.2.0.eb --- .../APR-util/APR-util-1.6.1-GCCcore-8.2.0.eb | 32 ++++++++++++ .../a/APR/APR-1.7.0-GCCcore-8.2.0.eb | 22 +++++++++ .../s/Serf/Serf-1.3.9-GCCcore-8.2.0.eb | 39 +++++++++++++++ .../Subversion-1.12.0-GCCcore-8.2.0.eb | 49 +++++++++++++++++++ 4 files changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/s/Subversion/Subversion-1.12.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..1490688cc56 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-8.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.1' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('APR', '1.7.0'), + ('SQLite', '3.27.2'), + ('expat', '2.2.6'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..7035b7d8458 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-8.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2'] + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..4d3eeadb5e9 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-8.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'SCons' +name = 'Serf' +version = '1.3.9' + +homepage = 'http://serf.apache.org/' +description = """The serf library is a high performance C-based HTTP client library + built upon the Apache Portable Runtime (APR) library""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Python', '2.7.15'), # Serfs build scripts are python 2 only + ('SCons', '3.0.5'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it is nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" + +sanity_check_paths = { + 'files': ['include/serf-1/serf.h'] + + ['lib/libserf-1.%s' % x for x in ['a', 'so']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.12.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.12.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..1f91ef5f2ac --- /dev/null +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.12.0-GCCcore-8.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'Subversion' +version = '1.12.0' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [ + 'http://apache.belnet.be/%(namelower)s', + 'http://www.eu.apache.org/dist/%(namelower)s', + 'http://www.us.apache.org/dist/%(namelower)s', + 'http://archive.apache.org/dist/%(namelower)s', +] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Subversion-%(version)s-no_swig.patch'] +checksums = [ + '7fae7c73d8a007c107c0ae5eb372bc0bb013dbfe966fcd5c59cd5a195a5e2edf', # subversion-1.12.0.tar.bz2 + '539ea2118f958d152d78438c81649eb727ff0b2e8491295702ee98e1f922041f', # Subversion-1.12.0-no_swig.patch +] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Autotools', '20180311'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('SQLite', '3.27.2'), + ('zlib', '1.2.11'), + ('lz4', '1.9.1'), + ('utf8proc', '2.3.0'), + ('Serf', '1.3.9'), +] + +preconfigopts = './autogen.sh && ' + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-lz4=$EBROOTLZ4 --with-serf=$EBROOTSERF" + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +moduleclass = 'tools' From 8f41925cbe550a64162a6027659d309caf229aaa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 27 Apr 2019 23:41:07 +0200 Subject: [PATCH 1309/5331] Add no-swig patch --- .../Subversion-1.12.0-no_swig.patch | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subversion/Subversion-1.12.0-no_swig.patch diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.12.0-no_swig.patch b/easybuild/easyconfigs/s/Subversion/Subversion-1.12.0-no_swig.patch new file mode 100644 index 00000000000..bab95872ff8 --- /dev/null +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.12.0-no_swig.patch @@ -0,0 +1,21 @@ +# Only way to disable SWIG/python bindings as --without-swig does nothing +# Mikael Öhman , 2019-04-27 +--- configure.ac.orig 2019-04-27 22:26:56.185082267 +0200 ++++ configure.ac 2019-04-27 22:27:14.038138415 +0200 +@@ -1341,11 +1341,11 @@ + fi + fi + +-SVN_CHECK_SWIG +-AC_ARG_VAR(SWIG_FEATURES, [SWIG feature flags common to all bindings]) +-AC_ARG_VAR(SWIG_RB_FEATURES, [SWIG feature flags specific to Ruby bindings]) +-AC_ARG_VAR(SWIG_PL_FEATURES, [SWIG feature flags specific to Perl bindings]) +-AC_ARG_VAR(SWIG_PY_FEATURES, [SWIG feature flags specific to Python bindings]) ++#SVN_CHECK_SWIG ++#AC_ARG_VAR(SWIG_FEATURES, [SWIG feature flags common to all bindings]) ++#AC_ARG_VAR(SWIG_RB_FEATURES, [SWIG feature flags specific to Ruby bindings]) ++#AC_ARG_VAR(SWIG_PL_FEATURES, [SWIG feature flags specific to Perl bindings]) ++#AC_ARG_VAR(SWIG_PY_FEATURES, [SWIG feature flags specific to Python bindings]) + + SVN_CHECK_CTYPESGEN + From acb872c81c3cabec8809b2d2d08232c8f445749c Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Sat, 27 Apr 2019 23:54:55 +0200 Subject: [PATCH 1310/5331] adding easyconfigs: SCons-3.0.5-GCCcore-8.2.0.eb --- .../s/SCons/SCons-3.0.5-GCCcore-8.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-3.0.5-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-3.0.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/SCons/SCons-3.0.5-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..ecccb7a2c0b --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-3.0.5-GCCcore-8.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '3.0.5' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['SCons-3.0.4_fix-pip-install.patch'] +checksums = [ + 'df676f23dc6d4bfa384fc389d95dcd21ab907e6349d4c848958ba4befb73c73e', # scons-3.0.5.tar.gz + 'c632a50184edbb0dc032943fd717e832577d4ad407eb7743e5331eddb842a69f', # SCons-3.0.4_fix-pip-install.patch +] + +builddependencies = [('binutils', '2.31.1')] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': [], +} + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' From 2fdda29df755da230bd44b07245b9e4dd24123eb Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Sun, 28 Apr 2019 00:07:32 +0200 Subject: [PATCH 1311/5331] Checksum + cleanup --- .../easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb index e34f81c79d2..b04ca54a116 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb @@ -2,7 +2,6 @@ easyblock = 'CMakeMake' name = 'utf8proc' version = '2.3.0' -#versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/JuliaStrings/utf8proc' description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, @@ -12,6 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['c0265a49b59bab95481cab1ae958ba034dedc47ad58676a61f5de1fa9347930e'] builddependencies = [ ('binutils', '2.31.1'), @@ -27,6 +27,4 @@ sanity_check_paths = { 'dirs': [], } -#sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - moduleclass = 'lib' From ee179213f9c0c8d50919a79a57b3745bea1bfcfd Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 01:15:49 +0200 Subject: [PATCH 1312/5331] adding easyconfigs: METIS-5.1.0-GCCcore-8.2.0.eb --- .../m/METIS/METIS-5.1.0-GCCcore-8.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..9557c598928 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-8.2.0.eb @@ -0,0 +1,38 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +# We use 32bit for indices and 64bit for content +patches = ['%(name)s-%(version)s-use-doubles.patch'] + +checksums = [ + '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2', # source + '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67', # patch +] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' From 5db1730c5d259406e265c756b9e769906f56c003 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 01:17:57 +0200 Subject: [PATCH 1313/5331] adding easyconfigs: ParMETIS-4.0.3-iimpi-2019a.eb, ParMETIS-4.0.3-gompi-2019a.eb --- .../p/ParMETIS/ParMETIS-4.0.3-gompi-2019a.eb | 23 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-iimpi-2019a.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2019a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2019a.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2019a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2019a.eb new file mode 100644 index 00000000000..f9c3495fcf3 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2019a.eb @@ -0,0 +1,23 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.13.3')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2019a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2019a.eb new file mode 100644 index 00000000000..b0218ea227b --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2019a.eb @@ -0,0 +1,23 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2019a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.13.3')] + +moduleclass = 'math' From a3b395ea208144dd118880e19bf64a8f3b97d955 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 29 Apr 2019 07:21:34 +0200 Subject: [PATCH 1314/5331] adding easyconfigs: Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb, libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb, Mako-1.0.9-fosscuda-2018b-Python-3.6.6.eb --- ...array-0.7.6-fosscuda-2018b-Python-3.6.6.eb | 48 +++++++++++++++++++ .../Mako-1.0.9-fosscuda-2018b-Python-3.6.6.eb | 26 ++++++++++ ...heano-1.0.4-fosscuda-2018b-Python-3.6.6.eb | 31 ++++++++++++ 3 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.9-fosscuda-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..ea64ed34d4e --- /dev/null +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'libgpuarray' +version = '0.7.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/%(name)s/' +description = "Library to manipulate tensors on the GPU." + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['https://github.com/Theano/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'] + +builddependencies = [('CMake', '3.12.1')] + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +dependencies = [ + ('Mako', '1.0.9', '-Python-%(pyver)s'), + ('NCCL', '2.3.7'), + ('Python', '3.6.6'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} +exts_list = [ + (name, version, { + 'buildcmd': 'build_ext', + 'modulename': 'pygpu', + 'source_tmpl': SOURCE_TAR_GZ, + 'source_urls': ['https://github.com/Theano/%(name)s/releases/download/v%(version)s/'], + 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s-static.a'], + 'dirs': ['include/gpuarray', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.9-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.9-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..01f421505f3 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.9-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.0.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.%(namelower)stemplates.org' +description = "A super-fast templating language that borrows the best ideas from the existing templating languages" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['0728c404877cd4ca72c409c0ea372dc5f3b53fa1ad2bb434e1d216c0444ff1fd'] + +dependencies = [('Python', '3.6.6')] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..b12b5dbabc2 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/%(namelower)s' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] + +dependencies = [ + ('cuDNN', '7.1.4.18'), + ('libgpuarray', '0.7.6', '-Python-%(pyver)s'), + ('Python', '3.6.6'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-cache', 'bin/%(namelower)s-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From 5d6964a9e81de178c0b4b09b374e402b31746c89 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 29 Apr 2019 07:51:08 +0200 Subject: [PATCH 1315/5331] adding easyconfigs: ncdu-1.14-foss-2018b.eb --- .../n/ncdu/ncdu-1.14-foss-2018b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdu/ncdu-1.14-foss-2018b.eb diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.14-foss-2018b.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.14-foss-2018b.eb new file mode 100644 index 00000000000..c4373a97550 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.14-foss-2018b.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'ncdu' +version = '1.14' + +homepage = 'https://dev.yorhel.nl/%(name)s' +description = """Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a + remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular + desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like + environment with ncurses installed.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://dev.yorhel.nl/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c694783aab21e27e64baad314b7c1ff34541bfa219fe9645ef6780f1c5558c44'] + +dependencies = [('ncurses', '6.1')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' From 9ad73535c68493bac310d0caf84385dffa15edd0 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 29 Apr 2019 08:59:44 +0100 Subject: [PATCH 1316/5331] Further things moved to easyblock --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb index c041c171982..4449dd4645d 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb @@ -25,9 +25,6 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] -buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' -installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" - # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' From b3be6ff2762f6e7b2702ab0369e538f3ca11b916 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Apr 2019 11:45:39 +0200 Subject: [PATCH 1317/5331] adding easyconfigs: simpy-3.0.11-intel-2018b-Python-3.6.6.eb --- .../simpy-3.0.11-intel-2018b-Python-3.6.6.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..91ddc59f674 --- /dev/null +++ b/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'simpy' +version = '3.0.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://simpy.readthedocs.io' +description = "SimPy is a process-based discrete-event simulation framework based on standard Python." + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d09625b9b01f34242ae100fe6bdb6c9508da181a08419ab00cc2bd47c7ec0f43'] + +dependencies = [ + ('Python', '3.6.6'), +] + +download_dep_fail = True +use_pip = True + +moduleclass = 'tools' From 0db9cf2910697a47609559aef1fa2056eb795339 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 29 Apr 2019 12:34:18 +0200 Subject: [PATCH 1318/5331] change to Mako 1.0.7 with Python 3 and apply style remarks --- .../libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb | 4 ++-- ...hon-3.6.6.eb => Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb} | 2 +- .../t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/Mako/{Mako-1.0.9-fosscuda-2018b-Python-3.6.6.eb => Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb} (97%) diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb index ea64ed34d4e..78364cb4e7e 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb @@ -18,9 +18,9 @@ builddependencies = [('CMake', '3.12.1')] configopts = '-DCMAKE_BUILD_TYPE=Release' dependencies = [ - ('Mako', '1.0.9', '-Python-%(pyver)s'), - ('NCCL', '2.3.7'), ('Python', '3.6.6'), + ('Mako', '1.0.7', versionsuffix), + ('NCCL', '2.3.7'), ] exts_defaultclass = 'PythonPackage' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.9-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb similarity index 97% rename from easybuild/easyconfigs/m/Mako/Mako-1.0.9-fosscuda-2018b-Python-3.6.6.eb rename to easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb index 01f421505f3..0d35cf684b4 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.9-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'Mako' -version = '1.0.9' +version = '1.0.7' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.%(namelower)stemplates.org' diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb index b12b5dbabc2..781edd4bef1 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2018b-Python-3.6.6.eb @@ -15,9 +15,9 @@ sources = [SOURCE_TAR_GZ] checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] dependencies = [ - ('cuDNN', '7.1.4.18'), - ('libgpuarray', '0.7.6', '-Python-%(pyver)s'), ('Python', '3.6.6'), + ('cuDNN', '7.1.4.18'), + ('libgpuarray', '0.7.6', versionsuffix), ] use_pip = True From bbb265f4977752268ea5f42589e4fb01aa771fe2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Apr 2019 12:58:55 +0200 Subject: [PATCH 1319/5331] add missing patch file for llvmlite, required by numba 0.43.1 easyconfig --- .../llvmlite-0.26.0_fix-ffi-Makefile.patch | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.26.0_fix-ffi-Makefile.patch diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.26.0_fix-ffi-Makefile.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.26.0_fix-ffi-Makefile.patch new file mode 100644 index 00000000000..f43c35713e4 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.26.0_fix-ffi-Makefile.patch @@ -0,0 +1,17 @@ +Make sure easybuild flags and libs are used for llvmlite +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ur llvmlite-0.26.0.orig/ffi/Makefile.linux llvmlite-0.26.0/ffi/Makefile.linux +--- llvmlite-0.26.0.orig/ffi/Makefile.linux 2019-02-01 21:16:16.000000000 +0100 ++++ llvmlite-0.26.0/ffi/Makefile.linux 2019-02-14 13:38:18.147608713 +0100 +@@ -5,9 +5,9 @@ + CXX_FLTO_FLAGS ?= -flto + LD_FLTO_FLAGS ?= -flto -Wl,--exclude-libs=ALL + +-CXXFLAGS = $(LLVM_CXXFLAGS) $(CXX_FLTO_FLAGS) ++CXXFLAGS := $(CXXFLAGS) $(LLVM_CXXFLAGS) $(CXX_FLTO_FLAGS) + LDFLAGS := $(LDFLAGS) $(LLVM_LDFLAGS) $(LD_FLTO_FLAGS) +-LIBS = $(LLVM_LIBS) ++LIBS := $(LIBS) $(LLVM_LIBS) + INCLUDE = core.h + SRC = assembly.cpp bitcode.cpp core.cpp initfini.cpp module.cpp value.cpp \ + executionengine.cpp transforms.cpp passmanagers.cpp targets.cpp dylib.cpp \ From ce24ad3898283ecc948f38f44f96e3bca3d33bd0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Apr 2019 14:17:46 +0200 Subject: [PATCH 1320/5331] adding easyconfigs: RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb --- .../RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..506bb38e123 --- /dev/null +++ b/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'RBFOpt' +version = '4.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/coin-or/rbfopt' +description = "RBFOpt is a Python library for black-box optimization (also known as derivative-free optimization)." + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('ply', '3.11', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ply/'], + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('appdirs', '1.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/a/appdirs/'], + 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], + }), + ('PyUtilib', '5.6.5', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PyUtilib/'], + 'checksums': ['4730084624be98f2c326da88f3852831c6aa919e11babab2c34b0299c8f5ce2a'], + }), + ('Pyomo', '5.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pyomo/'], + 'checksums': ['449be9a4c9b3caee7c89dbe5f0e4e5ad0eaeef8be110a860641cd249986e362c'], + 'modulename': 'pyomo', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/r/rbfopt/'], + 'source_tmpl': 'rbfopt-%(version)s.tar.gz', + 'checksums': ['fdcef4ca8272f3467d38fb061ce362fc372cc3494f5e75e84c91c9bdeb0db295'], + }), +] + +sanity_check_paths = { + 'files': ['bin/rbfopt_cl_interface.py', 'bin/rbfopt_test_interface.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 3b6289e04dee5783c6f538623233c8c3602af607 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 15:53:58 +0200 Subject: [PATCH 1321/5331] adding easyconfigs: sympy-1.4-foss-2019a.eb, sympy-1.4-intel-2019a.eb --- .../s/sympy/sympy-1.4-foss-2019a.eb | 33 +++++++++++++++++ .../s/sympy/sympy-1.4-intel-2019a.eb | 37 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb new file mode 100644 index 00000000000..6015cc673a5 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.4' + +homepage = 'http://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['sympy-1.3_allpython.patch'] + +builddependencies = [('binutils', '2.31.1')] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [('SciPy-bundle', '2019.03')] + +use_pip = True + +runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb new file mode 100644 index 00000000000..d6f1444d09c --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.4' + +homepage = 'http://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = [ + 'sympy-1.3_allpython.patch', + 'sympy-%(version)s_intel_precision.patch', +] + +builddependencies = [('binutils', '2.31.1')] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [('SciPy-bundle', '2019.03')] + +check_ldshared = True +use_pip = True + +runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From fffcc7ebd003653f15a3e6afb50ffac22f9f13aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 29 Apr 2019 15:55:49 +0200 Subject: [PATCH 1322/5331] Add sympy 1.4 intel patch --- .../s/sympy/sympy-1.4_intel_precision.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.4_intel_precision.patch diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.4_intel_precision.patch b/easybuild/easyconfigs/s/sympy/sympy-1.4_intel_precision.patch new file mode 100644 index 00000000000..1fddf4a898b --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.4_intel_precision.patch @@ -0,0 +1,13 @@ +# Precision of intel math functions are very slightly off, requires larger margin +# Mikael Öhman , 2019-04-26 +--- sympy/utilities/tests/test_lambdify.py.orig 2019-04-26 20:02:43.731512423 +0200 ++++ sympy/utilities/tests/test_lambdify.py 2019-04-26 20:02:25.064447329 +0200 +@@ -1059,7 +1059,7 @@ + tparams = tuple(numpy.random.randint(1, tn, size=1)) + vals = (tn,) + tparams + (tv,) + sympy_result = sympy_fn(*vals).evalf() +- assert abs(f(*vals) - sympy_result) < 1e-13*(1 + abs(sympy_result)) ++ assert abs(f(*vals) - sympy_result) < 2e-13*(1 + abs(sympy_result)) + + + def test_lambdify_inspect(): From e1ce14364c4443a645cfedb11729fe2e17643939 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 29 Apr 2019 16:06:04 +0200 Subject: [PATCH 1323/5331] Add missing checksums --- easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb | 4 ++++ easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb | 5 +++++ 2 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb index 6015cc673a5..b9b997f9629 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb @@ -14,6 +14,10 @@ toolchain = {'name': 'foss', 'version': '2019a'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['sympy-1.3_allpython.patch'] +checksums = [ + '71a11e5686ae7ab6cb8feb5bd2651ef4482f8fd43a7c27e645a165e4353b23e1', # sympy-1.4.tar.gz + '888aacedb1c722470e1b85fe39a12b926d694867fd2a187e2422474993f8f1b5', # sympy-1.3_allpython.patch +] builddependencies = [('binutils', '2.31.1')] diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb index d6f1444d09c..28fe260e4f0 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb @@ -17,6 +17,11 @@ patches = [ 'sympy-1.3_allpython.patch', 'sympy-%(version)s_intel_precision.patch', ] +checksums = [ + '71a11e5686ae7ab6cb8feb5bd2651ef4482f8fd43a7c27e645a165e4353b23e1', # sympy-1.4.tar.gz + '888aacedb1c722470e1b85fe39a12b926d694867fd2a187e2422474993f8f1b5', # sympy-1.3_allpython.patch + '84fdf317ebe47e258000248c37bde13d50474e0774e376406ad3db3ed71babc8', # sympy-1.4_intel_precision.patch +] builddependencies = [('binutils', '2.31.1')] From 6d7dcb6287dd25d33002fbbed4a5a09a41cf5b6f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 29 Apr 2019 17:11:40 +0200 Subject: [PATCH 1324/5331] also change checksum --- .../m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb index 0d35cf684b4..358e9210d53 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-fosscuda-2018b-Python-3.6.6.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['0728c404877cd4ca72c409c0ea372dc5f3b53fa1ad2bb434e1d216c0444ff1fd'] +checksums = ['4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae'] dependencies = [('Python', '3.6.6')] From a1feddb2bf509935903adeafb37c8acee3530ccc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 29 Apr 2019 17:22:32 +0200 Subject: [PATCH 1325/5331] download_dep_fail = True --- easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb | 1 + easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb index b9b997f9629..717aecb5894 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.4-foss-2019a.eb @@ -25,6 +25,7 @@ multi_deps = {'Python': ['3.7.2', '2.7.15']} dependencies = [('SciPy-bundle', '2019.03')] +download_dep_fail = True use_pip = True runtest = 'python setup.py test' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb index 28fe260e4f0..58f9fd8cb47 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.4-intel-2019a.eb @@ -30,6 +30,7 @@ multi_deps = {'Python': ['3.7.2', '2.7.15']} dependencies = [('SciPy-bundle', '2019.03')] check_ldshared = True +download_dep_fail = True use_pip = True runtest = 'python setup.py test' From ba766512abcbc81f03923fb613dec21526dd84fe Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 17:27:40 +0200 Subject: [PATCH 1326/5331] adding easyconfigs: SCOTCH-6.0.6-gompi-2019a.eb, SCOTCH-6.0.6-intel-2019a.eb --- .../s/SCOTCH/SCOTCH-6.0.6-gompi-2019a.eb | 19 +++++++++++++++++++ .../s/SCOTCH/SCOTCH-6.0.6-intel-2019a.eb | 19 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-gompi-2019a.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-intel-2019a.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-gompi-2019a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-gompi-2019a.eb new file mode 100644 index 00000000000..2757ed30f96 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-gompi-2019a.eb @@ -0,0 +1,19 @@ +name = 'SCOTCH' +version = '6.0.6' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gforge.inria.fr/frs/download.php/file/37622/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] +checksums = ['686f0cad88d033fe71c8b781735ff742b73a1d82a65b8b1586526d69729ac4cf'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-intel-2019a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-intel-2019a.eb new file mode 100644 index 00000000000..db3648672e1 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-intel-2019a.eb @@ -0,0 +1,19 @@ +name = 'SCOTCH' +version = '6.0.6' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gforge.inria.fr/frs/download.php/file/37622/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] +checksums = ['686f0cad88d033fe71c8b781735ff742b73a1d82a65b8b1586526d69729ac4cf'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' From a3cae9c05139974e384c2cb3d310b11844802cbd Mon Sep 17 00:00:00 2001 From: install Date: Mon, 29 Apr 2019 08:50:57 -0700 Subject: [PATCH 1327/5331] Moved 'configopts' below 'separate_build_dir' as requested. --- easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb index 0d14bfeac14..cb39af0e9bd 100644 --- a/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.0.0-fosscuda-2018b.eb @@ -12,8 +12,6 @@ source_urls = ['https://github.com/Syllo/nvtop/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['de3d7b6a889f886f3bc28c15c3c34cfb6fcb7cb7ebc9a0cc36c3c77d837029b1'] -configopts = '-DNVML_INCLUDE_DIRS=$EBROOTCUDA/include -DNVML_LIBRARIES=$EBROOTCUDA/lib64/stubs/libnvidia-ml.so' - dependencies = [ ('ncurses', '6.1'), ] @@ -24,6 +22,8 @@ builddependencies = [ separate_build_dir = True +configopts = '-DNVML_INCLUDE_DIRS=$EBROOTCUDA/include -DNVML_LIBRARIES=$EBROOTCUDA/lib64/stubs/libnvidia-ml.so' + sanity_check_paths = { 'files': ['bin/nvtop'], 'dirs': [], From 283785930b14eb1521c3aab4c961f9f3a6f9dbd4 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 18:05:34 +0200 Subject: [PATCH 1328/5331] adding easyconfigs: GSL-2.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb --- ....5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GSL/GSL-2.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..8f23266cf4e --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.5' + +homepage = 'http://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0460ad7c2542caaddc6729762952d345374784100223995eb14d614861f2258d'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' From 09f444317d3a959c3772ff94c9abdd921e4cd373 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 19:18:22 +0200 Subject: [PATCH 1329/5331] adding easyconfigs: CP2K-6.1-foss-2019a.eb --- .../easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb new file mode 100644 index 00000000000..d28aab3460b --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb @@ -0,0 +1,44 @@ +name = 'CP2K' +version = '6.1' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] +checksums = [ + 'af803558e0a6b9e9d9ce8a3ab955ba32bacd179922455424e061c82c9fefa34b', # cp2k-6.1.tar.bz2 + '02475cbe24c8d4ba27037c826adf8a534cad634c3c4e02c21d743f5284516bda', # CP2K-2.4.0-fix_compile_date_lastsvn.patch +] + +dependencies = [ + ('Libint', '1.1.6'), + ('libxc', '4.3.4'), + ('libxsmm', '1.10'), + ('FFTW', '3.3.8'), + ('PLUMED', '2.5.1'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.5'), +] + +# values to use here are +1 those used for building Libint +# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT +extradflags = "-D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5" +#extradflags = "-fno-exceptions -D__parallel -D__SCALAPACK -D__LIBINT -D__FFTW3 -D__LIBXC -D__PLUMED2" + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' From 217578da7bd47b97721b76235d73abb2d857fbc3 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 19:29:21 +0200 Subject: [PATCH 1330/5331] adding easyconfigs: Libint-1.1.6-GCC-8.2.0-2.31.1.eb --- .../l/Libint/Libint-1.1.6-GCC-8.2.0-2.31.1.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.6-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..6c07d7d3c23 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,32 @@ +name = 'Libint' +version = '1.1.6' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/evaleev/libint/archive/'] +sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] +checksums = ['f201b0c621df678cfe8bdf3990796b8976ff194aba357ae398f2f29b0e2985a6'] + +builddependencies = [('Autotools', '20180311')] + +preconfigopts = "aclocal -I lib/autoconf && libtoolize && autoconf && " + +# these are important for CP2K +# see https://github.com/cp2k/cp2k/tree/master/tools/hfx_tools/libint_tools +configopts = "--with-libint-max-am=5 --with-libderiv-max-am1=4 " + +configopts += " --enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'chem' From 2caa25af89866453f14906fa28558f039f35eb56 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 19:34:02 +0200 Subject: [PATCH 1331/5331] adding easyconfigs: PLUMED-2.5.1-foss-2019a.eb --- .../p/PLUMED/PLUMED-2.5.1-foss-2019a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.1-foss-2019a.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.1-foss-2019a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.1-foss-2019a.eb new file mode 100644 index 00000000000..4098fb0fc81 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.1-foss-2019a.eb @@ -0,0 +1,46 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.5.1' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['449e835a4778ee89007bd28643eb1c41d7cde4929978e2cf1c0f2e35c76c378d'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.5'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl --enable-modules=all' +prebuildopts = 'source sourceme.sh && ' +# make sure that ld.gold linker is used +# requires to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +buildopts = 'LD_RO="ld.gold -r -o"' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' From a7e2cccfe1105b3dd218397c721ff25e941c7127 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 29 Apr 2019 19:36:18 +0200 Subject: [PATCH 1332/5331] Switch level intel -> iimpi --- ...{SCOTCH-6.0.6-intel-2019a.eb => SCOTCH-6.0.6-iimpi-2019a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/SCOTCH/{SCOTCH-6.0.6-intel-2019a.eb => SCOTCH-6.0.6-iimpi-2019a.eb} (92%) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-intel-2019a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-iimpi-2019a.eb similarity index 92% rename from easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-intel-2019a.eb rename to easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-iimpi-2019a.eb index db3648672e1..00f3cf0869b 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-intel-2019a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.6-iimpi-2019a.eb @@ -5,7 +5,7 @@ homepage = 'http://gforge.inria.fr/projects/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" -toolchain = {'name': 'intel', 'version': '2019a'} +toolchain = {'name': 'iimpi', 'version': '2019a'} toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/file/37622/'] From c0da0ed88db11ddf9084639cfda03e88e3d5766a Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 19:41:52 +0200 Subject: [PATCH 1333/5331] adding easyconfigs: libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb, libxc-4.3.4-GCC-8.2.0-2.31.1.eb --- .../l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb | 27 +++++++++++++++++++ ....4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..5d662987600 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '4.3.4' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337'] + +configopts = '--enable-static --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..5509d4ea627 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '4.3.4' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} + +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337'] + +configopts = '--enable-static --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' From d7547f98449abedb836e72fd5e55fd43f7febaf4 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 19:51:08 +0200 Subject: [PATCH 1334/5331] Include iccifort version as well --- ....6-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.6-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..b9903864674 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,32 @@ +name = 'Libint' +version = '1.1.6' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/evaleev/libint/archive/'] +sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] +checksums = ['f201b0c621df678cfe8bdf3990796b8976ff194aba357ae398f2f29b0e2985a6'] + +builddependencies = [('Autotools', '20180311')] + +preconfigopts = "aclocal -I lib/autoconf && libtoolize && autoconf && " + +# these are important for CP2K +# see https://github.com/cp2k/cp2k/tree/master/tools/hfx_tools/libint_tools +configopts = "--with-libint-max-am=5 --with-libderiv-max-am1=4 " + +configopts += " --enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'chem' From dca4a3772f11d486b58bdcbb2de5f6baa0811dc7 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 19:55:20 +0200 Subject: [PATCH 1335/5331] Add intel version --- .../p/PLUMED/PLUMED-2.5.1-intel-2018b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.1-intel-2018b.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.1-intel-2018b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.1-intel-2018b.eb new file mode 100644 index 00000000000..912eb6b8397 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.1-intel-2018b.eb @@ -0,0 +1,46 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.5.1' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['449e835a4778ee89007bd28643eb1c41d7cde4929978e2cf1c0f2e35c76c378d'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.5'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl --enable-modules=all' +prebuildopts = 'source sourceme.sh && ' +# make sure that ld.gold linker is used +# requires to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +buildopts = 'LD_RO="ld.gold -r -o"' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' From dbfeb492923b97c065e406daaaca54a2567f6f36 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 29 Apr 2019 20:39:41 +0200 Subject: [PATCH 1336/5331] adding easyconfigs: libxsmm-1.10-GCC-8.2.0-2.31.1.eb, libxsmm-1.10-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb --- .../libxsmm/libxsmm-1.10-GCC-8.2.0-2.31.1.eb | 27 +++++++++++++++++++ ...10-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.10-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.10-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.10-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.10-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..003d695ab67 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.10-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.10' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2904f7983719fd5c5af081121c1d028d45b10b854aec9a9e67996a0602631abc'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.10-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.10-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..a14f0909fbc --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.10-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.10' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2904f7983719fd5c5af081121c1d028d45b10b854aec9a9e67996a0602631abc'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' From 3660282409985cfc1bdbbabdad32077a6c0db4f3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 30 Apr 2019 08:35:22 +0200 Subject: [PATCH 1337/5331] adding easyconfigs: protobuf-3.6.1.2-GCCcore-8.2.0.eb and patches: protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch --- .../protobuf-3.6.1.2-GCCcore-8.2.0.eb | 34 ++++++++++++++++ ...f-3.6.1.2_fix_TensorFlow_issue_26155.patch | 39 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..a983cd0a0af --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2-GCCcore-8.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '3.6.1.2' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch', +] +checksums = [ + '2244b0308846bb22b4ff0bcc675e99290ff9f1115553ae9671eba1030af31bc0', # protobuf-3.6.1.2.tar.gz + # protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch + '828e2843cba1f8457d6aee89a2cf9ab7310c772d54a29dbd54254feec719ca04', +] + +builddependencies = [ + ('binutils', '2.31.1'), + ('Autotools', '20180311'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch b/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch new file mode 100644 index 00000000000..a325689656f --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch @@ -0,0 +1,39 @@ +Fix problem with building protobuf with CUDA 10.1 +Taken from https://github.com/tensorflow/tensorflow/issues/26155 + +Slightly adapted to EB +Åke Sandgren, 20190430 +diff -ru protobuf-3.6.1.2.orig/src/google/protobuf/map.h protobuf-3.6.1.2/src/google/protobuf/map.h +--- protobuf-3.6.1.2.orig/src/google/protobuf/map.h 2018-12-05 00:52:48.000000000 +0100 ++++ protobuf-3.6.1.2/src/google/protobuf/map.h 2019-04-29 15:26:34.507536056 +0200 +@@ -419,10 +419,10 @@ + node_ = NULL; + for (bucket_index_ = start_bucket; bucket_index_ < m_->num_buckets_; + bucket_index_++) { +- if (m_->TableEntryIsNonEmptyList(bucket_index_)) { ++ if ((*m_).TableEntryIsNonEmptyList(bucket_index_)) { + node_ = static_cast(m_->table_[bucket_index_]); + break; +- } else if (m_->TableEntryIsTree(bucket_index_)) { ++ } else if ((*m_).TableEntryIsTree(bucket_index_)) { + Tree* tree = static_cast(m_->table_[bucket_index_]); + GOOGLE_DCHECK(!tree->empty()); + node_ = NodePtrFromKeyPtr(*tree->begin()); +@@ -481,7 +481,7 @@ + return true; + // Less common: the bucket is a linked list with node_ somewhere in it, + // but not at the head. +- if (m_->TableEntryIsNonEmptyList(bucket_index_)) { ++ if ((*m_).TableEntryIsNonEmptyList(bucket_index_)) { + Node* l = static_cast(m_->table_[bucket_index_]); + while ((l = l->next) != NULL) { + if (l == node_) { +@@ -495,7 +495,7 @@ + // find-like method that compares Node* instead of const Key&. + iterator_base i(m_->find(*KeyPtrFromNodePtr(node_), it)); + bucket_index_ = i.bucket_index_; +- return m_->TableEntryIsList(bucket_index_); ++ return (*m_).TableEntryIsList(bucket_index_); + } + + Node* node_; From 977cad9cdb7f8ca5800a6a5c96cb42e550630ae3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 30 Apr 2019 08:36:21 +0200 Subject: [PATCH 1338/5331] adding easyconfigs: cuDNN-7.4.2.24-gcccuda-2019a.eb --- .../c/cuDNN/cuDNN-7.4.2.24-gcccuda-2019a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-gcccuda-2019a.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-gcccuda-2019a.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-gcccuda-2019a.eb new file mode 100644 index 00000000000..11f6d790ca2 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-gcccuda-2019a.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# OriginalAuthor: Stephane Thiell +# Author: Ake Sandgren +## +easyblock = 'Tarball' + +# The full version of the library can be found using +# strings -a cuda/lib64/libcudnn_static.a | grep cudnn_version_ +# Download and rename. +name = 'cuDNN' +version = '7.4.2.24' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +# gcccuda 2019a uses CUDA 10.1 +toolchain = {'name': 'gcccuda', 'version': '2019a'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-10.0-linux-x64-v%(version)s.tgz'] +checksums = ['2edfc86a02b50d17e88c478955a332e6a1e8174e7e53a3458b4ea51faf02daa3'] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From d879f5e9e2309eaaa7df57df475ea28739f02b70 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 30 Apr 2019 08:44:10 +0200 Subject: [PATCH 1339/5331] Fix problems with CUDA 10.1 for TF 1.13.1 and protobuf. --- ...Flow-1.13.1-fosscuda-2019a-Python-3.7.2.eb | 64 ++++++++++------ ...w-1.13.1_dont_expand_cuda_cudnn_path.patch | 31 ++++++++ ...3.1_fix_cudalib_version_for_cuda10.1.patch | 73 +++++++++++++++++++ ...nsorFlow-1.13.1_fix_protobuf_problem.patch | 70 ++++++++++++++++++ ...ow-1.13.1_protobuf-3.6.1.2_fix_26155.patch | 39 ++++++++++ ...ove_usrbin_from_linker_bin_path_flag.patch | 16 ++++ 6 files changed, 270 insertions(+), 23 deletions(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_dont_expand_cuda_cudnn_path.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_fix_cudalib_version_for_cuda10.1.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_fix_protobuf_problem.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_protobuf-3.6.1.2_fix_26155.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_remove_usrbin_from_linker_bin_path_flag.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb index 73239118815..e9d9d63f875 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb @@ -13,12 +13,13 @@ toolchainopts = {'usempi': True} builddependencies = [ # must be Bazel <= 0.21, and Bazel 0.21.0 fails to install... ('Bazel', '0.20.0'), - ('protobuf', '3.7.1'), + ('protobuf', '3.6.1.2'), ] dependencies = [ ('Python', '3.7.2'), - ('h5py', '2.9.0', versionsuffix), + ('SciPy-bundle', '2019.03'), + ('h5py', '2.9.0'), ('cuDNN', '7.4.2.24'), ('NCCL', '2.4.2'), ] @@ -26,18 +27,22 @@ dependencies = [ use_pip = True exts_list = [ - ('protobuf-python', '3.7.1', { - 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + ('protobuf-python', '3.6.1', { + 'modulename': 'google.protobuf', 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', - 'checksums': ['40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6'], - 'use_pip': False, + 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + 'patches': ['TensorFlow-1.13.1_protobuf-3.6.1.2_fix_26155.patch'], 'start_dir': 'python', - 'modulename': 'google.protobuf', + 'use_pip': False, + 'checksums': [ + '40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6', + 'db514d3698d37e329cecdd2245dcd6ff65f2b739a66730f303e8a9f6c107392b', + ], }), ('absl-py', '0.7.1', { - 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], - 'checksums': ['8718189e4bd6013bf79910b9d1cb0a76aecad8ce664f78e1144980fabdd2cd23'], 'modulename': 'absl', + 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], + 'checksums': ['b943d1c567743ed0455878fcd60bc28ac9fae38d129d1ccfad58079da00b8951'], }), ('astor', '0.7.1', { 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], @@ -48,19 +53,19 @@ exts_list = [ 'checksums': ['fe939df4583692f0512161ec1c880e0a10e71e6a232da045ab8edd3756fbadf0'], }), ('grpcio', '1.20.1', { - 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], - 'checksums': ['2ddbca16c2e7b3f2ffc6e34c7cfa6886fb01de9f156ad3f77b72ad652d632097'], 'modulename': 'grpc', + 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], + 'checksums': ['84eb47b1a47e206e78f453fb92a155ed0d18d2ca8747f5c67e4b50b9c37180a7'], }), ('Markdown', '3.1', { 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], - 'checksums': ['d02e0f9b04c500cde6637c11ad7c72671f359b87b9fe924b2383649d8841db7c'], + 'checksums': ['fc4a6f69a656b8d858d7503bda633f4dd63c2d70cf80abdc6eafa64c4ae8c250'], }), - ('tensorboard', '1.13.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], + ('tensorboard', version, { 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', - 'checksums': ['82c9c711b76949b7b3794fc319dc3d3b0fad25f7c0c5260ec4a8371b02d23da6'], + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], 'unpack_sources': False, + 'checksums': ['b664fe7772be5670d8b04200342e681af7795a12cd752709aed565c06c0cc196'], }), ('termcolor', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], @@ -68,39 +73,52 @@ exts_list = [ }), ('Werkzeug', '0.15.2', { 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], - 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], + 'checksums': ['0a73e8bb2ff2feecfc5d56e6f458f5b99290ef34f565ffb2665801ff7de6af7a'], }), ('Keras-Applications', '1.0.7', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], + 'modulename': 'keras_applications', 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], 'checksums': ['60607b2b98868983e5153bf1cc6aa468ba73adc93bc977a90edaa4bc595e69fa'], - 'modulename': 'keras_applications', }), ('Keras-Preprocessing', '1.0.9', { - 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], + 'modulename': 'keras_preprocessing', 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], 'checksums': ['5e3700117981c2db762e512ed6586638124fac5842170701628088a11aeb51ac'], - 'modulename': 'keras_preprocessing', }), ('tensorflow-estimator', '1.13.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow-estimator'], 'source_tmpl': 'tensorflow_estimator-1.13.0-py2.py3-none-any.whl', + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow-estimator'], 'unpack_sources': False, + 'checksums': ['7cfdaa3e83e3532f31713713feb98be7ea9f3065722be4267e49b6c301271419'], }), (name, version, { - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], - 'source_tmpl': 'v%(version)s.tar.gz', 'patches': [ 'TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.13.1_lrt-flag.patch', + 'TensorFlow-1.13.1_dont_expand_cuda_cudnn_path.patch', + 'TensorFlow-1.13.1_remove_usrbin_from_linker_bin_path_flag.patch', + 'TensorFlow-1.13.1_fix_protobuf_problem.patch', + 'TensorFlow-1.13.1_fix_cudalib_version_for_cuda10.1.patch', ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'checksums': [ '7cd19978e6bc7edc2c847bce19f95515a742b34ea5e28e4389dade35348f58ed', # v1.13.1.tar.gz 'aa53c7f6d42b4a9e91e0ba639d79f69a7db3c0a88c3b8e43d332479b6368391a', # TensorFlow-1.11.0_swig-env.patch # TensorFlow-1.11.0_remove-msse-hardcoding.patch 'a0f00ee4d03bb4fd3a645ee06045cedaf97d0b85675ec35187e9dd7e479d7bb6', 'b388be35f2581786bcd533b1bfa375165d7f35e38a3aab74570019312816bf1b', # TensorFlow-1.13.1_lrt-flag.patch + # TensorFlow-1.13.1_dont_expand_cuda_cudnn_path.patch + '3722764db136c58a1310aa087b6be6c34dd10c6fb5b6b215a9ae83946fd1c4ae', + # TensorFlow-1.13.1_remove_usrbin_from_linker_bin_path_flag.patch + 'e6122f34557fbe9e705ce1999403053b0ac4bdd058e4a31a182a16446c87bdb3', + # TensorFlow-1.13.1_fix_protobuf_problem.patch + 'd2fab1497078a2980a68adeea4d0f8719be5bef03741ea4775163745a1e52d40', + # TensorFlow-1.13.1_fix_cudalib_version_for_cuda10.1.patch + '176237dc2736d99d343f7a086503f9c724e7747f9289884302a010e5dff2dd1b', ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_dont_expand_cuda_cudnn_path.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_dont_expand_cuda_cudnn_path.patch new file mode 100644 index 00000000000..4927e47660f --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_dont_expand_cuda_cudnn_path.patch @@ -0,0 +1,31 @@ +Don't expand path for cuda_toolkit and cudnn. +We want the EasyBuild created path to be used. + +Åke Sandgren, 20190427 +diff -ru tensorflow-1.13.1.orig/configure.py tensorflow-1.13.1/configure.py +--- tensorflow-1.13.1.orig/configure.py 2019-02-25 21:37:04.000000000 +0100 ++++ tensorflow-1.13.1/configure.py 2019-04-26 20:27:28.610727650 +0200 +@@ -903,8 +903,9 @@ + + # Result returned from "read" will be used unexpanded. That make "~" + # unusable. Going through one more level of expansion to handle that. +- cudnn_install_path = os.path.realpath( +- os.path.expanduser(cudnn_install_path)) ++# Don't expand symlinks ++# cudnn_install_path = os.path.realpath( ++# os.path.expanduser(cudnn_install_path)) + if is_windows() or is_cygwin(): + cudnn_install_path = cygpath(cudnn_install_path) + +diff -ru tensorflow-1.13.1.orig/third_party/gpus/cuda_configure.bzl tensorflow-1.13.1/third_party/gpus/cuda_configure.bzl +--- tensorflow-1.13.1.orig/third_party/gpus/cuda_configure.bzl 2019-02-25 21:37:04.000000000 +0100 ++++ tensorflow-1.13.1/third_party/gpus/cuda_configure.bzl 2019-04-27 09:23:45.220881697 +0200 +@@ -421,7 +421,7 @@ + cuda_toolkit_path = repository_ctx.os.environ[_CUDA_TOOLKIT_PATH].strip() + if not repository_ctx.path(cuda_toolkit_path).exists: + auto_configure_fail("Cannot find cuda toolkit path.") +- return str(repository_ctx.path(cuda_toolkit_path).realpath) ++ return cuda_toolkit_path + + + def _cudnn_install_basedir(repository_ctx): diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_fix_cudalib_version_for_cuda10.1.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_fix_cudalib_version_for_cuda10.1.patch new file mode 100644 index 00000000000..7b9fc95a5e6 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_fix_cudalib_version_for_cuda10.1.patch @@ -0,0 +1,73 @@ +Fix search and use of libcublas etc for CUDA 10.1 +CUDA 10.1 change soname to be only major version for cublas,fft,solver,rand etc. +Taken from https://github.com/tensorflow/tensorflow/issues/28093 + +Åke Sandgren, 20190430 +diff -ru tensorflow-1.13.1.orig/tensorflow/stream_executor/dso_loader.cc tensorflow-1.13.1/tensorflow/stream_executor/dso_loader.cc +--- tensorflow-1.13.1.orig/tensorflow/stream_executor/dso_loader.cc 2019-02-25 21:37:04.000000000 +0100 ++++ tensorflow-1.13.1/tensorflow/stream_executor/dso_loader.cc 2019-04-29 21:47:37.282470005 +0200 +@@ -46,7 +46,7 @@ + + /* static */ port::Status DsoLoader::GetCublasDsoHandle(void** dso_handle) { + return GetDsoHandle(FindDsoPath(port::Env::Default()->FormatLibraryFileName( +- "cublas", GetCudaVersion()), ++ "cublas", "10"), + GetCudaLibraryDirPath()), + dso_handle); + } +@@ -63,14 +63,14 @@ + + /* static */ port::Status DsoLoader::GetCufftDsoHandle(void** dso_handle) { + return GetDsoHandle(FindDsoPath(port::Env::Default()->FormatLibraryFileName( +- "cufft", GetCudaVersion()), ++ "cufft", "10"), + GetCudaLibraryDirPath()), + dso_handle); + } + + /* static */ port::Status DsoLoader::GetCurandDsoHandle(void** dso_handle) { + return GetDsoHandle(FindDsoPath(port::Env::Default()->FormatLibraryFileName( +- "curand", GetCudaVersion()), ++ "curand", "10"), + GetCudaLibraryDirPath()), + dso_handle); + } +diff -ru tensorflow-1.13.1.orig/third_party/gpus/cuda_configure.bzl tensorflow-1.13.1/third_party/gpus/cuda_configure.bzl +--- tensorflow-1.13.1.orig/third_party/gpus/cuda_configure.bzl 2019-02-25 21:37:04.000000000 +0100 ++++ tensorflow-1.13.1/third_party/gpus/cuda_configure.bzl 2019-04-29 21:48:17.258083455 +0200 +@@ -842,7 +842,7 @@ + repository_ctx, + cpu_value, + cuda_config.cuda_toolkit_path, +- cuda_config.cuda_version, ++ '10', + ), + "cusolver": + _find_cuda_lib( +@@ -850,7 +850,7 @@ + repository_ctx, + cpu_value, + cuda_config.cuda_toolkit_path, +- cuda_config.cuda_version, ++ '10', + ), + "curand": + _find_cuda_lib( +@@ -858,7 +858,7 @@ + repository_ctx, + cpu_value, + cuda_config.cuda_toolkit_path, +- cuda_config.cuda_version, ++ '10', + ), + "cufft": + _find_cuda_lib( +@@ -866,7 +866,7 @@ + repository_ctx, + cpu_value, + cuda_config.cuda_toolkit_path, +- cuda_config.cuda_version, ++ '10', + ), + "cudnn": + _find_cuda_lib( diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_fix_protobuf_problem.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_fix_protobuf_problem.patch new file mode 100644 index 00000000000..ce5f33d1a9c --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_fix_protobuf_problem.patch @@ -0,0 +1,70 @@ +Fix problem with building protobuf with CUDA 10.1 +Taken from https://github.com/tensorflow/tensorflow/issues/26155 + +Slightly adapted to EB +Åke Sandgren, 20190430 +diff -rNu tensorflow-1.13.1.orig/tensorflow/workspace.bzl tensorflow-1.13.1/tensorflow/workspace.bzl +--- tensorflow-1.13.1.orig/tensorflow/workspace.bzl 2019-02-25 21:37:04.000000000 +0100 ++++ tensorflow-1.13.1/tensorflow/workspace.bzl 2019-04-29 17:54:13.739857564 +0200 +@@ -364,6 +364,7 @@ + "//third_party/systemlibs:protobuf.bzl": "protobuf.bzl", + }, + urls = PROTOBUF_URLS, ++ patch_file = clean_dep("//third_party:protobuf-3.6.1.2_fix_26155.patch"), + ) + + # We need to import the protobuf library under the names com_google_protobuf +@@ -378,6 +379,7 @@ + "//third_party/systemlibs:protobuf.bzl": "protobuf.bzl", + }, + urls = PROTOBUF_URLS, ++ patch_file = clean_dep("//third_party:protobuf-3.6.1.2_fix_26155.patch"), + ) + + tf_http_archive( +@@ -389,6 +391,7 @@ + "//third_party/systemlibs:protobuf.bzl": "protobuf.bzl", + }, + urls = PROTOBUF_URLS, ++ patch_file = clean_dep("//third_party:protobuf-3.6.1.2_fix_26155.patch"), + ) + + tf_http_archive( +diff -rNu tensorflow-1.13.1.orig/third_party/protobuf-3.6.1.2_fix_26155.patch tensorflow-1.13.1/third_party/protobuf-3.6.1.2_fix_26155.patch +--- tensorflow-1.13.1.orig/third_party/protobuf-3.6.1.2_fix_26155.patch 1970-01-01 01:00:00.000000000 +0100 ++++ tensorflow-1.13.1/third_party/protobuf-3.6.1.2_fix_26155.patch 2019-04-29 20:14:13.397392169 +0200 +@@ -0,0 +1,34 @@ ++diff -ru a/src/google/protobuf/map.h b/src/google/protobuf/map.h ++--- a/src/google/protobuf/map.h 2018-12-05 00:52:48.000000000 +0100 +++++ b/src/google/protobuf/map.h 2019-04-29 15:26:34.507536056 +0200 ++@@ -419,10 +419,10 @@ ++ node_ = NULL; ++ for (bucket_index_ = start_bucket; bucket_index_ < m_->num_buckets_; ++ bucket_index_++) { ++- if (m_->TableEntryIsNonEmptyList(bucket_index_)) { +++ if ((*m_).TableEntryIsNonEmptyList(bucket_index_)) { ++ node_ = static_cast(m_->table_[bucket_index_]); ++ break; ++- } else if (m_->TableEntryIsTree(bucket_index_)) { +++ } else if ((*m_).TableEntryIsTree(bucket_index_)) { ++ Tree* tree = static_cast(m_->table_[bucket_index_]); ++ GOOGLE_DCHECK(!tree->empty()); ++ node_ = NodePtrFromKeyPtr(*tree->begin()); ++@@ -481,7 +481,7 @@ ++ return true; ++ // Less common: the bucket is a linked list with node_ somewhere in it, ++ // but not at the head. ++- if (m_->TableEntryIsNonEmptyList(bucket_index_)) { +++ if ((*m_).TableEntryIsNonEmptyList(bucket_index_)) { ++ Node* l = static_cast(m_->table_[bucket_index_]); ++ while ((l = l->next) != NULL) { ++ if (l == node_) { ++@@ -495,7 +495,7 @@ ++ // find-like method that compares Node* instead of const Key&. ++ iterator_base i(m_->find(*KeyPtrFromNodePtr(node_), it)); ++ bucket_index_ = i.bucket_index_; ++- return m_->TableEntryIsList(bucket_index_); +++ return (*m_).TableEntryIsList(bucket_index_); ++ } ++ ++ Node* node_; diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_protobuf-3.6.1.2_fix_26155.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_protobuf-3.6.1.2_fix_26155.patch new file mode 100644 index 00000000000..5f1d01e40d9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_protobuf-3.6.1.2_fix_26155.patch @@ -0,0 +1,39 @@ +Fix problem with building protobuf with CUDA 10.1 +Taken from https://github.com/tensorflow/tensorflow/issues/26155 + +Slightly adapted to EB +Åke Sandgren, 20190430 +diff -ru a/src/google/protobuf/map.h b/src/google/protobuf/map.h +--- a/src/google/protobuf/map.h 2018-12-05 00:52:48.000000000 +0100 ++++ b/src/google/protobuf/map.h 2019-04-29 15:26:34.507536056 +0200 +@@ -419,10 +419,10 @@ + node_ = NULL; + for (bucket_index_ = start_bucket; bucket_index_ < m_->num_buckets_; + bucket_index_++) { +- if (m_->TableEntryIsNonEmptyList(bucket_index_)) { ++ if ((*m_).TableEntryIsNonEmptyList(bucket_index_)) { + node_ = static_cast(m_->table_[bucket_index_]); + break; +- } else if (m_->TableEntryIsTree(bucket_index_)) { ++ } else if ((*m_).TableEntryIsTree(bucket_index_)) { + Tree* tree = static_cast(m_->table_[bucket_index_]); + GOOGLE_DCHECK(!tree->empty()); + node_ = NodePtrFromKeyPtr(*tree->begin()); +@@ -481,7 +481,7 @@ + return true; + // Less common: the bucket is a linked list with node_ somewhere in it, + // but not at the head. +- if (m_->TableEntryIsNonEmptyList(bucket_index_)) { ++ if ((*m_).TableEntryIsNonEmptyList(bucket_index_)) { + Node* l = static_cast(m_->table_[bucket_index_]); + while ((l = l->next) != NULL) { + if (l == node_) { +@@ -495,7 +495,7 @@ + // find-like method that compares Node* instead of const Key&. + iterator_base i(m_->find(*KeyPtrFromNodePtr(node_), it)); + bucket_index_ = i.bucket_index_; +- return m_->TableEntryIsList(bucket_index_); ++ return (*m_).TableEntryIsList(bucket_index_); + } + + Node* node_; diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_remove_usrbin_from_linker_bin_path_flag.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_remove_usrbin_from_linker_bin_path_flag.patch new file mode 100644 index 00000000000..103f6bd1c38 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_remove_usrbin_from_linker_bin_path_flag.patch @@ -0,0 +1,16 @@ +# Remove -B/usr/bin from linker_bin_path_flag, as it causes a possibly +# incompatible linker from the system to be used. +# +# Fokke Dijkstra, 20190228 +diff -ru tensorflow-1.13.1.orig/third_party/gpus/cuda_configure.bzl tensorflow-1.13.1/third_party/gpus/cuda_configure.bzl +--- tensorflow-1.13.1.orig/third_party/gpus/cuda_configure.bzl 2019-04-27 09:51:24.892509614 +0200 ++++ tensorflow-1.13.1/third_party/gpus/cuda_configure.bzl 2019-04-27 09:51:47.920282539 +0200 +@@ -1410,7 +1410,7 @@ + if should_download_clang: + cuda_defines["%{linker_bin_path_flag}"] = "" + else: +- cuda_defines["%{linker_bin_path_flag}"] = 'flag: "-B/usr/bin"' ++ cuda_defines["%{linker_bin_path_flag}"] = '' + + if is_cuda_clang: + cuda_defines["%{host_compiler_path}"] = str(cc) From c0a1b32b029c18620d6a216ba618a889c01a61d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Apr 2019 11:01:44 +0200 Subject: [PATCH 1340/5331] adding easyconfigs: scikit-learn-0.20.3-intel-2019a-Python-3.7.2.eb --- ...t-learn-0.20.3-intel-2019a-Python-3.7.2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a-Python-3.7.2.eb new file mode 100755 index 00000000000..7b14973720b --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.20.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c503802a81de18b8b4d40d069f5e363795ee44b1605f38bc104160ca3bfe2c41'] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), # required for numpy/scipy + ('matplotlib', '3.0.3', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' From 907179d0a5107a660d85ce7e4cf9d17ab939bfae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Apr 2019 11:05:45 +0200 Subject: [PATCH 1341/5331] adding easyconfigs: NiBabel-2.4.0-intel-2019a.eb --- .../n/NiBabel/NiBabel-2.4.0-intel-2019a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-intel-2019a.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-intel-2019a.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-intel-2019a.eb new file mode 100644 index 00000000000..7c443e522cc --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-2.4.0-intel-2019a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '2.4.0' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [ + ('SciPy-bundle', '2019.03'), + ('Pillow', '6.0.0'), +] + +use_pip = True + +exts_list = [ + ('pydicom', '1.2.0', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pydicom/pydicom/archive/'], + 'checksums': ['56068467f6d339223349717fe2a4f6edd219bb299eed8f15a9a875a357942949'], + }), + ('bz2file', '0.98', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/nibabel'], + 'checksums': ['dd0c41715d0391c724e2828bba2c16690dbd6aafbca8e920ee8448ed0086e4c1'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +moduleclass = 'vis' From d2c844d7483d305e4e2250fd9ba2367fbf60206c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 30 Apr 2019 11:43:55 +0200 Subject: [PATCH 1342/5331] adding easyconfigs: INTEGRATE-0.2.6-foss-2018b.eb --- .../i/INTEGRATE/INTEGRATE-0.2.6-foss-2018b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-foss-2018b.eb diff --git a/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-foss-2018b.eb b/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-foss-2018b.eb new file mode 100644 index 00000000000..bbf7927089a --- /dev/null +++ b/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-foss-2018b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'INTEGRATE' +version = '0.2.6' + +homepage = "https://sourceforge.net/p/integrate-fusion/wiki/Home/" +description = """\ + INTEGRATE is a tool calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq + and WGS data. It is highly sensitive and accurate by applying a fast split-read mapping algorithm based on + Burrow-Wheeler transform. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://download.sourceforge.net/integrate-fusion/'] +sources = ['%(name)s.%(version)s.tar.gz'] +checksums = ['b65b14432b7184900d1f777f96fa73f4d0dffda4418936e8334613d6aa876e38'] + +builddependencies = [('CMake', '3.12.1')] + +separate_build_dir = True + +parallel = 1 + +skipsteps = ['install'] + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin', + 'cp -a bin/Integrate %(installdir)s/bin/', + 'cp -a vendor/divsufsort/lib %(installdir)s/', + 'cp -a vendor/divsufsort/include %(installdir)s/', +] + +sanity_check_paths = { + 'files': ['bin/Integrate'], + 'dirs': [''], +} + +moduleclass = 'bio' From 55df75903c351c1249a0fa015d42f326ebf8b522 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 30 Apr 2019 12:17:53 +0200 Subject: [PATCH 1343/5331] Need to use -std=gnu89 to avoid problems with u_char etc being undefined in some cases. --- easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb index babebf7387b..18daf7f5528 100644 --- a/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb @@ -10,6 +10,7 @@ applications, and also has a synchronous API, for use in threaded applications.""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'cstd': 'gnu89'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] From fc98395d34366c30eef598ad9de5896fb2485ac1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 30 Apr 2019 12:28:05 +0200 Subject: [PATCH 1344/5331] Fix comment in patch (and name of it) to better describe its purpose. --- .../p/protobuf/protobuf-3.6.1.2-GCCcore-8.2.0.eb | 6 +++--- ...obuf-3.6.1.2_make_include_file_CUDA_10.1_friendly.patch} | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/p/protobuf/{protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch => protobuf-3.6.1.2_make_include_file_CUDA_10.1_friendly.patch} (96%) diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2-GCCcore-8.2.0.eb index a983cd0a0af..483ab68183e 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2-GCCcore-8.2.0.eb @@ -11,12 +11,12 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ - 'protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch', + 'protobuf-3.6.1.2_make_include_file_CUDA_10.1_friendly.patch', ] checksums = [ '2244b0308846bb22b4ff0bcc675e99290ff9f1115553ae9671eba1030af31bc0', # protobuf-3.6.1.2.tar.gz - # protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch - '828e2843cba1f8457d6aee89a2cf9ab7310c772d54a29dbd54254feec719ca04', + # protobuf-3.6.1.2_make_include_file_CUDA_10.1_friendly.patch + '17c81fe38b503d3bf8aa3b07ddc9e412d46dd5babd32b5c61c43b50c1df47459', ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch b/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2_make_include_file_CUDA_10.1_friendly.patch similarity index 96% rename from easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch rename to easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2_make_include_file_CUDA_10.1_friendly.patch index a325689656f..50643021358 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2_fix_TensorFlow_issue_26155.patch +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.6.1.2_make_include_file_CUDA_10.1_friendly.patch @@ -1,4 +1,4 @@ -Fix problem with building protobuf with CUDA 10.1 +Fix problem with building against protobuf with CUDA 10.1 Taken from https://github.com/tensorflow/tensorflow/issues/26155 Slightly adapted to EB From 351f36d8371db2ae585ea6060fb9dda4366eda0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Apr 2019 13:12:54 +0200 Subject: [PATCH 1345/5331] adding easyconfigs: FFTW-3.3.8-intel-2019a.eb --- .../f/FFTW/FFTW-3.3.8-intel-2019a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2019a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2019a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2019a.eb new file mode 100644 index 00000000000..1d1b11b5580 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-intel-2019a.eb @@ -0,0 +1,26 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails on AMD systems when configuring with --enable-avx-128-fma, +# because Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' From 9e87e1ed1c6a9a0452b10d8a9aa646c6bc3c1363 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 30 Apr 2019 13:31:32 +0200 Subject: [PATCH 1346/5331] Use better sanity checks, and drop libdir flag which is no longer needed thanks to https://github.com/easybuilders/easybuild-easyblocks/pull/1673 --- .../easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb index 18daf7f5528..664db99778e 100644 --- a/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.66.1-GCCcore-8.2.0.eb @@ -31,15 +31,15 @@ dependencies = [ ('cURL', '7.63.0'), ] -configopts = '--libdir lib -Dgssapi=false -Dvapi=false ' +configopts = '-Dgssapi=false -Dvapi=false ' modextrapaths = { 'XDG_DATA_DIRS': 'share', } sanity_check_paths = { - 'files': [], - 'dirs': ['include', 'lib'] + 'files': ['lib/libsoup-2.4.%s' % SHLIB_EXT, 'lib/libsoup-gnome-2.4.%s' % SHLIB_EXT], + 'dirs': ['include/libsoup-2.4/libsoup', 'include/libsoup-gnome-2.4/libsoup', 'lib/pkgconfig'] } moduleclass = 'lib' From bfd8fcf2a4f150729337a5e521aef21ecd474513 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Tue, 30 Apr 2019 12:39:27 +0100 Subject: [PATCH 1347/5331] adding easyconfigs: Nextflow-19.04.0.eb --- .../n/Nextflow/Nextflow-19.04.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb new file mode 100644 index 00000000000..49f503e1005 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb @@ -0,0 +1,32 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock='Binary' + +name = "Nextflow" +version = "19.04.0" + +homepage = 'https://www.nextflow.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-all'] +checksums = ['10d96864489a5d6b4de3a730307871ca865e2f1c49a14cd5c4051cae5dca8d8e'] + +# specify dependency on Java/1.8 "wrapper", rather than a specific Java version +dependencies = [('Java', '1.8', '', True)] + +install_cmd = "[ -d %(builddir)s/bin ] || mkdir -p %(installdir)s/bin &&" +install_cmd += "cp %(builddir)s/nextflow-%(version)s-all %(installdir)s/bin &&" +install_cmd += "cd %(installdir)s/bin && ln -s nextflow-%(version)s-all nextflow &&" +install_cmd += "chmod +x %(installdir)s/bin/nextflow-%(version)s-all" + +sanity_check_paths = { + 'files': ['bin/nextflow-%(version)s-all', 'bin/nextflow'], + 'dirs': [] +} + +moduleclass = 'tools' From b50e2ffa9a22a4e903d74ebcd078e0acdf01cd76 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 30 Apr 2019 14:29:00 +0200 Subject: [PATCH 1348/5331] adding easyconfigs: Boost-1.70.0-gompi-2019a.eb, Boost-1.70.0-gompic-2019a.eb, Boost-1.70.0-iimpi-2019a.eb, Boost-1.70.0-iimpic-2019a.eb --- .../b/Boost/Boost-1.70.0-gompi-2019a.eb | 25 +++++++++++++++++++ .../b/Boost/Boost-1.70.0-gompic-2019a.eb | 25 +++++++++++++++++++ .../b/Boost/Boost-1.70.0-iimpi-2019a.eb | 25 +++++++++++++++++++ .../b/Boost/Boost-1.70.0-iimpic-2019a.eb | 25 +++++++++++++++++++ 4 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.70.0-gompi-2019a.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.70.0-gompic-2019a.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.70.0-iimpi-2019a.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.70.0-iimpic-2019a.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.70.0-gompi-2019a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.70.0-gompi-2019a.eb new file mode 100644 index 00000000000..27c1c0486ea --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.70.0-gompi-2019a.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.70.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['882b48708d211a5f48e60b0124cf5863c1534cd544ecd0664bb534a4b5d506e9'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('XZ', '5.2.4'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.70.0-gompic-2019a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.70.0-gompic-2019a.eb new file mode 100644 index 00000000000..e573b7b5a38 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.70.0-gompic-2019a.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.70.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompic', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['882b48708d211a5f48e60b0124cf5863c1534cd544ecd0664bb534a4b5d506e9'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('XZ', '5.2.4'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.70.0-iimpi-2019a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.70.0-iimpi-2019a.eb new file mode 100644 index 00000000000..82bdcd4488e --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.70.0-iimpi-2019a.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.70.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'iimpi', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['882b48708d211a5f48e60b0124cf5863c1534cd544ecd0664bb534a4b5d506e9'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('XZ', '5.2.4'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.70.0-iimpic-2019a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.70.0-iimpic-2019a.eb new file mode 100644 index 00000000000..c9efa32d049 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.70.0-iimpic-2019a.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.70.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'iimpic', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['882b48708d211a5f48e60b0124cf5863c1534cd544ecd0664bb534a4b5d506e9'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('XZ', '5.2.4'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' From 98ddcd957f575bc096f9250bb98424d92fac695b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Apr 2019 17:18:14 +0200 Subject: [PATCH 1349/5331] adding easyconfigs: pyFFTW-0.11.1-intel-2019a.eb --- .../p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb new file mode 100644 index 00000000000..5b722669eec --- /dev/null +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pyFFTW' +version = '0.11.1' + +homepage = 'https://github.com/pyFFTW/pyFFTW' +description = """A pythonic wrapper around FFTW, the FFT library, presenting a unified interface + for all the supported transforms.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['05ea28dede4c3aaaf5c66f56eb0f71849d0d50f5bc0f53ca0ffa69534af14926'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [ + ('SciPy-bundle', '2019.03'), + ('FFTW', '3.3.8'), +] + +download_dep_fail = True +use_pip = True + +moduleclass = 'lib' From 2e88bf7583056a8233248e16b1fd4771e8c262ac Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Tue, 30 Apr 2019 16:18:23 +0100 Subject: [PATCH 1350/5331] Missing whitespace addressed --- easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb index 49f503e1005..987bb25c7c0 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb @@ -1,7 +1,7 @@ # Contribution from the Crick HPC team # uploaded by J. Sassmannshausen -easyblock='Binary' +easyblock = 'Binary' name = "Nextflow" version = "19.04.0" From 06ff48c15b2e6a919c5c7fcc139b77a9e2a72211 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 May 2019 09:56:25 +0200 Subject: [PATCH 1351/5331] matplotlib is not an actual dependency of scikit-learn, so remove it and change easyconfig to multi-dep on Python 3.7.2 & 2.7.15 --- ...ython-3.7.2.eb => scikit-learn-0.20.3-intel-2019a.eb} | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/s/scikit-learn/{scikit-learn-0.20.3-intel-2019a-Python-3.7.2.eb => scikit-learn-0.20.3-intel-2019a.eb} (84%) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a.eb similarity index 84% rename from easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a-Python-3.7.2.eb rename to easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a.eb index 7b14973720b..6652590033a 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-intel-2019a.eb @@ -2,7 +2,6 @@ easyblock = 'PythonPackage' name = 'scikit-learn' version = '0.20.3' -versionsuffix = '-Python-%(pyver)s' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -16,11 +15,9 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['c503802a81de18b8b4d40d069f5e363795ee44b1605f38bc104160ca3bfe2c41'] -dependencies = [ - ('Python', '3.7.2'), - ('SciPy-bundle', '2019.03'), # required for numpy/scipy - ('matplotlib', '3.0.3', versionsuffix), -] +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [('SciPy-bundle', '2019.03')] download_dep_fail = True use_pip = True From d11faa21c95b56ea873f3684b4010cdf3653c5b8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 1 May 2019 14:17:22 +0200 Subject: [PATCH 1352/5331] adding easyconfigs: GROMACS-2019.2-fosscuda-2019a.eb --- .../GROMACS/GROMACS-2019.2-fosscuda-2019a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2019.2-fosscuda-2019a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.2-fosscuda-2019a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.2-fosscuda-2019a.eb new file mode 100644 index 00000000000..d113178b9ba --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.2-fosscuda-2019a.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2019.2' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. +""" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', +] +checksums = [ + 'bcbf5cc071926bc67baa5be6fb04f0986a2b107e1573e15fadcb7d7fc4fb9f7e', # gromacs-2019.2.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', +] + +builddependencies = [ + ('CMake', '3.13.3'), +] + +moduleclass = 'bio' From 4cbf999dd2816cd17c8b3d107ec0296e6dceb92e Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 1 May 2019 14:51:10 +0200 Subject: [PATCH 1353/5331] Added support for pkg-config via pkgconfig/bzip2.pc --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-8.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-8.2.0.eb index c7a553de5f3..64bb0f026a7 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-8.2.0.eb @@ -15,7 +15,11 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '97ba60fc236049d38a42934da0b94cadd7d56d0d2309c04da58781837c622f65', # bzip2-1.0.6-pkgconfig.patch +] builddependencies = [ ('binutils', '2.31.1'), From 003221d97ae2d5c40d32c74b35acef0c5b29c1fe Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 1 May 2019 14:56:58 +0200 Subject: [PATCH 1354/5331] Added support for pkg-config via pkgconfig/bzip2.pc --- .../b/bzip2/bzip2-1.0.6-pkgconfig.patch | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-pkgconfig.patch diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-pkgconfig.patch b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-pkgconfig.patch new file mode 100644 index 00000000000..8f20eb0c991 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-pkgconfig.patch @@ -0,0 +1,31 @@ +#- Adds a pkgconfig/bzip2.pc file +# +# author: Jiri Furst +diff -Nau bzip2-1.0.6.orig/bzip2.pc.in bzip2-1.0.6/bzip2.pc.in +--- bzip2-1.0.6.orig/bzip2.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ bzip2-1.0.6/bzip2.pc.in 2019-05-01 11:47:29.795517973 +0200 +@@ -0,0 +1,11 @@ ++exec_prefix=${prefix} ++bindir=${exec_prefix}/bin ++libdir=${exec_prefix}/lib ++includedir=${prefix}/include ++ ++Name: bzip2 ++Description: Lossless, block-sorting data compression ++Version: 1.0.6 ++Libs: -L${libdir} -lbz2 ++Cflags: -I${includedir} ++ +diff -Nau bzip2-1.0.6.orig/Makefile bzip2-1.0.6/Makefile +--- bzip2-1.0.6.orig/Makefile 2019-05-01 11:28:04.788206974 +0200 ++++ bzip2-1.0.6/Makefile 2019-05-01 11:46:20.911324226 +0200 +@@ -107,6 +107,9 @@ + echo ".so man1/bzgrep.1" > $(PREFIX)/man/man1/bzfgrep.1 + echo ".so man1/bzmore.1" > $(PREFIX)/man/man1/bzless.1 + echo ".so man1/bzdiff.1" > $(PREFIX)/man/man1/bzcmp.1 ++ if ( test ! -d $(PREFIX)/lib/pkgconfig ) ; then mkdir -p $(PREFIX)/lib/pkgconfig ; fi ++ echo "prefix=$(PREFIX)" > $(PREFIX)/lib/pkgconfig/bzip2.pc ++ cat bzip2.pc.in >> $(PREFIX)/lib/pkgconfig/bzip2.pc + + clean: + rm -f *.o libbz2.a bzip2 bzip2recover \ From 2ff0baa38e10f06bb55ade5402dd44914eb125d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 May 2019 15:07:03 +0200 Subject: [PATCH 1355/5331] adding easyconfigs: Qt5-5.12.3-GCCcore-8.2.0.eb --- .../q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..e16a228c3c5 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.12.3' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +checksums = ['6462ac74c00ff466487d8ef8d0922971aa5b1d5b33c0753308ec9d57711f5a42'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), + ('Bison', '3.0.5'), + ('flex', '2.6.4'), + ('Python', '2.7.15'), +] + +dependencies = [ + ('GLib', '2.60.1'), + ('libpng', '1.6.36'), + ('X11', '20190311'), + ('libGLU', '9.0.0'), + ('NSS', '3.42.1'), + ('DBus', '1.13.8'), + ('gperf', '3.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +# make sure QtWebEngine component is being built & installed +check_qtwebengine = True + +moduleclass = 'devel' From 08f5b73f7d95474b59a5367d9fe3c7a3df87a4a3 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 1 May 2019 15:59:54 +0200 Subject: [PATCH 1356/5331] Added support for pkg-config via pkgconfig/bzip2.pc --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-pkgconfig.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-pkgconfig.patch b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-pkgconfig.patch index 8f20eb0c991..f477e4a134b 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-pkgconfig.patch +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-pkgconfig.patch @@ -1,6 +1,8 @@ #- Adds a pkgconfig/bzip2.pc file # # author: Jiri Furst +# inspired by OpenSUSE patch by Stanislav Brabec , see +# http://ftp.suse.com/pub/people/sbrabec/bzip2/ diff -Nau bzip2-1.0.6.orig/bzip2.pc.in bzip2-1.0.6/bzip2.pc.in --- bzip2-1.0.6.orig/bzip2.pc.in 1970-01-01 01:00:00.000000000 +0100 +++ bzip2-1.0.6/bzip2.pc.in 2019-05-01 11:47:29.795517973 +0200 From 65651a698797ee88fe103161e2d280aec5e92e5b Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 1 May 2019 16:46:52 +0200 Subject: [PATCH 1357/5331] Updated checksums --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-8.2.0.eb index 64bb0f026a7..fe70a62f692 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-8.2.0.eb @@ -18,7 +18,7 @@ sources = [SOURCE_TAR_GZ] patches = ['bzip2-%(version)s-pkgconfig.patch'] checksums = [ 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz - '97ba60fc236049d38a42934da0b94cadd7d56d0d2309c04da58781837c622f65', # bzip2-1.0.6-pkgconfig.patch + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch ] builddependencies = [ From 914f9dbe94f348a5663c04711eda7b77486b8042 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 May 2019 16:48:43 +0200 Subject: [PATCH 1358/5331] add patch to fix build of Qt5 5.12.3 on non-AVX2 systems --- .../easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb | 6 +++++- .../easyconfigs/q/Qt5/Qt5-5.12.3_fix-avx2.patch | 14 ++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-avx2.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb index e16a228c3c5..41c7d2155b4 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb @@ -15,7 +15,11 @@ source_urls = [ 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' ] sources = ['qt-everywhere-src-%(version)s.tar.xz'] -checksums = ['6462ac74c00ff466487d8ef8d0922971aa5b1d5b33c0753308ec9d57711f5a42'] +patches = ['Qt5-%(version)s_fix-avx2.patch'] +checksums = [ + '6462ac74c00ff466487d8ef8d0922971aa5b1d5b33c0753308ec9d57711f5a42', # qt-everywhere-src-5.12.3.tar.xz + '40f19bfc3233cdc9fba487f64c830856c0ee34664483965d79ac08311ffcd5d6', # Qt5-5.12.3_fix-avx2.patch +] builddependencies = [ ('binutils', '2.31.1'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-avx2.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-avx2.patch new file mode 100644 index 00000000000..4dbc4ceac5a --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-avx2.patch @@ -0,0 +1,14 @@ +build qdrawhelper_avx2.cpp with -mavx2 rather than -march=core-avx2 to avoid compilation failures on non-AVX2 systems +cfr. https://bugreports.qt.io/browse/QTBUG-71564 (and https://gcc.gnu.org/bugzilla/show_bug.cgi?id=69471) +author: Kenneth Hoste (HPC-UGent) +--- qt-everywhere-src-5.12.3/qtbase/src/gui/Makefile.orig 2019-05-01 16:37:30.802829447 +0200 ++++ qt-everywhere-src-5.12.3/qtbase/src/gui/Makefile 2019-05-01 16:38:30.204257192 +0200 +@@ -3076,7 +3076,7 @@ + painting/qdrawingprimitive_sse2_p.h \ + painting/qrgba64_p.h \ + .pch/Qt5Gui.gch/c++ +- g++ -c $(CXXFLAGS) -march=core-avx2 $(INCPATH) painting/qdrawhelper_avx2.cpp -o .obj/qdrawhelper_avx2.o ++ g++ -c $(CXXFLAGS) -mavx2 $(INCPATH) painting/qdrawhelper_avx2.cpp -o .obj/qdrawhelper_avx2.o + + compiler_arch_haswell_c_compiler_make_all: + compiler_arch_haswell_c_compiler_clean: From dd46366b7ae68109f88f8d8dd14a9a904d7480ce Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 1 May 2019 17:02:08 +0200 Subject: [PATCH 1359/5331] Support for pkgconfig for all bzip2 packages --- .../easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb | 6 +++++- .../easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb | 6 +++++- .../easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2016.03.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.1.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.2.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.2.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.3-2.25.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-7.2.0.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-7.3.0.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2014b.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015a.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015b.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016a.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016b.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2.11.5.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2017a.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.4.10.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.14.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.2.0.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.3.0.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.4.0.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.5.0.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-6.2.5.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-7.1.2.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014b.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015a.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.eb | 6 +++++- .../b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016a.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016b.eb | 6 +++++- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb | 6 +++++- .../b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb | 6 +++++- 45 files changed, 225 insertions(+), 45 deletions(-) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb index 5e0abca6af5..eb52023752b 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.06.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb index 85dc1040816..8a16aff150c 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2015.11.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2016.03.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2016.03.eb index ffade220bb8..0400f85dbe4 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2016.03.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.1.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.1.eb index 2fa90ff3367..c7edb2ab915 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.1.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.2.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.2.eb index cdfa5b94893..9d50e3aeea3 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.2.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb index c35f939592d..62481c78728 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.8.4.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.2.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.2.eb index 293e21b83d7..c36dae00372 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.2.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.3-2.25.eb index 2e6b2c04690..4cf06fe534c 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-4.9.3-2.25.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.eb index 6e7f1090d16..0c1c69f35bd 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb index 327e3d5254b..37441762499 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb @@ -11,7 +11,11 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] builddependencies = [ ('binutils', '2.25'), diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb index 5806b7c50f0..ef7b74223fe 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb @@ -11,7 +11,11 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] # use same binutils version that was used when building GCCcore toolchain builddependencies = [('binutils', '2.26', '', True)] diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb index b570a3b40e3..afaa5714028 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb @@ -11,7 +11,11 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] # use same binutils version that was used when building GCCcore toolchain builddependencies = [('binutils', '2.27', '', True)] diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb index b5d10c82c19..25eb9437b1d 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.4.0.eb @@ -15,7 +15,11 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-7.2.0.eb index 8da8429c12c..055a3349f4d 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-7.2.0.eb @@ -15,7 +15,11 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] builddependencies = [ ('binutils', '2.29'), diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-7.3.0.eb index 826ea48849c..1b84405bc0c 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-7.3.0.eb @@ -15,7 +15,11 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] builddependencies = [ ('binutils', '2.30'), diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.eb index 76b5abe9484..9ceafd8990a 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2014b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2014b.eb index 6eacc835424..38b598cafe9 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2014b.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2014b.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb index 3146b98d07a..0a1802e3f7a 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015a.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015a.eb index 632a9f38ca7..f25396c6433 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015a.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015a.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015b.eb index 5dbb19d7a47..d1dd4fc2927 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015b.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015b.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb index 249fd25614e..4d4e4303360 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016.04.eb @@ -12,6 +12,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016a.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016a.eb index 544c7e27d93..7f8134abe9e 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016a.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016a.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016b.eb index 77377e1573d..405d7e0e8ce 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016b.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016b.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2.11.5.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2.11.5.eb index e9f6860bcae..761dbe486a1 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2.11.5.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2017a.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2017a.eb index 3318502d5f0..eb274b40ccf 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2017a.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gimkl-2017a.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb index 80612f4810b..edd8ed2e00d 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gompi-1.5.16.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.4.10.eb index 67f16f87fd8..7d90abb893e 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.4.10.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.14.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.14.eb index 466bd203660..7d7bad06dba 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.14.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb index 6efc0e17e4e..616914296e7 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.5.16.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb index 6e5804a218c..69f44a23cc7 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.2.0.eb index 3f048ad622a..c3b2aaf6620 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.2.0.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.3.0.eb index 71f78928844..2edb5215e79 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.3.0.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.4.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.4.0.eb index 8695d000421..3b240e654b8 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.4.0.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.5.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.5.0.eb index c9d2d644259..9bc28621acc 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-5.5.0.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-6.2.5.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-6.2.5.eb index 2eb69fd0b92..d89acf8a980 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-6.2.5.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-7.1.2.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-7.1.2.eb index 98fda248157..ceccb0d103c 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-ictce-7.1.2.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb index aa991af52fe..c9a74a84a88 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014b.eb index 8e22a6b83e5..173a6258037 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014b.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014b.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015a.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015a.eb index 3cf08495ebe..bd1d0142faf 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015a.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015a.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.eb index c3f33dcc8e7..cc73862ed4e 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb index cce64bccb38..9dc055a4585 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016.02-GCC-4.9.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016a.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016a.eb index b057c598813..b3ee78cd416 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016a.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016a.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016b.eb index 5431a03c4d0..05453a3d0be 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016b.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016b.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb index 2cf4dc76251..4bad1dbc504 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.07.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb index 182b7334898..6ead5500cd5 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -11,6 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] moduleclass = 'tools' From f0f7f11bdf49533eb1bed9d7c4f4ff7fa7e524ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 May 2019 19:17:18 +0200 Subject: [PATCH 1360/5331] remove download_dep_fail in RBFOpt easyconfig (not required when using PythonBundle) --- .../r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb index 506bb38e123..7f3482ebb6d 100644 --- a/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RBFOpt/RBFOpt-4.1.1-intel-2018b-Python-3.6.6.eb @@ -13,7 +13,6 @@ dependencies = [ ('Python', '3.6.6'), ] -download_dep_fail = True use_pip = True exts_list = [ From 78a69f4da276f83db0ccc8f41d0eb65316ad7e03 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 1 May 2019 19:51:51 +0200 Subject: [PATCH 1361/5331] Support for pkgconfig for all bzip2 packages --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb index 702538bade1..1110fd72bcf 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb @@ -11,7 +11,11 @@ toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] sources = [SOURCE_TAR_GZ] -checksums = ['a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd', # bzip2-1.0.6.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] buildopts = "CC=gcc CFLAGS='-Wall -Winline -O3 -fPIC -g $(BIGFILES)'" From 9da55e0bcec08f9645b2e37559d2e024348a98e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 May 2019 22:14:47 +0200 Subject: [PATCH 1362/5331] fix patch for Qt5 --- .../q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb | 2 +- .../q/Qt5/Qt5-5.12.3_fix-avx2.patch | 20 +++++++++---------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb index 41c7d2155b4..441e75e10e5 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb @@ -18,7 +18,7 @@ sources = ['qt-everywhere-src-%(version)s.tar.xz'] patches = ['Qt5-%(version)s_fix-avx2.patch'] checksums = [ '6462ac74c00ff466487d8ef8d0922971aa5b1d5b33c0753308ec9d57711f5a42', # qt-everywhere-src-5.12.3.tar.xz - '40f19bfc3233cdc9fba487f64c830856c0ee34664483965d79ac08311ffcd5d6', # Qt5-5.12.3_fix-avx2.patch + '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.12.3_fix-avx2.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-avx2.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-avx2.patch index 4dbc4ceac5a..a2c9a0cdf28 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-avx2.patch +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-avx2.patch @@ -1,14 +1,14 @@ build qdrawhelper_avx2.cpp with -mavx2 rather than -march=core-avx2 to avoid compilation failures on non-AVX2 systems cfr. https://bugreports.qt.io/browse/QTBUG-71564 (and https://gcc.gnu.org/bugzilla/show_bug.cgi?id=69471) author: Kenneth Hoste (HPC-UGent) ---- qt-everywhere-src-5.12.3/qtbase/src/gui/Makefile.orig 2019-05-01 16:37:30.802829447 +0200 -+++ qt-everywhere-src-5.12.3/qtbase/src/gui/Makefile 2019-05-01 16:38:30.204257192 +0200 -@@ -3076,7 +3076,7 @@ - painting/qdrawingprimitive_sse2_p.h \ - painting/qrgba64_p.h \ - .pch/Qt5Gui.gch/c++ -- g++ -c $(CXXFLAGS) -march=core-avx2 $(INCPATH) painting/qdrawhelper_avx2.cpp -o .obj/qdrawhelper_avx2.o -+ g++ -c $(CXXFLAGS) -mavx2 $(INCPATH) painting/qdrawhelper_avx2.cpp -o .obj/qdrawhelper_avx2.o +--- qt-everywhere-src-5.12.3.orig/qtbase/mkspecs/common/gcc-base.conf 2019-04-09 11:51:26.000000000 +0200 ++++ qt-everywhere-src-5.12.3/qtbase/mkspecs/common/gcc-base.conf 2019-05-01 19:21:50.683489624 +0200 +@@ -109,7 +109,7 @@ + QMAKE_CFLAGS_MIPS_DSPR2 += -mdspr2 - compiler_arch_haswell_c_compiler_make_all: - compiler_arch_haswell_c_compiler_clean: + # -march=haswell is supported as of GCC 4.9 and Clang 3.6 +-QMAKE_CFLAGS_ARCH_HASWELL = -march=core-avx2 ++QMAKE_CFLAGS_ARCH_HASWELL = -mavx2 + + # Wrapper tools that understand .o/.a files with GIMPLE instead of machine code + QMAKE_AR_LTCG = gcc-ar cqs From 20ec84290ad780cc75464d307146efccccb6d8f0 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 1 May 2019 15:44:20 -0500 Subject: [PATCH 1363/5331] adding easyconfigs: charmm-43b2-foss-2017b.eb, charmm-43b2-intel-2017b.eb and patches: charmm-43b2_Use_xhost.patch --- .../c/charmm/charmm-43b2-foss-2017b.eb | 30 +++++++++++++++++++ .../c/charmm/charmm-43b2-intel-2017b.eb | 29 ++++++++++++++++++ .../c/charmm/charmm-43b2_Use_xhost.patch | 16 ++++++++++ 3 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/c/charmm/charmm-43b2-foss-2017b.eb create mode 100644 easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb create mode 100644 easybuild/easyconfigs/c/charmm/charmm-43b2_Use_xhost.patch diff --git a/easybuild/easyconfigs/c/charmm/charmm-43b2-foss-2017b.eb b/easybuild/easyconfigs/c/charmm/charmm-43b2-foss-2017b.eb new file mode 100644 index 00000000000..62ad10b31e1 --- /dev/null +++ b/easybuild/easyconfigs/c/charmm/charmm-43b2-foss-2017b.eb @@ -0,0 +1,30 @@ +# Authors:: Ward Poelmans +easyblock = 'EB_CHARMM' + +name = 'charmm' +version = '43b2' + +homepage = "http://www.charmm.org" +description = """CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile +and widely used molecular simulation program with broad application to many-particle systems. +charmm provides all the functionality of CHARMM except its performance enhancements.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True, 'opt': True} + +# Request the download link from http://charmm.chemistry.harvard.edu/request_license.php?version=charmm +# and rename the file with the latest version reported in the ChangeLogs directory +sources = ["charmm-c%(version)s.tar.gz"] +patches = ["charmm-43b2_Use_xhost.patch"] +checksums = [ + 'de0d5e2fa8508c73292355918b2bc43eef44c5b6bcae050848862400b64e51f8', # charmm-c43b2.tar.gz + '3b1f1ac371578d9bd814bf4ac223b839ac293ae3aa6156611beba26b2dc25163', # charmm-43b2_Use_xhost.patch +] + +# MKL activated automatically when the intel toolchain is used +build_options = "FULL COLFFT PIPF -CMPI" + +# Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +system_size = "medium" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb b/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb new file mode 100644 index 00000000000..9ca9d1daf5f --- /dev/null +++ b/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb @@ -0,0 +1,29 @@ +# Authors:: Ward Poelmans +easyblock = 'EB_CHARMM' + +name = 'charmm' +version = '43b2' + +homepage = "http://www.charmm.org" +description = """CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile +and widely used molecular simulation program with broad application to many-particle systems. +charmm provides all the functionality of CHARMM except its performance enhancements.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'usempi': True, 'opt': True} + +# Request the download link from http://charmm.chemistry.harvard.edu/request_license.php?version=charmm +# and rename the file with the latest version reported in the ChangeLogs directory +sources = ["charmm-c%(version)s.tar.gz"] +patches = ["charmm-43b2_Use_xhost.patch"] + +# Ensure that mpiifort is used instead of mpif90 +prebuildopts = 'MPIIFORT=YES' + +# MKL activated automatically when the intel toolchain is used +build_options = "FULL COLFFT PIPF -CMPI" + +# Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +system_size = "medium" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/charmm/charmm-43b2_Use_xhost.patch b/easybuild/easyconfigs/c/charmm/charmm-43b2_Use_xhost.patch new file mode 100644 index 00000000000..77ad335588e --- /dev/null +++ b/easybuild/easyconfigs/c/charmm/charmm-43b2_Use_xhost.patch @@ -0,0 +1,16 @@ +# Use the optimization options from EasyBuild +# Davide Vanzo (Vanderbilt University) +diff -ru charmm.orig/build/UNX/Makefile_em64t charmm/build/UNX/Makefile_em64t +--- charmm.orig/build/UNX/Makefile_em64t 2019-04-16 15:08:16.873426458 -0500 ++++ charmm/build/UNX/Makefile_em64t 2019-04-16 15:09:31.909428534 -0500 +@@ -88,8 +88,8 @@ + + FC0 = $(FC) -c -O0 -free -fp-model strict + FC1 = $(FC) -c -O1 -free -fp-model strict +-FC2 = $(FC) -c -O3 -mp1 -axSSE4.1 -free -fp-model strict +-FC3 = $(FC) -c -O3 -mp1 -axSSE4.1 -free -fp-model strict ++FC2 = $(FC) -c -mp1 -free $(F90FLAGS) ++FC3 = $(FC) -c -mp1 -free $(F90FLAGS) + FCR = $(FC) -c -u -V -free -fp-model strict + FCD = $(FC) -c -g -O0 -u -traceback -free + From c134252890a7c17249fa6e210df07818ab6a40ca Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Wed, 1 May 2019 22:50:42 +0200 Subject: [PATCH 1364/5331] adding easyconfigs: PETSc-3.11.1-foss-2019a.eb, PETSc-3.11.1-intel-2019a.eb --- .../p/PETSc/PETSc-3.11.1-foss-2019a.eb | 40 ++++++++++++++++++ .../p/PETSc/PETSc-3.11.1-intel-2019a.eb | 42 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-foss-2019a.eb create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-intel-2019a.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-foss-2019a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-foss-2019a.eb new file mode 100644 index 00000000000..b5e13f1fec9 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-foss-2019a.eb @@ -0,0 +1,40 @@ +name = 'PETSc' +version = '3.11.1' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', + 'PETSc-3.9.3_fix-AVX512.patch', +] +checksums = [ + 'cb627f99f7ce1540ebbbf338189f89a5f1ecf3ab3b5b0e357f9e46c209f1fb23', # petsc-3.11.1.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch + 'f11e3d7c36ec9939b10550c9913320e0ee4b34585bdf9458977548686f90bfa8', # PETSc-3.9.3_fix-AVX512.patch +] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [ + ('Boost', '1.70.0'), + ('METIS', '5.1.0'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '6.0.6'), + ('SuiteSparse', '5.4.0', '-METIS-5.1.0'), + ('Hypre', '2.15.1'), +] + +configopts = '--LIBS="$LIBS -lrt"' + +# only required when building PETSc in a SLURM job environment +# configopts = '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-intel-2019a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-intel-2019a.eb new file mode 100644 index 00000000000..602d0a0bb41 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-intel-2019a.eb @@ -0,0 +1,42 @@ +name = 'PETSc' +version = '3.11.1' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', + 'PETSc-3.9.3_fix-AVX512.patch', +] +checksums = [ + 'cb627f99f7ce1540ebbbf338189f89a5f1ecf3ab3b5b0e357f9e46c209f1fb23', # petsc-3.11.1.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch + 'f11e3d7c36ec9939b10550c9913320e0ee4b34585bdf9458977548686f90bfa8', # PETSc-3.9.3_fix-AVX512.patch +] + +builddependencies = [('CMake', '3.13.3')] + +#parmetis = 'ParMETIS' +#parmetis_ver = '4.0.3' +dependencies = [ + ('Boost', '1.70.0'), + ('METIS', '5.1.0'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '6.0.6'), + ('SuiteSparse', '5.4.0', '-METIS-5.1.0'), + ('Hypre', '2.15.1'), +] + +configopts = '--LIBS="$LIBS -lrt"' + +# only required when building PETSc in a SLURM job environment +# configopts = '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' From 9133c4313f754911a5ddc5eed6c6354b43f42227 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 1 May 2019 16:14:26 -0500 Subject: [PATCH 1365/5331] Added missing checksums --- easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb b/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb index 9ca9d1daf5f..6a43c53d199 100644 --- a/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb +++ b/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb @@ -16,6 +16,10 @@ toolchainopts = {'usempi': True, 'opt': True} # and rename the file with the latest version reported in the ChangeLogs directory sources = ["charmm-c%(version)s.tar.gz"] patches = ["charmm-43b2_Use_xhost.patch"] +checksums = [ + 'de0d5e2fa8508c73292355918b2bc43eef44c5b6bcae050848862400b64e51f8', # charmm-c43b2.tar.gz + '3b1f1ac371578d9bd814bf4ac223b839ac293ae3aa6156611beba26b2dc25163', # charmm-43b2_Use_xhost.patch +] # Ensure that mpiifort is used instead of mpif90 prebuildopts = 'MPIIFORT=YES' From 088ef293882e339bc2ab9fd171ccd6e525772fed Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 2 May 2019 00:26:24 +0200 Subject: [PATCH 1366/5331] adding easyconfigs: Hypre-2.15.1-foss-2019a.eb, Hypre-2.15.1-intel-2019a.eb --- .../h/Hypre/Hypre-2.15.1-foss-2019a.eb | 18 ++++++++++++++++++ .../h/Hypre/Hypre-2.15.1-intel-2019a.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-foss-2019a.eb create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-intel-2019a.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-foss-2019a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-foss-2019a.eb new file mode 100644 index 00000000000..e31136e3c07 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-foss-2019a.eb @@ -0,0 +1,18 @@ +name = 'Hypre' +version = '2.15.1' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['58d215146e1c7c2c11be4cb1eac0d1663a45584efbe5f603205d8c4766b7579f'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-intel-2019a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-intel-2019a.eb new file mode 100644 index 00000000000..759501b07d9 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-intel-2019a.eb @@ -0,0 +1,18 @@ +name = 'Hypre' +version = '2.15.1' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['58d215146e1c7c2c11be4cb1eac0d1663a45584efbe5f603205d8c4766b7579f'] + +start_dir = 'src' + +moduleclass = 'numlib' From c2acb65177398a26da9c214f8c28ac74d38cc5d6 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 2 May 2019 00:28:34 +0200 Subject: [PATCH 1367/5331] adding easyconfigs: SuiteSparse-5.4.0-intel-2019a-METIS-5.1.0.eb, SuiteSparse-5.4.0-foss-2019a-METIS-5.1.0.eb --- ...uiteSparse-5.4.0-foss-2019a-METIS-5.1.0.eb | 26 +++++++++++++++++++ ...iteSparse-5.4.0-intel-2019a-METIS-5.1.0.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2019a-METIS-5.1.0.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-intel-2019a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2019a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2019a-METIS-5.1.0.eb new file mode 100644 index 00000000000..2331ba184ff --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-foss-2019a-METIS-5.1.0.eb @@ -0,0 +1,26 @@ +name = 'SuiteSparse' +version = '5.4.0' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] +checksums = ['374dd136696c653e34ef3212dc8ab5b61d9a67a6791d5ec4841efb838e94dbd1'] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [('METIS', metis_ver)] + +parallel = 1 + +prebuildopts = "sed -i 's/-openmp/-fopenmp/g' SuiteSparse_config/SuiteSparse_config.mk && " +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts += "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-intel-2019a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-intel-2019a-METIS-5.1.0.eb new file mode 100644 index 00000000000..d8155ac7f7a --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.4.0-intel-2019a-METIS-5.1.0.eb @@ -0,0 +1,26 @@ +name = 'SuiteSparse' +version = '5.4.0' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] +checksums = ['374dd136696c653e34ef3212dc8ab5b61d9a67a6791d5ec4841efb838e94dbd1'] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [('METIS', metis_ver)] + +parallel = 1 + +prebuildopts = "sed -i 's/-openmp/-fopenmp/g' SuiteSparse_config/SuiteSparse_config.mk && " +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts += "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From ba44fddae1a975770cd2ec5a871dea9d2c933cce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2019 10:27:45 +0200 Subject: [PATCH 1368/5331] enable check_ldshared for pyFFTW built with intel toolchain on top of Python built with GCCcore --- easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb index 5b722669eec..dd407dfc5a3 100644 --- a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.11.1-intel-2019a.eb @@ -23,4 +23,7 @@ dependencies = [ download_dep_fail = True use_pip = True +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + moduleclass = 'lib' From e3d9ae418aaa8ea24b28b6b550d2bfe5b7b8815c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 11:25:31 +0200 Subject: [PATCH 1369/5331] adding easyconfigs: fmt-5.3.0-GCCcore-8.2.0.eb --- .../f/fmt/fmt-5.3.0-GCCcore-8.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-5.3.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-5.3.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-5.3.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..14aef7c2479 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-5.3.0-GCCcore-8.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '5.3.0' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['4c0741e10183f75d7d6f730b8708a99b329b2f942dad5a9da3385ab92bb4a15c'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' From 030093d9016799830964d6e4c0e015821188acdc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 13:20:21 +0200 Subject: [PATCH 1370/5331] adding easyconfigs: ADDA-1.3b4-foss-2019a.eb and patches: ADDA-1.3b4_add_install_target.patch, ADDA-1.3b4_fix_bad_cmd_name_code.patch, ADDA-1.3b4_remove_bad_MPI_detection_code.patch, ADDA-1.3b4_remove_xxOPTSFILE_targets.patch --- .../a/ADDA/ADDA-1.3b4-foss-2019a.eb | 45 +++++++++++ .../ADDA/ADDA-1.3b4_add_install_target.patch | 29 +++++++ .../ADDA-1.3b4_fix_bad_cmd_name_code.patch | 21 +++++ ...-1.3b4_remove_bad_MPI_detection_code.patch | 48 ++++++++++++ ...ADDA-1.3b4_remove_xxOPTSFILE_targets.patch | 77 +++++++++++++++++++ 5 files changed, 220 insertions(+) create mode 100644 easybuild/easyconfigs/a/ADDA/ADDA-1.3b4-foss-2019a.eb create mode 100644 easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_add_install_target.patch create mode 100644 easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_fix_bad_cmd_name_code.patch create mode 100644 easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_remove_bad_MPI_detection_code.patch create mode 100644 easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_remove_xxOPTSFILE_targets.patch diff --git a/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4-foss-2019a.eb b/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4-foss-2019a.eb new file mode 100644 index 00000000000..2962e12d575 --- /dev/null +++ b/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4-foss-2019a.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'ADDA' +version = '1.3b4' + +homepage = 'https://github.com/adda-team/adda/wiki' +description = """ADDA is an open-source parallel implementation of the +discrete dipole approximation, capable to simulate light scattering by +particles of arbitrary shape and composition in a wide range of particle +sizes.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/adda-team/adda/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_add_install_target.patch', + '%(name)s-%(version)s_remove_xxOPTSFILE_targets.patch', + '%(name)s-%(version)s_remove_bad_MPI_detection_code.patch', + '%(name)s-%(version)s_fix_bad_cmd_name_code.patch', +] +checksums = [ + 'fb6eb6ac721a0dc97754198daf6c3ff321394e1e2921758b0fda56ee00a40ffa', # v1.3b4.tar.gz + '8d07d5eafab22c727ca57f51c98cddfbf84b86129a4cdd340cf086e8c8fb51c6', # ADDA-1.3b4_add_install_target.patch + 'fa6946ddbf5249a3c75609202d3dabf8633b34717704595250fb807ccf0da007', # ADDA-1.3b4_remove_xxOPTSFILE_targets.patch + # ADDA-1.3b4_remove_bad_MPI_detection_code.patch + '362c1c556e1f98a5d29522076b076ca629faa8567019057ab9f95a6d28df4027', + '67c516b35a5318840ec946d1c06cb211a1a6fd39c1e6ac88907969274b0a8b16', # ADDA-1.3b4_fix_bad_cmd_name_code.patch +] + +skipsteps = ['configure'] + +start_dir = 'src' + +buildopts = ' COMPILER=other OPTIONS="USE_SSE3" CF=$F90 CCPP=$CXX seq mpi ' + +installopts = 'TARGETS="seq mpi" DESTDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['adda']], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_add_install_target.patch b/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_add_install_target.patch new file mode 100644 index 00000000000..5847497dcbc --- /dev/null +++ b/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_add_install_target.patch @@ -0,0 +1,29 @@ +Add install target. + +Åke Sandgren, 20190502 +diff -ru adda-1.3b4.orig/src/common.mk adda-1.3b4/src/common.mk +--- adda-1.3b4.orig/src/common.mk 2014-02-20 15:48:03.000000000 +0100 ++++ adda-1.3b4/src/common.mk 2019-05-02 10:29:45.487297028 +0200 +@@ -108,3 +108,7 @@ + echo -n "$(subst ",\",$(CPPCMD))" > $@ + + -include $(CDEPEND) ++ ++install: $(PROG) ++ mkdir -p $(DESTDIR)/bin ++ cp $(PROG) $(DESTDIR)/bin +diff -ru adda-1.3b4.orig/src/Makefile adda-1.3b4/src/Makefile +--- adda-1.3b4.orig/src/Makefile 2014-02-20 15:48:03.000000000 +0100 ++++ adda-1.3b4/src/Makefile 2019-05-02 10:44:48.222497406 +0200 +@@ -467,6 +467,11 @@ + @echo "Compiling OpenCL version of ADDA" + $(MAKE) -C $(OCL) + ++install: ++ for i in $(TARGETS); do \ ++ make -C $$i install; \ ++ done ++ + cleanfull: clean cleanruns + + clean: cleanseq cleanmpi cleanocl diff --git a/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_fix_bad_cmd_name_code.patch b/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_fix_bad_cmd_name_code.patch new file mode 100644 index 00000000000..96de7e95430 --- /dev/null +++ b/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_fix_bad_cmd_name_code.patch @@ -0,0 +1,21 @@ +Fix bad code for detecting executables name. + +Åke Sandgren, 20190502 +diff -ru adda-1.3b4.orig/src/param.c adda-1.3b4/src/param.c +--- adda-1.3b4.orig/src/param.c 2014-02-20 15:48:03.000000000 +0100 ++++ adda-1.3b4/src/param.c 2019-05-02 12:53:34.618014688 +0200 +@@ -1919,9 +1919,11 @@ + // try to determine terminal width + if ((p1=getenv("COLUMNS"))!=NULL && sscanf(p1,"%d",&tmp)==1 && tmp>=MIN_TERM_WIDTH) term_width=tmp; + // get name of executable; remove all path overhead +- if ((p1=strrchr(argv[0],'\\'))==NULL) p1=argv[0]; +- if ((p2=strrchr(argv[0],'/'))==NULL) p2=argv[0]; +- exename=MAX(p1,p2)+1; ++ if ((exename = strrchr(argv[0],'/')) == NULL) { ++ if ((exename = strrchr(argv[0],'\\')) == NULL) { ++ exename = argv[0]; ++ } ++ } + // initialize option + opt.l1=UNDEF; + // check first argument diff --git a/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_remove_bad_MPI_detection_code.patch b/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_remove_bad_MPI_detection_code.patch new file mode 100644 index 00000000000..86fca784288 --- /dev/null +++ b/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_remove_bad_MPI_detection_code.patch @@ -0,0 +1,48 @@ +Remove bad MPI compiler detection code. + +Åke Sandgren, 20190502 +diff -ru adda-1.3b4.orig/src/mpi/Makefile adda-1.3b4/src/mpi/Makefile +--- adda-1.3b4.orig/src/mpi/Makefile 2014-02-20 15:48:03.000000000 +0100 ++++ adda-1.3b4/src/mpi/Makefile 2019-05-02 12:27:30.173683945 +0200 +@@ -19,17 +19,6 @@ + # for compilation. However, the default set of options may work out-of-box on some systems. + #======================================================================================================================= + +-# Heurestics to determine if MPI wrapper is available. If $(MPICC) is defined it is used as is. Otherwise we try to +-# locate 'mpicc' wrapper through system call, and reverse to $(CC) as the last resort. This should work fine in many +-# cases, but can be replaced by a simple assignment of MPICC. +-ifndef MPICC +- ifeq ($(shell which mpicc > /dev/null 2>&1 && echo 0),0) +- MPICC := mpicc +- else +- MPICC := $(CC) +- endif +-endif +- + # Compiler dependent options + # These are options for a particular Alpha system + ifeq ($(COMPILER),compaq) +@@ -37,23 +26,6 @@ + LDFLAGS += -lmpi -lelan + endif + +-# If the compiler is used directly, a few additional options are needed +-ifeq ($(MPICC),$(CC)) +- # Depending on a particular MPI installation one may need to manually specify paths to MPI headers and libraries. +- # Path should be absolute or relative to the location of this Makefile. +- #CFLAGS += -I"C:/Program Files/MPICH2/include" +- #LDFLAGS += -L"C:/Program Files/MPICH2/lib" +- +- LDFLAGS += -lmpi +-# If MPI compiler wrapper is used, environmental variables are set to define C compiler and linker +-else +- # for MPICH +- export MPICH_CC = $(CC) +- export MPICH_CLINKER = $(CC) +- # for OpenMPI +- export OMPI_CC = $(CC) +-endif +- + #======================================================================================================================= + # !!! End of control section. Everything below is not designed to be modified by user + #======================================================================================================================= diff --git a/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_remove_xxOPTSFILE_targets.patch b/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_remove_xxOPTSFILE_targets.patch new file mode 100644 index 00000000000..765dec6a87e --- /dev/null +++ b/easybuild/easyconfigs/a/ADDA/ADDA-1.3b4_remove_xxOPTSFILE_targets.patch @@ -0,0 +1,77 @@ +Remove xxOPTSFILE targets, they interfere with installation. + +Åke Sandgren, 20190502 +diff -ru adda-1.3b4.orig/src/common.mk adda-1.3b4/src/common.mk +--- adda-1.3b4.orig/src/common.mk 2019-05-02 10:53:25.301453425 +0200 ++++ adda-1.3b4/src/common.mk 2019-05-02 10:55:31.580222293 +0200 +@@ -43,19 +43,6 @@ + + READ_FILE = $(shell if [ -f $(1) ]; then cat $(1); fi) + +-ifneq ($(call READ_FILE,$(LDOPTSFILE)),$(LDCMD)) +- $(shell rm -f $(LDOPTSFILE)) +-endif +-ifneq ($(call READ_FILE,$(COPTSFILE)),$(CCMD)) +- $(shell rm -f $(COPTSFILE)) +-endif +-ifneq ($(call READ_FILE,$(FOPTSFILE)),$(FCMD)) +- $(shell rm -f $(FOPTSFILE)) +-endif +-ifneq ($(call READ_FILE,$(CPPOPTSFILE)),$(CPPCMD)) +- $(shell rm -f $(CPPOPTSFILE)) +-endif +- + vpath %.c $(PARENT) + vpath %.cpp $(PARENT)/$(CPPFOLDER) + vpath %.h $(PARENT) +@@ -68,22 +55,22 @@ + .DELETE_ON_ERROR: + + # C linker is used, while Fortran and C++ is handled by addition of libraries for linking +-$(PROG): $(COBJECTS) $(FOBJECTS) $(F90OBJECTS) $(CPPOBJECTS) $(LDOPTSFILE) ++$(PROG): $(COBJECTS) $(FOBJECTS) $(F90OBJECTS) $(CPPOBJECTS) + @echo "Building $@" + $(MYCC) -o $@ $(COBJECTS) $(FOBJECTS) $(F90OBJECTS) $(CPPOBJECTS) $(LDFLAGS) + +-$(COBJECTS): %.o: %.c $(COPTSFILE) ++$(COBJECTS): %.o: %.c + $(MYCC) -c $(CFLAGS) $(DEPFLAG) $< + + # Dependencies are only generated for C and C++ sources; we assume that each Fortran file is completely independent or + # all of the files from dependent set are compiled at once. +-$(FOBJECTS): %.o: %.f $(FOPTSFILE) ++$(FOBJECTS): %.o: %.f + $(MYCF) -c $(FFLAGS) $< + +-$(F90OBJECTS): %.o: %.f90 $(FOPTSFILE) ++$(F90OBJECTS): %.o: %.f90 + $(MYCF) -c $(FFLAGS) $< + +-$(CPPOBJECTS): %.o: %.cpp $(CPPOPTSFILE) ++$(CPPOBJECTS): %.o: %.cpp + $(MYCCPP) -c $(CPPFLAGS) $(DEPFLAG) $< + + # Special rule for generation of stringified CL source. Used only for ocl. All relevant variables are defined in +@@ -91,22 +78,6 @@ + $(addprefix $(CLSPREFIX),$(CLSTRING)): $(CLSPREFIX)%.clstr:%.cl + $(CLSCOMMAND) $< > $@ + +-$(LDOPTSFILE): +- @echo Linking needs to be redone +- echo -n "$(subst ",\",$(LDCMD))" > $@ +- +-$(COPTSFILE): +- @echo C sources need to be recompiled +- echo -n "$(subst ",\",$(CCMD))" > $@ +- +-$(FOPTSFILE): +- @echo Fortran sources need to be recompiled +- echo -n "$(subst ",\",$(FCMD))" > $@ +- +-$(CPPOPTSFILE): +- @echo C++ sources need to be recompiled +- echo -n "$(subst ",\",$(CPPCMD))" > $@ +- + -include $(CDEPEND) + + install: $(PROG) From 5aa9bb4ead7eda4bf0b3df41ca3535097056fe19 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 13:22:31 +0200 Subject: [PATCH 1371/5331] adding easyconfigs: fmt-5.3.0-GCCcore-7.3.0.eb --- .../f/fmt/fmt-5.3.0-GCCcore-7.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-5.3.0-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-5.3.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-5.3.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..df92af2d899 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-5.3.0-GCCcore-7.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '5.3.0' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['4c0741e10183f75d7d6f730b8708a99b329b2f942dad5a9da3385ab92bb4a15c'] + +builddependencies = [ + ('binutils', '2.30'), + ('CMake', '3.12.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' From 2ec9b69514f98dceebf23d7e84859dfaf595a2b2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 13:45:44 +0200 Subject: [PATCH 1372/5331] adding easyconfigs: libgpuarray-0.7.6-fosscuda-2019a.eb --- .../libgpuarray-0.7.6-fosscuda-2019a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb new file mode 100644 index 00000000000..97742e3f66c --- /dev/null +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'libgpuarray' +version = '0.7.6' + +homepage = 'http://deeplearning.net/software/libgpuarray/' +description = "Library to manipulate tensors on the GPU." + +toolchain = {'name': 'fosscuda', 'version': '2019a'} + +source_urls = ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'] + +builddependencies = [('CMake', '3.13.3')] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [ + ('SciPy-bundle', '2019.03'), + ('Mako', '1.0.8'), + ('NCCL', '2.4.2'), +] + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} +exts_list = [ + (name, version, { + 'buildcmd': 'build_ext', + 'modulename': 'pygpu', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], + 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgpuarray.%s' % SHLIB_EXT, 'lib/libgpuarray-static.a'], + 'dirs': ['include/gpuarray', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From f66a9ec7c8e405a29d817a9e2cd1c51000484344 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 13:56:24 +0200 Subject: [PATCH 1373/5331] adding easyconfigs: PyYAML-5.1-GCCcore-8.2.0.eb --- .../l/libyaml/libyaml-0.2.2-GCCcore-8.2.0.eb | 32 +++++++++++++++++++ .../p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb | 30 +++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.2.2-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..3e8dd3f6b4c --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.2-GCCcore-8.2.0.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.2' + +homepage = 'http://pyyaml.org/wiki/LibYAML' + +description = """LibYAML is a YAML parser and emitter written in C.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://pyyaml.org/download/libyaml/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['4a9100ab61047fd9bd395bcef3ce5403365cafd55c1e0d0299cde14958e47be9'] + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.%s" % SHLIB_EXT], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..4082ce69f4e --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '5.1' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['436bc774ecf7c103814098159fbb84c2715d25980175292c648f2da143909f95'] + +builddependencies = [('binutils', '2.31.1')] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [ + ('libyaml', '0.2.2'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 5e6285215486afe25631b0000c5871bd92dd2b93 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2019 14:02:36 +0200 Subject: [PATCH 1374/5331] fix PCMSolver build by not overriding CMAKE_CXX_FLAGS + fix sanity_check_paths --- .../p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb index 730cb4b72e6..de126d2763b 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb @@ -26,17 +26,14 @@ builddependencies = [ ] configopts = '-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN' -configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS $LIBLAPACK_MT"' separate_build_dir = True runtest = 'test' -postinstallcmds = ["chmod +x %(installdir)s/bin/pcmsolver.py"] - sanity_check_paths = { - 'files': ['bin/pcmsolver.py', 'lib/libpcm.a', 'lib/libpcm.%s' % SHLIB_EXT], - 'dirs': ['include'] + 'files': ['bin/run_pcm', 'lib/libpcm.a', 'lib/libpcm.%s' % SHLIB_EXT], + 'dirs': ['include/PCMSolver'] } moduleclass = 'chem' From 454aa54422efad177cfc07136803e6e4d9cabf88 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2019 14:10:27 +0200 Subject: [PATCH 1375/5331] remove unused toolchainopts in PCMSolver easyconfig --- .../p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb index de126d2763b..a28c1b6eabd 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb @@ -8,7 +8,6 @@ homepage = 'https://pcmsolver.readthedocs.org' description = """An API for the Polarizable Continuum Model.""" toolchain = {'name': 'foss', 'version': '2018b'} -#toolchainopts = {'cstd': 'c99'} source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] sources = ['v%(version)s.tar.gz'] From 93052e84edba11be8be7ef8303b2505794a5f2b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2019 14:17:42 +0200 Subject: [PATCH 1376/5331] {tools}[intel/2019a] networkx v2.3 w/ Python 3.7.2 --- .../networkx-2.3-intel-2019a-Python-3.7.2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.3-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/n/networkx/networkx-2.3-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..6f812aa169d --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.3-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] +checksums = ['8311ddef63cf5c5c5e7c1d0212dd141d9a1fe3f474915281b73597ed5f1d4e3d'] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True + +moduleclass = 'tools' From f70f35935b3ecfe386485bbf22330ef1a1db5902 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2019 14:18:12 +0200 Subject: [PATCH 1377/5331] {bio}[foss/2018b] MEGAHIT v1.1.4 w/ Python 3.6.6 --- .../MEGAHIT-1.1.4-foss-2018b-Python-3.6.6.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.4-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.4-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..26f52d87518 --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.1.4-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'MEGAHIT' +version = '1.1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex + metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ecd64c8bfa516ef6b19f9b2961ede281ec814db836f1a91953c213c944e1575f'] + +dependencies = [ + ('Python', '3.6.6'), +] + +# This is the CPU-only version. +# +# We're specifying 'version' because otherwise the Makefile will try to +# guess it using 'git describe --tag', which seems less reliable. +buildopts = 'version=v%(version)s verbose=1 use_gpu=0' + +files_to_copy = [ + (['%(namelower)s', '%(namelower)s_asm_core', '%(namelower)s_sdbg_build', '%(namelower)s_toolkit'], 'bin'), + 'LICENSE', + 'README.md', +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s_asm_core', 'bin/%(namelower)s_sdbg_build'], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s -v'] + +moduleclass = 'bio' From 42702ef0b4778dfe9c8e5f9bf688dd4649fce9ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2019 14:18:59 +0200 Subject: [PATCH 1378/5331] adding easyconfigs: ARWEN-1.2.3-GCCcore-7.3.0.eb --- .../a/ARWEN/ARWEN-1.2.3-GCCcore-7.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/ARWEN/ARWEN-1.2.3-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/a/ARWEN/ARWEN-1.2.3-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/ARWEN/ARWEN-1.2.3-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..56f31b01e0e --- /dev/null +++ b/easybuild/easyconfigs/a/ARWEN/ARWEN-1.2.3-GCCcore-7.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CmdCp' + +name = 'ARWEN' +version = '1.2.3' + +homepage = 'http://mbio-serv2.mbioekol.lu.se/ARWEN' +description = "ARWEN, tRNA detection in metazoan mitochondrial sequences" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://mbio-serv2.mbioekol.lu.se/ARWEN/'] +sources = [{'filename': 'arwen%(version)s.c', 'extract_cmd': "cp %s ."}] +checksums = ['0e843b6b9d71d943aab66882ac0091165e646103b194b0aecfd293f839b8df84'] + +builddependencies = [('binutils', '2.30')] + +cmds_map = [('.*', "$CC $CFLAGS %(source)s -o arwen")] + +files_to_copy = [(['arwen'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/arwen'], + 'dirs': [], +} + +sanity_check_commands = ["arwen -h"] + +moduleclass = 'bio' From b13f4521d1388164aa3c4e9faa6efe3f2e0e0b12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2019 14:36:28 +0200 Subject: [PATCH 1379/5331] adding easyconfigs: CheMPS2-1.8.9-intel-2019a.eb --- .../c/CheMPS2/CheMPS2-1.8.9-intel-2019a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2019a.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2019a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2019a.eb new file mode 100644 index 00000000000..6320d33cd9e --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2019a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.8.9' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ccd4c0d9432759d97690bf37a0333440f93513960c62d1f75842f090406a224d'] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [ + ('HDF5', '1.10.5') +] + +pretestopts = 'export OMP_NUM_THREADS=1 && ' +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' From 68f7b10d5824fb82e1fcc1f2974844b28afcc4b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2019 14:41:17 +0200 Subject: [PATCH 1380/5331] {tools}[GCCcore/8.2.0] deepdiff v4.0.6 w/ Python 3.7.2 --- ...epdiff-4.0.6-GCCcore-8.2.0-Python-3.7.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/d/deepdiff/deepdiff-4.0.6-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-4.0.6-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-4.0.6-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..78560569fa2 --- /dev/null +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-4.0.6-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'deepdiff' +version = '4.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://deepdiff.readthedocs.io/en/latest/' +description = """DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +builddependencies = [('binutils', '2.31.1')] +dependencies = [('Python', '3.7.2')] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('jsonpickle', '1.1', { + 'checksums': ['625098cc8e5854b8c23b587aec33bc8e33e0e597636bfaca76152249c78fe5c1'], + }), + ('ordered-set', '3.1.1', { + 'checksums': ['a7bfa858748c73b096e43db14eb23e2bc714a503f990c89fac8fab9b0ee79724'], + }), + (name, version, { + 'checksums': ['55e461f56dcae3dc540746b84434562fb7201e5c27ecf28800e4cfdd17f61e56'], + }), +] + +moduleclass = 'tools' From 323f4eecb0204a8ab57577ab0fc0047d0fc08158 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2019 14:44:47 +0200 Subject: [PATCH 1381/5331] use %(namelower)s in ARWEN easyconfig to make tests happy --- easybuild/easyconfigs/a/ARWEN/ARWEN-1.2.3-GCCcore-7.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ARWEN/ARWEN-1.2.3-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/ARWEN/ARWEN-1.2.3-GCCcore-7.3.0.eb index 56f31b01e0e..66b65689418 100644 --- a/easybuild/easyconfigs/a/ARWEN/ARWEN-1.2.3-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/a/ARWEN/ARWEN-1.2.3-GCCcore-7.3.0.eb @@ -14,7 +14,7 @@ checksums = ['0e843b6b9d71d943aab66882ac0091165e646103b194b0aecfd293f839b8df84'] builddependencies = [('binutils', '2.30')] -cmds_map = [('.*', "$CC $CFLAGS %(source)s -o arwen")] +cmds_map = [('.*', "$CC $CFLAGS %%(source)s -o %(namelower)s")] files_to_copy = [(['arwen'], 'bin')] From 014eb645615b49bf7e6860cfc2f5fa98c3062d8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2019 14:57:42 +0200 Subject: [PATCH 1382/5331] disable use of -march=native for PCMSolver built with foss/2018b, because of failing test if it's enabled... --- .../p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb index a28c1b6eabd..f8ba46b7525 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb @@ -8,6 +8,9 @@ homepage = 'https://pcmsolver.readthedocs.org' description = """An API for the Polarizable Continuum Model.""" toolchain = {'name': 'foss', 'version': '2018b'} +# we have to disable use of -march=native to ensure a correct build on recent Intel systems +# see also https://github.com/PCMSolver/pcmsolver/issues/159 +toolchainopts = {'optarch': False} source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] sources = ['v%(version)s.tar.gz'] From 16c8a36d3588c01cb081fa17f63d9611a65e2b86 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 15:14:12 +0200 Subject: [PATCH 1383/5331] Add "-python" suffix to pkgconfig to make it more distinct from pkg-config. --- ...-GCCcore-8.2.0.eb => pkgconfig-1.5.1-GCCcore-8.2.0-python.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/p/pkgconfig/{pkgconfig-1.5.1-GCCcore-8.2.0.eb => pkgconfig-1.5.1-GCCcore-8.2.0-python.eb} (97%) diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb similarity index 97% rename from easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb rename to easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb index 4e7799f3499..cf1b1654490 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb @@ -2,6 +2,7 @@ easyblock = 'PythonBundle' name = 'pkgconfig' version = '1.5.1' +versionsuffix = '-python' homepage = 'http://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" From e66c5b9abb354c7db755c1720d69f5cc7ef9bec6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 15:30:36 +0200 Subject: [PATCH 1384/5331] Adapt to the new name for pkgconfig. --- easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb | 2 +- easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb | 2 +- easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb | 2 +- easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb index 6c8e0052524..e510a14f5e2 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb @@ -20,7 +20,7 @@ prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' multi_deps = {'Python': ['3.7.2', '2.7.15']} -builddependencies = [('pkgconfig', '1.5.1')] +builddependencies = [('pkgconfig', '1.5.1', '-python')] dependencies = [ ('SciPy-bundle', '2019.03'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb index 57596bed860..fd4cb0d3487 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb @@ -20,7 +20,7 @@ prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' multi_deps = {'Python': ['3.7.2', '2.7.15']} -builddependencies = [('pkgconfig', '1.5.1')] +builddependencies = [('pkgconfig', '1.5.1', '-python')] dependencies = [ ('SciPy-bundle', '2019.03'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb index cffe3725772..eda050deb44 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb @@ -23,7 +23,7 @@ prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' multi_deps = {'Python': ['3.7.2', '2.7.15']} -builddependencies = [('pkgconfig', '1.5.1')] +builddependencies = [('pkgconfig', '1.5.1', '-python')] dependencies = [ ('SciPy-bundle', '2019.03'), diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb index d542a413e23..8fa44e84f3c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb @@ -23,7 +23,7 @@ prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' multi_deps = {'Python': ['3.7.2', '2.7.15']} -builddependencies = [('pkgconfig', '1.5.1')] +builddependencies = [('pkgconfig', '1.5.1', '-python')] dependencies = [ ('SciPy-bundle', '2019.03'), From 142153fcabdba0315a1deaab5bc950793213afde Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 15:33:06 +0200 Subject: [PATCH 1385/5331] Add comment on why use_pip=False is needed. --- .../p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb index cf1b1654490..2eff1adbab8 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb @@ -15,6 +15,7 @@ builddependencies = [('binutils', '2.31.1')] dependencies = [('pkg-config', '0.29.2')] +# Due to poetry doing the actual build of pkgconfig we need use_pip=False use_pip = False exts_list = [ From 19096c915c19a448ccb1d75c29a5bb719f3e0435 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 15:40:28 +0200 Subject: [PATCH 1386/5331] adding easyconfigs: gomkl-2018b.eb --- easybuild/easyconfigs/g/gomkl/gomkl-2018b.eb | 19 ++++++++++ .../i/imkl/imkl-2018.3.222-gompi-2018b.eb | 36 +++++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/gomkl/gomkl-2018b.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2018b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2018b.eb new file mode 100644 index 00000000000..e98ea3e910d --- /dev/null +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2018b.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gomkl' +version = '2018b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp = ('GCC', '7.3.0-2.30') + +dependencies = [ + comp, + ('OpenMPI', '3.1.1', '', comp), + ('imkl', '2018.3.222', '', ('gompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb new file mode 100644 index 00000000000..a5bcee241c9 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb @@ -0,0 +1,36 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2018.3.222' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'gompi', 'version': '2018b'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] + +dontcreateinstalldir = 'True' + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' From f0ff7e0b1017fab960544905cc1a3f7aa82b2e6b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 16:02:41 +0200 Subject: [PATCH 1387/5331] Drop sanity_check_paths, it is already the default with PythonBundle. --- .../p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb index 2eff1adbab8..b3341c2f66d 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.1-GCCcore-8.2.0-python.eb @@ -29,9 +29,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - moduleclass = 'devel' From 33c072995ac5e64dd0980194f206b6984a44bbd7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 16:05:38 +0200 Subject: [PATCH 1388/5331] Add missing use_pip and download_dep_fail. --- easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb index 4082ce69f4e..c9e5dc94be2 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.1-GCCcore-8.2.0.eb @@ -20,6 +20,9 @@ dependencies = [ ('libyaml', '0.2.2'), ] +use_pip = True +download_dep_fail = True + options = {'modulename': 'yaml'} sanity_check_paths = { From 67bad3ab4e4460f3b3e539353ee80b05af12c0df Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 2 May 2019 16:25:57 +0200 Subject: [PATCH 1389/5331] adding easyconfigs: freeglut-3.0.0-GCCcore-8.2.0.eb, glew-2.1.0-GCCcore-8.2.0.eb --- .../freeglut/freeglut-3.0.0-GCCcore-8.2.0.eb | 39 +++++++++++++++++++ .../g/glew/glew-2.1.0-GCCcore-8.2.0.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..993e07161cf --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-GCCcore-8.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['2a43be8515b01ea82bcfa17d29ae0d40bd128342f0930cd1f375f1ff999f76a2'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), +] + +dependencies = [ + ('X11', '20190311'), + ('Mesa', '19.0.1'), + ('libGLU', '9.0.0'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.%s" ' % SHLIB_EXT +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..9a81f27a923 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.1.0-GCCcore-8.2.0.eb @@ -0,0 +1,39 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'glew' +version = '2.1.0' + +homepage = 'http://glew.sourceforge.net/' +description = """The OpenGL Extension Wrangler Library + +The OpenGL Extension Wrangler Library (GLEW) is a cross-platform +open-source C/C++ extension loading library. GLEW provides +efficient run-time mechanisms for determining which OpenGL +extensions are supported on the target platform. OpenGL +core and extension functionality is exposed in a single header +file. GLEW has been tested on a variety of operating systems, +including Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['04de91e7e6763039bc11940095cd9c7f880baba82196a7765f727ac05a993c95'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [('Mesa', '19.0.1')] + +files_to_copy = ['bin', 'lib', 'include', ] + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/glew.h', 'include/GL/glxew.h', 'include/GL/wglew.h'], + 'dirs': ['', ] +} + +moduleclass = 'devel' From f4bb0e58274d999a935a7634c9cb6b15c4da97cb Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 2 May 2019 09:31:34 -0500 Subject: [PATCH 1390/5331] Prefer https over ftp --- .../easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2017b.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2018.2-intelcuda-2017b.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2017b.eb index 7962ab7e415..4ae76f19b5f 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2017b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-fosscuda-2017b.eb @@ -26,7 +26,10 @@ This is a GPU enabled build, containing both MPI and threadMPI binaries. toolchain = {'name': 'fosscuda', 'version': '2017b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = [ '4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857', # gromacs-2018.2.tar.gz diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intelcuda-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intelcuda-2017b.eb index b3d12eea76b..202b4cc7c85 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intelcuda-2017b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intelcuda-2017b.eb @@ -26,7 +26,10 @@ This is a GPU enabled build, containing both MPI and threadMPI binaries. toolchain = {'name': 'intelcuda', 'version': '2017b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = [ '4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857', # gromacs-2018.2.tar.gz From 44202adf9623a833976bc3471075ec05431c1a47 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 16:32:31 +0200 Subject: [PATCH 1391/5331] Use https instead of http for homepage. --- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb index a5bcee241c9..0694f6c68b6 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb @@ -3,7 +3,7 @@ name = 'imkl' version = '2018.3.222' -homepage = 'http://software.intel.com/en-us/intel-mkl/' +homepage = 'https://software.intel.com/en-us/intel-mkl/' description = """Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include From 1dd3fc04880720602b0284449da648fa050e855c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 16:34:32 +0200 Subject: [PATCH 1392/5331] adding easyconfigs: gomkl-2019a.eb --- easybuild/easyconfigs/g/gomkl/gomkl-2019a.eb | 19 ++++++++++ .../i/imkl/imkl-2019.1.144-gompi-2019a.eb | 37 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/g/gomkl/gomkl-2019a.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2019a.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2019a.eb new file mode 100644 index 00000000000..4781ecb3865 --- /dev/null +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2019a.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gomkl' +version = '2019a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp = ('GCC', '8.2.0-2.31.1') + +dependencies = [ + comp, + ('OpenMPI', '3.1.3', '', comp), + ('imkl', '2019.1.144', '', ('gompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb new file mode 100644 index 00000000000..524a75c4f95 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2019.1.144-gompi-2019a.eb @@ -0,0 +1,37 @@ +name = 'imkl' +version = '2019.1.144' + +homepage = 'https://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14895/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['5205a460a9c685f7a442868367389b2d0c25e1455346bc6a37c5b8ff90a20fbb'] + +dontcreateinstalldir = 'True' + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' From 21531c7a7cd702f2f9b6231ea4712c5f3fca3be1 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 2 May 2019 09:34:41 -0500 Subject: [PATCH 1393/5331] Prefer https over ftp --- easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2017b.eb | 5 ++++- .../easyconfigs/g/GROMACS/GROMACS-2018.2-intel-2017b.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2017b.eb index b4db7222d37..310ad864484 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-foss-2017b.eb @@ -26,7 +26,10 @@ This is a CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = [ '4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857', # gromacs-2018.2.tar.gz diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intel-2017b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intel-2017b.eb index 686667772c1..f00ec0534a0 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2018.2-intel-2017b.eb @@ -26,7 +26,10 @@ This is a CPU only build, containing both MPI and threadMPI builds. toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] sources = [SOURCELOWER_TAR_GZ] checksums = [ '4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857', # gromacs-2018.2.tar.gz From b4ffb5048666dd8d893d25b68ccbb47e81bf3268 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 May 2019 17:09:26 +0200 Subject: [PATCH 1394/5331] allow use of 'use_pip = False' in easyconfigs if pip doesn't work --- test/easyconfigs/easyconfigs.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 5da46a777cc..5a3ed92b63b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -390,12 +390,12 @@ def check_python_packages(self, changed_ecs): # download_dep_fail should be set when using PythonPackage if easyblock == 'PythonPackage': - if not download_dep_fail: + if download_dep_fail is None: failing_checks.append("'download_dep_fail' set in %s" % ec_fn) # use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs) if easyblock in ['PythonBundle', 'PythonPackage']: - if not use_pip and not any(re.match(regex, ec_fn) for regex in whitelist_pip): + if use_pip is None and not any(re.match(regex, ec_fn) for regex in whitelist_pip): failing_checks.append("'use_pip' set in %s" % ec_fn) # download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set @@ -414,7 +414,7 @@ def check_python_packages(self, changed_ecs): # when installing Python packages as extensions exts_default_options = ec.get('exts_default_options', {}) for key in ['download_dep_fail', 'use_pip']: - if not exts_default_options.get(key): + if exts_default_options.get(key) is None: failing_checks.append("'%s' set in exts_default_options in %s" % (key, ec_fn)) # if Python is a dependency, that should be reflected in the versionsuffix From 6c5823cbc1b85e07b8ac9b5366a0dc7d06906046 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 18:13:41 +0200 Subject: [PATCH 1395/5331] Add missing checksum --- .../GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb index abd483fb871..de2892cf741 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['4093aa7b51e28fb24dfd603893fead8d1b7782f088b05ed0f22a21ef176fb5ae'] builddependencies = [ ('Autotools', '20180311'), From 5eda3e1611257f99340c40cacb4610e6acc0c4ac Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 2 May 2019 11:20:39 -0500 Subject: [PATCH 1396/5331] Fixed typo --- .../IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb | 2 +- .../IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb index 68a5b87a247..a820375ca7e 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-foss-2017b-R-3.4.3-Python-2.7.14.eb @@ -46,7 +46,7 @@ exts_list = [ modextrapaths = {'R_LIBS': ''} -# IPython notebook looks for the json kernel file in kernels/octave_kernels +# IPython notebook looks for the json kernel file in kernels/IRkernel kerneldir = '%(installdir)s/IRkernel' postinstallcmds = [ 'mkdir -p %s/kernels/ir' % kerneldir, diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb index b9fe7d46c25..cc6416348dd 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-0.8.15-intel-2017b-R-3.4.3-Python-2.7.14.eb @@ -46,7 +46,7 @@ exts_list = [ modextrapaths = {'R_LIBS': ''} -# IPython notebook looks for the json kernel file in kernels/octave_kernels +# IPython notebook looks for the json kernel file in kernels/IRkernel kerneldir = '%(installdir)s/IRkernel' postinstallcmds = [ 'mkdir -p %s/kernels/ir' % kerneldir, From c2eddf5eb118e4377dc2a9cb7cf2adce6b1817fc Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 2 May 2019 11:24:24 -0500 Subject: [PATCH 1397/5331] Added gettext build dep --- easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb index c169aa9070c..8a6486a35be 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.0.1-GCCcore-8.2.0.eb @@ -42,6 +42,7 @@ builddependencies = [ ('Mako', '1.0.8'), ('libxml2', '2.9.8'), ('expat', '2.2.6'), + ('gettext', '0.19.8.1'), ] dependencies = [ From c56010e00532ef110a5b14750a7368463e3988ed Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 18:24:36 +0200 Subject: [PATCH 1398/5331] Whitelist Toolchain easyconfigs from having sanity_check_paths. --- test/easyconfigs/easyconfigs.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 5da46a777cc..e49929fa20e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -429,7 +429,8 @@ def check_sanity_check_paths(self, changed_ecs): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # PythonBundle & PythonPackage already have a decent customised sanity_check_paths - whitelist = ['PythonBundle', 'PythonPackage'] + # Toolchain doesn't install anything so there is nothing to check. + whitelist = ['PythonBundle', 'PythonPackage', 'Toolchain'] failing_checks = [] From 380074c730c20fc46409cdb5f9a2116c61b44bdd Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Thu, 2 May 2019 11:42:54 -0500 Subject: [PATCH 1399/5331] Added X11 dependency --- .../easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb index ef38d0386b3..be85ca935c0 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb @@ -32,6 +32,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.2'), ('libpng', '1.6.36'), ('LibTIFF', '4.0.10'), + ('X11', '20190311'), ] configopts = "--buildtype=release --default-library=both " From 36502f528226e4d0b195a9e2ddc285efac721bb8 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 2 May 2019 20:08:12 +0200 Subject: [PATCH 1400/5331] R: make sure hdf5r picks up HDF5 from EB + fix checksum --- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 3 ++- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index d17b5098e9d..0fadb700a08 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -559,7 +559,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], + 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], @@ -1951,6 +1951,7 @@ exts_list = [ 'checksums': ['58e36d3b8a67d01194c4e5099499657d017f77fc2081213633964b1d57a7e32f'], }), ('hdf5r', '1.0.0', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', 'patches': ['hdf5r-1.0.0_fix-HDF5-1.10.2.patch'], 'preinstallopts': "unset LIBS && ", 'checksums': [ diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 6d2e61ebf7d..975f1235d76 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -557,7 +557,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], + 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], @@ -1949,6 +1949,7 @@ exts_list = [ 'checksums': ['58e36d3b8a67d01194c4e5099499657d017f77fc2081213633964b1d57a7e32f'], }), ('hdf5r', '1.0.0', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', 'patches': ['hdf5r-1.0.0_fix-HDF5-1.10.2.patch'], 'preinstallopts': "unset LIBS && ", 'checksums': [ From 395a2391956d716135235834cb0c950c5bf67327 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 2 May 2019 20:14:04 +0200 Subject: [PATCH 1401/5331] GRASS: add zstd compression --- .../GRASS-7.6.0-foss-2018b-Python-2.7.15.eb | 2 ++ .../z/zstd/zstd-1.4.0-foss-2018b.eb | 35 +++++++++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.4.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb index 6cb57dbfaf0..e510b702e29 100644 --- a/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb @@ -48,6 +48,7 @@ dependencies = [ ('Mesa', '18.1.1'), ('libGLU', '9.0.0'), ('wxPython', '3.0.2.0', versionsuffix), + ('zstd', '1.4.0'), ] preconfigopts = "sed -e 's/-lblas/\$LIBBLAS/g' -e 's/-llapack/\$LIBLAPACK/g' -i configure &&" @@ -87,6 +88,7 @@ configopts += '--with-wxwidgets=$EBROOTWXPYTHON/bin/wx-config ' configopts += '--with-x ' configopts += '--with-zlib --with-zlib-libs=$EBROOTZLIB/lib --with-zlib-includes=$EBROOTZLIB/include ' configopts += '--with-bzlib --with-bzlib-libs=$EBROOTBZIP2/lib --with-ibzlib-includes=$EBROOTBZIP2/include ' +configopts += '--with-zstd --with-zstd-libs=$EBROOTZSTD/lib --with-zstd-includes=$EBROOTZSTD/include ' sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.4.0-foss-2018b.eb b/easybuild/easyconfigs/z/zstd/zstd-1.4.0-foss-2018b.eb new file mode 100644 index 00000000000..f3522147efa --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.4.0-foss-2018b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.4.0' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/facebook/zstd/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.11'), + ('gzip', '1.9'), + ('XZ', '5.2.4'), + ('lz4', '1.9.0'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From a1c2a53b612b666cf7fb5f9f1dc4be03b5990c90 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 20:41:14 +0200 Subject: [PATCH 1402/5331] Add HPL/2.2 for gomkl/2018b as test case. --- .../easyconfigs/h/HPL/HPL-2.2-gomkl-2018b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-gomkl-2018b.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-gomkl-2018b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-gomkl-2018b.eb new file mode 100644 index 00000000000..8329439ff10 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-gomkl-2018b.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gomkl', 'version': '2018b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +checksums = [ + 'ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440', # hpl-2.2.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' From 8baa0c0c724d1aedeefe65f3bf1248e38c7c11b9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 20:42:42 +0200 Subject: [PATCH 1403/5331] Add HPL/2.3 for gomkl/2019a as test case. --- .../easyconfigs/h/HPL/HPL-2.3-gomkl-2019a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2019a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2019a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2019a.eb new file mode 100644 index 00000000000..b4f5c99f1e8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2019a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gomkl', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' From 3b675445c3e072781b0b2d7d078d33846b3ccc94 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 May 2019 20:53:40 +0200 Subject: [PATCH 1404/5331] Add missing "components" line. --- easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb index 0694f6c68b6..3bc1636a4ef 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gompi-2018b.eb @@ -11,11 +11,14 @@ description = """Intel Math Kernel Library is a library of highly optimized, toolchain = {'name': 'gompi', 'version': '2018b'} +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] sources = ['l_mkl_%(version)s.tgz'] checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] dontcreateinstalldir = 'True' +components = ['intel-mkl'] + license_file = HOME + '/licenses/intel/license.lic' interfaces = True From 68ffcfa061142408fb052a2c973f4f3acb1dfece Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 2 May 2019 23:22:58 +0200 Subject: [PATCH 1405/5331] adding easyconfigs: VTK-8.2.0-intel-2019a-Python-3.7.2.eb, VTK-8.2.0-foss-2019a-Python-3.7.2.eb --- .../VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb | 80 +++++++++++++++++++ .../VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb | 80 +++++++++++++++++++ 2 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..a7b3880c086 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,80 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '8.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('XZ', '5.2.4'), + ('HDF5', '1.10.5'), + ('netCDF', '4.6.2'), + ('libGLU', '9.0.0'), + ('X11', '20190311'), +] + +separate_build_dir = True + +# Third party modules +configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " +configopts += "-DVTK_USE_SYSTEM_LZMA=ON " +configopts += "-DVTK_USE_SYSTEM_HDF5=ON " +configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " +# OpenGL +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON " +configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)sm " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)sm.%s " % SHLIB_EXT +# Other +configopts += "-DVTK_Group_MPI:BOOL=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +# preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in + ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] + + ['bin/pvtkpython', 'bin/vtkpython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..fc5af50aa22 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,80 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '8.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('XZ', '5.2.4'), + ('HDF5', '1.10.5'), + ('netCDF', '4.6.2'), + ('libGLU', '9.0.0'), + ('X11', '20190311'), +] + +separate_build_dir = True + +# Third party modules +configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " +configopts += "-DVTK_USE_SYSTEM_LZMA=ON " +configopts += "-DVTK_USE_SYSTEM_HDF5=ON " +configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " +# OpenGL +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON " +configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)sm " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)sm.%s " % SHLIB_EXT +# Other +configopts += "-DVTK_Group_MPI:BOOL=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +# preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in + ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] + + ['bin/pvtkpython', 'bin/vtkpython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(namelower)s'")] + +moduleclass = 'vis' From c9ebc2d85a5429306215f81ac6b917b768f6457f Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 2 May 2019 23:38:08 +0200 Subject: [PATCH 1406/5331] Remove leftover line --- easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb index d28aab3460b..c4e7a556d0d 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb @@ -36,7 +36,6 @@ builddependencies = [ # values to use here are +1 those used for building Libint # see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT extradflags = "-D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5" -#extradflags = "-fno-exceptions -D__parallel -D__SCALAPACK -D__LIBINT -D__FFTW3 -D__LIBXC -D__PLUMED2" # regression test reports failures ignore_regtest_fails = True From 02db4ba1acebde1699cb3348755c90e046ff710a Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 2 May 2019 23:43:54 +0200 Subject: [PATCH 1407/5331] Remove old code --- easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-intel-2019a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-intel-2019a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-intel-2019a.eb index 602d0a0bb41..434d00bc046 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-intel-2019a.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.11.1-intel-2019a.eb @@ -22,8 +22,6 @@ checksums = [ builddependencies = [('CMake', '3.13.3')] -#parmetis = 'ParMETIS' -#parmetis_ver = '4.0.3' dependencies = [ ('Boost', '1.70.0'), ('METIS', '5.1.0'), From 9266b5c25f18d3bdbecccaf9be89564c8785bf5d Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 2 May 2019 23:53:26 +0200 Subject: [PATCH 1408/5331] Add checksums --- .../easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb | 4 ++++ .../easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb index a7b3880c086..c78bb632dff 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb @@ -30,6 +30,10 @@ sources = [ SOURCE_TAR_GZ, '%(name)sData-%(version)s.tar.gz', ] +checksums = [ + '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz + 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz +] builddependencies = [('CMake', '3.13.3')] diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb index fc5af50aa22..9dc8eba2c6f 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb @@ -30,6 +30,10 @@ sources = [ SOURCE_TAR_GZ, '%(name)sData-%(version)s.tar.gz', ] +checksums = [ + '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz + 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz +] builddependencies = [('CMake', '3.13.3')] From 092c5acedda6d124ebb28a87f706161db595371b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 May 2019 08:18:17 +0200 Subject: [PATCH 1409/5331] Switch to MesonNinja, add some missing dependencies. --- .../GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb index de2892cf741..2923fcf8285 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MesonNinja' name = 'GST-plugins-base' version = '1.16.0' @@ -13,17 +13,23 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['4093aa7b51e28fb24dfd603893fead8d1b7782f088b05ed0f22a21ef176fb5ae'] builddependencies = [ - ('Autotools', '20180311'), + ('Meson', '0.50.0', '-Python-3.7.2'), + ('Ninja', '1.9.0'), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), + ('gettext', '0.19.8.1'), ('pkg-config', '0.29.2'), ('Bison', '3.0.5'), ] dependencies = [ + ('zlib', '1.2.11'), + ('GLib', '2.60.1'), + ('GTK+', '3.24.8'), ('GStreamer', '1.16.0'), - ('gettext', '0.19.8.1'), + ('Gdk-Pixbuf', '2.38.1'), + ('X11', '20190311'), ('Mesa', '19.0.1'), ] From 7d0f2a0781f9ee18b239dbe1047f1c1f82222676 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 May 2019 08:19:55 +0200 Subject: [PATCH 1410/5331] Re-add checksum. --- .../GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb index 2923fcf8285..248c36798ff 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.0-GCC-8.2.0-2.31.1.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['http://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['4093aa7b51e28fb24dfd603893fead8d1b7782f088b05ed0f22a21ef176fb5ae'] builddependencies = [ ('Meson', '0.50.0', '-Python-3.7.2'), From ad659fcb3001b6828c2675da80a85d2ce8548255 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 May 2019 09:00:53 +0200 Subject: [PATCH 1411/5331] Add missing dependency on ICU. --- easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb index c6eb4a4fd8d..a8e5eb418f4 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.4.0-GCCcore-8.2.0.eb @@ -20,6 +20,7 @@ builddependencies = [ dependencies = [ ('GLib', '2.60.1'), + ('ICU', '64.2'), ('cairo', '1.16.0'), ('freetype', '2.9.1'), ] From ef1d85d7b5d6dc841d2b487712e574b112522fcc Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 3 May 2019 09:42:25 +0200 Subject: [PATCH 1412/5331] add checksums for zstd --- easybuild/easyconfigs/z/zstd/zstd-1.4.0-foss-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.4.0-foss-2018b.eb b/easybuild/easyconfigs/z/zstd/zstd-1.4.0-foss-2018b.eb index f3522147efa..e9453a8201a 100644 --- a/easybuild/easyconfigs/z/zstd/zstd-1.4.0-foss-2018b.eb +++ b/easybuild/easyconfigs/z/zstd/zstd-1.4.0-foss-2018b.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/facebook/zstd/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['63be339137d2b683c6d19a9e34f4fb684790e864fee13c7dd40e197a64c705c1'] dependencies = [ ('zlib', '1.2.11'), From 42295209283734f8fc6961b929fec2c62ea0070d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 May 2019 10:34:38 +0200 Subject: [PATCH 1413/5331] Disable the AVX512 DGEMM kernel as per OpenBLAS PR #2061 --- .../OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb | 1 + ...AS-0.3.5_disable_AVX512_dgemm_kernel.patch | 21 +++++++++++++++++++ 2 files changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb index 86d125db417..cc5594b90eb 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb @@ -20,6 +20,7 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + '%(name)s-%(version)s_disable_AVX512_dgemm_kernel.patch', ] checksums = [ '0950c14bd77c90a6427e26210d6dab422271bc86f9fc69126725833ecdaa0e85', # v0.3.5.tar.gz diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch new file mode 100644 index 00000000000..abc64ee3f2e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch @@ -0,0 +1,21 @@ +commit e608d4f7fe1a2085b22af206d0c8c2cc128c1e9a +Author: Martin Kroeker +Date: Wed Mar 13 22:10:28 2019 +0100 + + Disable the AVX512 DGEMM kernel (again) + + Due to as yet unresolved errors seen in #1955 and #2029 + +diff --git a/kernel/x86_64/KERNEL.SKYLAKEX b/kernel/x86_64/KERNEL.SKYLAKEX +index acc6356..5d0a300 100644 +--- a/kernel/x86_64/KERNEL.SKYLAKEX ++++ b/kernel/x86_64/KERNEL.SKYLAKEX +@@ -7,7 +7,7 @@ SGEMMITCOPY = sgemm_tcopy_16_skylakex.c + SGEMMONCOPY = sgemm_ncopy_4_skylakex.c + SGEMMOTCOPY = ../generic/gemm_tcopy_4.c + +-DGEMMKERNEL = dgemm_kernel_4x8_skylakex.c ++#DGEMMKERNEL = dgemm_kernel_4x8_skylakex.c + + DGEMMINCOPY = dgemm_ncopy_8_skylakex.c + DGEMMITCOPY = dgemm_tcopy_8_skylakex.c From 100c9d803b98fde5faaaa2e69fb6a203da206146 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 May 2019 10:58:32 +0200 Subject: [PATCH 1414/5331] Add missing checksum. --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb index cc5594b90eb..dc9ad24d9c7 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb @@ -26,6 +26,8 @@ checksums = [ '0950c14bd77c90a6427e26210d6dab422271bc86f9fc69126725833ecdaa0e85', # v0.3.5.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch + '1b43496a5bd71ee2c7d9b8adb6789a018da400050a6e3313839d5471c72d3b47', ] skipsteps = ['configure'] From 8a9110237467364c89426cc8fadb47f8fa25d6aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 3 May 2019 11:14:41 +0200 Subject: [PATCH 1415/5331] add cURL for all easyconfigs from version 1.4 onwards --- easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-GCC-6.4.0-2.28.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-foss-2017a.eb | 1 + .../SAMtools/SAMtools-1.6-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-intel-2017b.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-foss-2018a.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-intel-2018a.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.8-intel-2018a.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCC-6.4.0-2.28.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCC-7.3.0-2.30.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-intel-2018b.eb | 1 + 17 files changed, 17 insertions(+) mode change 100755 => 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb mode change 100755 => 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb mode change 100755 => 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-foss-2017a.eb mode change 100755 => 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-intel-2017b.eb mode change 100755 => 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-foss-2018a.eb mode change 100755 => 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-intel-2018a.eb mode change 100755 => 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.8-intel-2018a.eb mode change 100755 => 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-intel-2018b.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb index becb1e33dff..497f16a4df5 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb @@ -32,6 +32,7 @@ dependencies = [ ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ('XZ', '5.2.2'), + ('cURL', '7.49.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb index a590f0e5c55..a5b10bc0459 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb @@ -35,6 +35,7 @@ dependencies = [ ('zlib', '1.2.7'), ('bzip2', '1.0.6'), ('XZ', '5.2.2'), + ('cURL', '7.29.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb index 5fc351ad684..c2147ff22d0 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb @@ -32,6 +32,7 @@ dependencies = [ ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ('XZ', '5.2.2'), + ('cURL', '7.49.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb index a9362a745f1..a8ea91d3fc1 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb @@ -32,6 +32,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), + ('cURL', '7.53.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb index 1cb0955d191..0488bdebe6d 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb @@ -32,6 +32,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), + ('cURL', '7.53.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb old mode 100755 new mode 100644 index 30006e4f3c0..77ddfe2035c --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb @@ -33,6 +33,7 @@ dependencies = [ ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ('XZ', '5.2.2'), + ('cURL', '7.49.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb old mode 100755 new mode 100644 index ae85c244273..9c48a788178 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb @@ -32,6 +32,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), + ('cURL', '7.53.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-GCC-6.4.0-2.28.eb index f8cedd5875a..770f9ce3971 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-GCC-6.4.0-2.28.eb @@ -33,6 +33,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), + ('cURL', '7.58.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-foss-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-foss-2017a.eb old mode 100755 new mode 100644 index 7c9997f8bc1..1933a2350e8 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-foss-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-foss-2017a.eb @@ -33,6 +33,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), + ('cURL', '7.53.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 6ec0fbd7093..093b740aa3e 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -33,6 +33,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), + ('cURL', '7.58.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-intel-2017b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-intel-2017b.eb old mode 100755 new mode 100644 index a0bf05f899a..48029ca2f9f --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-intel-2017b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-intel-2017b.eb @@ -33,6 +33,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), + ('cURL', '7.56.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-foss-2018a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-foss-2018a.eb old mode 100755 new mode 100644 index f491e0e75a2..ba3bd2c46c3 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-foss-2018a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-foss-2018a.eb @@ -33,6 +33,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), + ('cURL', '7.58.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-intel-2018a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-intel-2018a.eb old mode 100755 new mode 100644 index efe8cfdf284..f7655217bc2 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-intel-2018a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.7-intel-2018a.eb @@ -33,6 +33,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), + ('cURL', '7.58.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.8-intel-2018a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.8-intel-2018a.eb old mode 100755 new mode 100644 index 64e9f58d6fb..97206d9e4fd --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.8-intel-2018a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.8-intel-2018a.eb @@ -33,6 +33,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), + ('cURL', '7.58.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCC-6.4.0-2.28.eb index 55f803f4341..e9221b9c66a 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCC-6.4.0-2.28.eb @@ -26,6 +26,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), + ('cURL', '7.58.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCC-7.3.0-2.30.eb index 55399fa396d..157f67240ec 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCC-7.3.0-2.30.eb @@ -26,6 +26,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.4'), + ('cURL', '7.60.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-intel-2018b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-intel-2018b.eb old mode 100755 new mode 100644 index fd17bb57da9..47436c9cdfb --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-intel-2018b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-intel-2018b.eb @@ -33,6 +33,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.4'), + ('cURL', '7.60.0'), ] moduleclass = 'bio' From 6b1a8958d838fa2187fa71565001fc03a50f107f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 3 May 2019 11:33:22 +0200 Subject: [PATCH 1416/5331] add missing checksums --- easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb | 1 + easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb | 1 + 6 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb index 497f16a4df5..cc748b0e581 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb @@ -24,6 +24,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9aae5bf835274981ae22d385a390b875aef34db91e6355337ca8b4dd2960e3f4'] # The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. # The latter is currently provided by XZ. diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb index a5b10bc0459..1efba02c096 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb @@ -26,6 +26,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9aae5bf835274981ae22d385a390b875aef34db91e6355337ca8b4dd2960e3f4'] # The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. # The latter is currently provided by XZ. diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb index c2147ff22d0..12ec373a875 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb @@ -24,6 +24,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9aae5bf835274981ae22d385a390b875aef34db91e6355337ca8b4dd2960e3f4'] # The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. # The latter is currently provided by XZ. diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb index a8ea91d3fc1..9e43b582181 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb @@ -24,6 +24,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9aae5bf835274981ae22d385a390b875aef34db91e6355337ca8b4dd2960e3f4'] # The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. # The latter is currently provided by XZ. diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb index 0488bdebe6d..ab0003de7fb 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb @@ -24,6 +24,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['bda7ded75909327135ea6145d5aa121a67600a0d556b76a8f57fbfb94b95fd6f'] # The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. # The latter is currently provided by XZ. diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb index 9c48a788178..416549cb221 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb @@ -24,6 +24,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['8542da26832ee08c1978713f5f6188ff750635b50d8ab126a0c7bb2ac1ae2df6'] # The htslib component of SAMtools 1.4 uses zlib, bzip2 and lzma compression. # The latter is currently provided by XZ. From 6dd6412a188aa2e05a05103431fde3116f6f7d6c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 3 May 2019 12:10:46 +0200 Subject: [PATCH 1417/5331] adding easyconfigs: FlexiDot-1.06-foss-2018b-Python-2.7.15.eb --- .../FlexiDot-1.06-foss-2018b-Python-2.7.15.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..e30d9dab1cf --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,71 @@ +easyblock = 'PackedBinary' + +name = 'FlexiDot' +version = '1.06' +commit = 'be8397a' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/molbio-dresden/flexidot' +description = """ Highly customizable, ambiguity-aware dotplots for visual sequence analyses """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/molbio-dresden/flexidot/archive/'] +sources = [{'download_filename': '%s.tar.gz' % commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['edb182e2fcb879fe45d72127909e8c0b98b19bc71f87dd070b4a5bad04af0268'] + +dependencies = [ + ('Python', '2.7.15'), + ('Biopython', '1.72', versionsuffix), + ('matplotlib', '2.2.3', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('regex', '2019.04.14', { + 'source_urls': ['https://pypi.python.org/packages/source/r/regex/'], + 'checksums': ['d56ce4c7b1a189094b9bee3b81c4aeb3f1ba3e375e91627ec8561b6ab483d0a8'], + }), + ('colorama', '0.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], + 'checksums': ['05eed71e2e327246ad6b38c540c4a3117230b19679b875190486ddd2d721422d'], + }), + ('colorlog', '4.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colorlog/'], + 'checksums': ['3cf31b25cbc8f86ec01fef582ef3b840950dea414084ed19ab922c8b493f9b42'], + }), + ('pexpect', '4.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + 'checksums': ['9e2c1fd0e6ee3a49b28f95d4b33bc389c89b20af6a1255906e90ff1262ce62eb'], + }), + ('easydev', '0.9.37', { + 'source_urls': ['https://pypi.python.org/packages/source/e/easydev/'], + 'checksums': ['38bd1a7e489673847e109c27f83f8e373e45907b70ea78eb2d38d96464f3a4e3'], + }), + ('colormap', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colormap/'], + 'checksums': ['c0193efe8f7d626cfc78225fc03a56513a4cfb8d3fc43856ccfb97b9646cc1b1'], + }), + ('colour', '0.1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colour/'], + 'checksums': ['af20120fefd2afede8b001fbef2ea9da70ad7d49fafdb6489025dae8745c3aee'], + }), +] + +postinstallcmds = [ + 'mv %(installdir)s/code/flexidot_v%(version)s.py %(installdir)s/bin/flexidot.py', + 'chmod +x %(installdir)s/bin/flexidot.py', + "sed -i -e 's/\x0D$//' -e '1 s|^.*$|#!/usr/bin/env python|' %(installdir)s/bin/flexidot.py", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_commands = ['flexidot.py -h'] + +moduleclass = 'vis' From 950d6f1d177f8051f756fc5daf46bcdbbe8a5192 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 3 May 2019 12:14:22 +0200 Subject: [PATCH 1418/5331] adding easyconfigs: imgaug-0.2.8-foss-2018b-Python-3.6.6.eb, OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb --- .../imgaug-0.2.8-foss-2018b-Python-3.6.6.eb | 40 +++++++++++++++++ .../OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb | 45 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.2.8-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.2.8-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.2.8-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..573a44b437e --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.2.8-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'imgaug' +version = '0.2.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('Pillow', '5.3.0', versionsuffix), + ('matplotlib', '3.0.0', versionsuffix), + ('scikit-image', '0.14.1', versionsuffix), + ('OpenCV', '4.0.1', versionsuffix), + ('GEOS', '3.6.2', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('Shapely', '1.6.4.post2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/Shapely/'], + 'checksums': ['c4b87bb61fc3de59fc1f85e71a79b0c709dc68364d9584473697aad4aa13240f'], + }), + ('imageio', '2.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/imageio/'], + 'checksums': ['42e65aadfc3d57a1043615c92bdf6319b67589e49a0aae2b985b82144aceacad'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/aleju/imgaug/archive/'], + 'checksums': ['3c40c8e9b06277d258368129376151d2cb41c2523353719f646b2448c9d18fea'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..0aa61fe1e65 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,45 @@ +name = 'OpenCV' +version = '4.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [ + 'https://github.com/opencv/opencv/archive/', + # the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake + 'https://raw.githubusercontent.com/opencv/opencv_3rdparty/32e315a5b106a7b89dbed51c28f8120a48b368b4/ippicv', +] +sources = [ + '%(version)s.zip', + {'filename': 'ippicv_2019_lnx_intel64_general_20180723.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + 'b79ccdc4797a959c5ab17249a8a302c066248ae070e4d7010e2d77a625fdb30a', # 4.0.1.zip + 'fc167cb60deb8924339a7050f3da168bb02e221b2d6b8c00139d1fa7eace0c7d', # ippicv_2019_lnx_intel64_general_20180723.tgz +] + +builddependencies = [ + ('CMake', '3.12.1'), +] + +dependencies = [ + ('Python', '3.6.6'), + ('zlib', '1.2.11'), + ('FFmpeg', '4.1'), + ('libjpeg-turbo', '2.0.0'), + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), + ('JasPer', '2.0.14'), + ('Java', '1.8', '', True), + ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('GLib', '2.54.3'), + ('GTK+', '2.24.32'), +] + +moduleclass = 'vis' From 5c279a255c96a4d3052606ef8034df19f03b543f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 May 2019 12:47:12 +0200 Subject: [PATCH 1419/5331] adding easyconfigs: gnuplot-5.2.6-fosscuda-2018b.eb --- .../g/gnuplot/gnuplot-5.2.6-fosscuda-2018b.eb | 49 +++++++++++++++++++ .../n/nettle/nettle-3.4-GCCcore-7.3.0.eb | 40 +++++++++++++++ .../q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb | 41 ++++++++++++++++ 3 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-fosscuda-2018b.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-fosscuda-2018b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-fosscuda-2018b.eb new file mode 100644 index 00000000000..cb62e93cf58 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-fosscuda-2018b.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.2.6' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['35dd8f013139e31b3028fac280ee12d4b1346d9bb5c501586d1b5a04ae7a94ee'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('cairo', '1.14.12'), + ('libjpeg-turbo', '2.0.0'), + ('libpng', '1.6.34'), + ('libgd', '2.2.5'), + ('Pango', '1.42.4'), + ('libcerf', '1.7'), + ('Qt5', '5.10.1'), +] + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..32251b81658 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.4' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' + +description = """ + Nettle is a cryptographic library that is designed to fit easily in more or + less any context: In crypto toolkits for object-oriented languages (C++, + Python, Pike, ...), in applications like LSH or GNUPG, or even in + kernel space. +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ae7a42df026550b85daca8389b6a60ba6313b0567f374392e54918588a411e94'] + +builddependencies = [ + ('binutils', '2.30'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' \ No newline at end of file diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb new file mode 100644 index 00000000000..bce316f6a0e --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb @@ -0,0 +1,41 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.10.1' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +checksums = ['05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Bison', '3.0.4'), + ('flex', '2.6.4'), + ('Python', '2.7.15'), +] + +dependencies = [ + ('GLib', '2.54.3'), + ('libpng', '1.6.34'), + ('X11', '20180604'), + ('libGLU', '9.0.0'), + ('NSS', '3.39'), + ('DBus', '1.13.6'), + ('gperf', '3.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +configopts = '-skip qtgamepad' + +# make sure QtWebEngine component is being built & installed +check_qtwebengine = True + +moduleclass = 'devel' From ce6da8edd7edf36bfb9f74554492c52f63d0a883 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 3 May 2019 13:25:50 +0200 Subject: [PATCH 1420/5331] add missing sanity_check_paths --- .../f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb index e30d9dab1cf..a8be3f507b4 100644 --- a/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb @@ -66,6 +66,12 @@ postinstallcmds = [ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} +sanity_check_paths = { + 'files': ['bin/flexidot.py'], + 'dirs': [], +} + + sanity_check_commands = ['flexidot.py -h'] moduleclass = 'vis' From 1f39a32611434ed771ebaadb6ea59b33967b3474 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 May 2019 13:46:53 +0200 Subject: [PATCH 1421/5331] Fix missing newline on last line. --- easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb index 32251b81658..6e7872c651b 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.4-GCCcore-7.3.0.eb @@ -37,4 +37,4 @@ sanity_check_paths = { 'dirs': ['include/nettle'], } -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' From 62eb7be5a650983e83fd6b8e160bb6beb8ae2c3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 May 2019 14:55:35 +0200 Subject: [PATCH 1422/5331] adding easyconfigs: Gurobi-8.1.1.eb --- easybuild/easyconfigs/g/Gurobi/Gurobi-8.1.1.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-8.1.1.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-8.1.1.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-8.1.1.eb new file mode 100644 index 00000000000..4239a554559 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-8.1.1.eb @@ -0,0 +1,18 @@ +name = 'Gurobi' +version = '8.1.1' + +homepage = 'http://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +checksums = ['c030414603d88ad122246fe0e42a314fab428222d98e26768480f1f870b53484'] + +license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' + +moduleclass = 'math' From c60228813025f58439fcdd26d7224fd9df62ba5c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 3 May 2019 15:01:00 +0200 Subject: [PATCH 1423/5331] Add use_pip=True to PyQtGraph-0.10.0-intel-2018a-Python-3.6.4.eb --- .../p/PyQtGraph/PyQtGraph-0.10.0-intel-2018a-Python-3.6.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2018a-Python-3.6.4.eb index 7b68b3d1c4a..9ef7f652bcb 100644 --- a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2018a-Python-3.6.4.eb @@ -20,6 +20,7 @@ dependencies = [ ('PyQt5', '5.9.2', versionsuffix), ] +use_pip = True download_dep_fail = True sanity_check_paths = { From f473b22b972cc59f29337c109f38845f9c5c9aae Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Fri, 3 May 2019 09:27:35 -0500 Subject: [PATCH 1424/5331] adding easyconfigs: SimpleElastix-0.10.0-foss-2017b-Python-3.6.3.eb --- ...eElastix-0.10.0-foss-2017b-Python-3.6.3.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-0.10.0-foss-2017b-Python-3.6.3.eb diff --git a/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-0.10.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-0.10.0-foss-2017b-Python-3.6.3.eb new file mode 100644 index 00000000000..92e30c1620e --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-0.10.0-foss-2017b-Python-3.6.3.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'SimpleElastix' +version = '0.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://simpleelastix.github.io/' +description = " Multi-lingual medical image registration library. " + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/SuperElastix/SimpleElastix/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['SimpleElastix-%(version)s_git-version.patch'] +checksums = [ + 'e4c08412a97871b171da2873e0ac76ab1ebfcf171c2d4a0958cc4b4f92a7b14b', # v0.10.0.tar.gz + 'fdb8d558ea295bda13b7483db0ec2a44def9e5066b794c42ae89a962c57804c7', # SimpleElastix-0.10.0_git-version.patch +] + +builddependencies = [('CMake', '3.9.5')] + +dependencies = [ + ('Python', '3.6.3'), +] + +configopts = '-DBUILD_EXAMPLES=OFF ' +configopts += '-DWRAP_TCL=OFF -DWRAP_LUA=OFF -DWRAP_RUBY=OFF -DWRAP_JAVA=OFF -DWRAP_CSHARP=OFF -DWRAP_R=OFF ' + +start_dir = 'SuperBuild' + +separate_build_dir = True + +skipsteps = ['install'] + +postinstallcmds = [ + # install SimpleITK Python wrapper: + "cd %(builddir)s/easybuild_obj/SimpleITK-build/Wrapping/Python/Packaging && " + + "python setup.py install --prefix=%(installdir)s", + # install elastix, ITK, and SimpleITK binaries: + 'mkdir -p %(installdir)s/bin && ' + + 'cp %(builddir)s/easybuild_obj/elastix-build/src/bin/* %(installdir)s/bin && ' + + 'cp %(builddir)s/easybuild_obj/ITK-build/bin/* %(installdir)s/bin && ' + + 'cp %(builddir)s/easybuild_obj/SimpleITK-build/bin/* %(installdir)s/bin' +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/SimpleITK-%(version_major_minor)s', 'lib', 'share'] +} + +sanity_check_commands = ["python -c 'import SimpleITK'"] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' From d12d768a0dcce179c2977d1e4cb4e3ec1df93549 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 May 2019 16:32:04 +0200 Subject: [PATCH 1425/5331] adding easyconfigs: scp-0.13.2-intel-2018b-Python-2.7.15.eb --- .../scp-0.13.2-intel-2018b-Python-2.7.15.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/scp/scp-0.13.2-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/s/scp/scp-0.13.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/scp/scp-0.13.2-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..20b81c1155f --- /dev/null +++ b/easybuild/easyconfigs/s/scp/scp-0.13.2-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'scp' +version = '0.13.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jbardin/scp.py' +description = """The scp.py module uses a paramiko transport to send and recieve files via the scp1 protocol.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ef9d6e67c0331485d3db146bf9ee9baff8a48f3eb0e6c08276a8584b13bf34b3'] + +dependencies = [('Python', '2.7.15')] + +download_dep_fail = True +use_pip = True + +moduleclass = 'lib' From 2c59519fc323668ffdae949cd505f0c62b80ab46 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 May 2019 16:37:43 +0200 Subject: [PATCH 1426/5331] fix homepage/description in OrthoFinder easyconfig --- .../OrthoFinder-2.2.7-intel-2018a-Python-2.7.14.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.2.7-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.2.7-intel-2018a-Python-2.7.14.eb index 42dae35ccd2..182ccd5ea8a 100644 --- a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.2.7-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.2.7-intel-2018a-Python-2.7.14.eb @@ -4,8 +4,8 @@ name = 'OrthoFinder' version = '2.2.7' versionsuffix = '-Python-%(pyver)s' -homepage = '' -description = "" +homepage = 'https://github.com/davidemms/OrthoFinder' +description = "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics" toolchain = {'name': 'intel', 'version': '2018a'} From 8c59a63de109e4b8ff1c66382d9ceb9928003f99 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 3 May 2019 16:44:59 +0200 Subject: [PATCH 1427/5331] Update comments in libutempter-1.1.6.2-GCC-6.4.0-2.28.eb --- .../l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb index 13cb6c68203..faeaa9459da 100644 --- a/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/l/libutempter/libutempter-1.1.6.2-GCC-6.4.0-2.28.eb @@ -10,7 +10,8 @@ description = """libutempter is library that provides an interface for terminal toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} # Download from http://git.altlinux.org/people/ldv/packages/?p=libutempter.git;a=snapshot;h=1.1.6-alt2;sf=tgz -# and unzip / rename libutempter-1.1.6-alt2-3c6e555.tar.gz to libutempter-1.1.6.2.tar +# and unpack (required to obtain a consistent checksum) + rename to obtain libutempter-1.1.6.2.tar: +# gunzip libutempter-1.1.6-alt2-3c6e555.tar.gz && mv libutempter-1.1.6-alt2-3c6e555.tar libutempter-1.1.6.tar sources = [{ 'filename': SOURCE_TAR, 'extract_cmd': "tar xfv %s --strip 1", From 683d5ca8c228627671fbb755b936b6794539ea8d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 May 2019 17:20:11 +0200 Subject: [PATCH 1428/5331] {bio}[intel/2018b] OrthoFinder v2.3.3 w/ Python 2.7.15 (+ deps) --- .../d/DIAMOND/DIAMOND-0.9.22-intel-2018b.eb | 24 ++++++++++++ .../f/FastME/FastME-2.1.6.1-intel-2018b.eb | 20 ++++++++++ .../MCL-14.137-GCCcore-7.3.0-Perl-5.28.0.eb | 39 +++++++++++++++++++ .../m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb | 26 +++++++++++++ ...oFinder-2.3.3-intel-2018b-Python-2.7.15.eb | 36 +++++++++++++++++ 5 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.22-intel-2018b.eb create mode 100644 easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-intel-2018b.eb create mode 100644 easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-7.3.0-Perl-5.28.0.eb create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb create mode 100644 easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.3.3-intel-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.22-intel-2018b.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.22-intel-2018b.eb new file mode 100644 index 00000000000..d3cd1fcb701 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-0.9.22-intel-2018b.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '0.9.22' + +homepage = 'https://github.com/bbuchfink/diamond' +description = """DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance + analysis of big sequence data.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/bbuchfink/diamond/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['35e518cfa0ac2fbc57e422d380bdb5123c6335742dd7965b76c34c95f241b729'] + +builddependencies = [('CMake', '3.12.1')] +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['bin/diamond'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-intel-2018b.eb b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-intel-2018b.eb new file mode 100644 index 00000000000..f29f9bb8719 --- /dev/null +++ b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-intel-2018b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'FastME' +version = '2.1.6.1' + +homepage = 'http://www.atgc-montpellier.fr/fastme/' +description = """FastME: a comprehensive, accurate and fast distance-based phylogeny inference program.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://gite.lirmm.fr/atgc/FastME/raw/master/tarball/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ac05853bc246ccb3d88b8bc075709a82cfe096331b0f4682b639f37df2b30974'] + +sanity_check_paths = { + 'files': ['bin/fastme'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-7.3.0-Perl-5.28.0.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-7.3.0-Perl-5.28.0.eb new file mode 100644 index 00000000000..ee81413a698 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-7.3.0-Perl-5.28.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '14.137' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://micans.org/%(namelower)s/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fixperl.patch', +] +checksums = [ + 'b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497', # mcl-14-137.tar.gz + '46988a287b2ee400a54fa485176d043b2a2d6589b6257cc6cf9c21689ea3842d', # MCL-14.137_fixperl.patch +] + +builddependencies = [ + ('binutils', '2.30'), +] + +dependencies = [ + ('Perl', '5.28.0'), +] + +configopts = '--enable-blast ' + +sanity_check_paths = { + 'files': ['bin/mcl', 'bin/mcxdeblast'], + 'dirs': ['share'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb new file mode 100644 index 00000000000..aa1307b0c4e --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +version = '8-fac81' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/soedinglab/MMseqs2/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['035d1c9a5fcfae50bc2d201f177722bd79d95d3ba32342972baa7b142b52aa82'] + +builddependencies = [('CMake', '3.12.1')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE' + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.3.3-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.3.3-intel-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..a5236e15f1a --- /dev/null +++ b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.3.3-intel-2018b-Python-2.7.15.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'OrthoFinder' +version = '2.3.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/davidemms/OrthoFinder' +description = "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/davidemms/OrthoFinder/releases/download/%(version)s/'] +sources = ['OrthoFinder-%(version)s_source.tar.gz'] +checksums = ['2a0752544b116f9e5e5c3848460832b5a63e615765e588884b50942904fb948a'] + +dependencies = [ + ('Python', '2.7.15'), + ('DIAMOND', '0.9.22'), + ('MMseqs2', '8-fac81'), + ('MCL', '14.137', '-Perl-5.28.0'), + ('FastME', '2.1.6.1'), + ('BLAST+', '2.7.1'), +] + +postinstallcmds = ["cd %(installdir)s; ln -s orthofinder.py orthofinder"] + +sanity_check_paths = { + 'files': ['orthofinder.py', 'orthofinder'], + 'dirs': [], +} + +sanity_check_commands = ["orthofinder --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 05057341fd1d61e5160acb66d9120f398e685076 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 May 2019 18:10:14 +0200 Subject: [PATCH 1429/5331] bump to MaSuRCA 3.3.1, add missing bzip2 dep, also fix 'bin' in runCA-dedup script --- ...8.0.eb => MaSuRCA-3.3.1-foss-2018b-Perl-5.28.0.eb} | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/MaSuRCA/{MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb => MaSuRCA-3.3.1-foss-2018b-Perl-5.28.0.eb} (79%) diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.1-foss-2018b-Perl-5.28.0.eb similarity index 79% rename from easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb rename to easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.1-foss-2018b-Perl-5.28.0.eb index 48ab80bad8f..fccda53d234 100644 --- a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.0-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-3.3.1-foss-2018b-Perl-5.28.0.eb @@ -11,7 +11,7 @@ easyblock = 'ConfigureMake' name = 'MaSuRCA' -version = '3.3.0' +version = '3.3.1' versionsuffix = '-Perl-%(perlver)s' homepage = 'http://www.genome.umd.edu/masurca.html' @@ -23,10 +23,9 @@ description = '''MaSuRCA is whole genome assembly software. It combines the effi toolchain = {'name': 'foss', 'version': '2018b'} -# note: the tagged 3.3.0 release is (slightly) older than the 3.3.0 tarball included *in* the repo... -source_urls = ['https://github.com/alekseyzimin/masurca/raw/9b3771/'] +source_urls = ['https://github.com/alekseyzimin/masurca/releases/download/v%(version)s'] sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['f4625de837c54311d2ff4a53cd7e60d28bae49c1e5e9f2c1cbd75b688454d078'] +checksums = ['587d0ee2c6b9fbd3436ca2a9001e19f251b677757fe5e88e7f94a0664231e020'] dependencies = [ ('libreadline', '7.0'), @@ -34,15 +33,17 @@ dependencies = [ ('Boost', '1.67.0'), ('zlib', '1.2.11'), ('Perl', '5.28.0'), + ('bzip2', '1.0.6'), ] buildopts = "install-special" start_dir = "global-1" postinstallcmds = [ - # fix location of 'bin' in install prefix in runCA script + # fix location of 'bin' in install prefix in runCA and runCA-dedupe scripts # escaping single quotes within single quotes is tricky, so we use $'...' to use ANSI C-like escaping "sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA", + "sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA-dedupe", # fix hardcoded path in masurca script, just point back to 'bin' subdirectory instead "sed -i 's@../CA8/Linux-amd64/bin@../bin@g' %(installdir)s/bin/masurca", ] From 625ab491c037b1aa639d09b94434aa7f38ec22d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 May 2019 18:50:59 +0200 Subject: [PATCH 1430/5331] {toolchains} GCC 9.1.0 + binutils 2.32 --- .../b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb | 28 +++++++++++ .../b/binutils/binutils-2.32-GCCcore-9.1.0.eb | 22 +++++++++ .../f/flex/flex-2.6.4-GCCcore-9.1.0.eb | 34 +++++++++++++ easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb | 25 ++++++++++ .../easyconfigs/g/GCCcore/GCCcore-9.1.0.eb | 49 +++++++++++++++++++ .../help2man-1.47.10-GCCcore-9.1.0.eb | 25 ++++++++++ .../m/M4/M4-1.4.18-GCCcore-9.1.0.eb | 34 +++++++++++++ .../z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb | 26 ++++++++++ 8 files changed, 243 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb new file mode 100644 index 00000000000..01768c26d5c --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.3.2' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '9.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.32', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb new file mode 100644 index 00000000000..9dcc984d3a2 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb @@ -0,0 +1,22 @@ +name = 'binutils' +version = '2.32' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '9.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.3.2'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb new file mode 100644 index 00000000000..256f72bf9e9 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.3.2'), + ('help2man', '1.47.10'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.32', '', True), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb b/easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb new file mode 100644 index 00000000000..e295ebfc924 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '9.1.0' + +binutilsver = '2.32' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb new file mode 100644 index 00000000000..b145edd8135 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb @@ -0,0 +1,49 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '9.1.0' + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +mpfr_version = '4.0.2' + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.1.2.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.1.0.tar.gz', + 'isl-0.21.tar.bz2', +] +patches = ['GCCcore-6.2.0-fix-find-isl.patch'] +checksums = [ + 'be303f7a8292982a35381489f5a9178603cbe9a4715ee4fa4a815d6bcd2b658d', # gcc-9.1.0.tar.gz + '5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2', # gmp-6.1.2.tar.bz2 + 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc', # mpfr-4.0.2.tar.bz2 + '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz + 'd18ca11f8ad1a39ab6d03d3dcb3365ab416720fcb65b42d69f34f51bf0a0e859', # isl-0.21.tar.bz2 + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.32'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb new file mode 100644 index 00000000000..2c4fe36c213 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.47.10' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '9.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['f371cbfd63f879065422b58fa6b81e21870cd791ef6e11d4528608204aa4dcfb'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.32', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb new file mode 100644 index 00000000000..46d56136336 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.18' + +homepage = 'http://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '9.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['M4-1.4.18_glibc_2.28.patch'] +checksums = [ + 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz + 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.32', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb new file mode 100644 index 00000000000..d78aa50d923 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '9.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.32', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 839c3fef6b3f3e31634a03b7eb9e32491efab55e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 May 2019 20:21:00 +0200 Subject: [PATCH 1431/5331] don't require custom sanity_check_paths for GCC bundle --- test/easyconfigs/easyconfigs.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2a38154c916..9e9b14acd4c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -431,6 +431,8 @@ def check_sanity_check_paths(self, changed_ecs): # PythonBundle & PythonPackage already have a decent customised sanity_check_paths # Toolchain doesn't install anything so there is nothing to check. whitelist = ['PythonBundle', 'PythonPackage', 'Toolchain'] + # GCC is just a bundle of GCCcore+binutils + bundles_whitelist = ['GCC'] failing_checks = [] @@ -438,9 +440,12 @@ def check_sanity_check_paths(self, changed_ecs): easyblock = ec.get('easyblock') - if is_generic_easyblock(easyblock) and easyblock not in whitelist and not ec.get('sanity_check_paths'): - ec_fn = os.path.basename(ec.path) - failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) + if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): + if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): + pass + else: + ec_fn = os.path.basename(ec.path) + failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) self.assertFalse(failing_checks, '\n'.join(failing_checks)) From 1de23aadfd422c450a68d279e49138eb6c2c7eae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 May 2019 10:20:17 +0200 Subject: [PATCH 1432/5331] adding easyconfigs: MAFFT-7.427-intel-2018b-with-extensions.eb --- ...MAFFT-7.427-intel-2018b-with-extensions.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-intel-2018b-with-extensions.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-intel-2018b-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-intel-2018b-with-extensions.eb new file mode 100644 index 00000000000..4fcefc97a5d --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-intel-2018b-with-extensions.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 7.305 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'MAFFT' +version = '7.427' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program + for unix-like operating systems. It offers a range of multiple + alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), + FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://mafft.cbrc.jp/alignment/software/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s-src.tgz'] +checksums = ['068abcbc20965cbfa4e14c138cbfbcd0d311874ac2fdde384a580ac774f40e26'] + +skipsteps = ['configure'] +start_dir = 'core' +installopts = 'PREFIX=%(installdir)s' + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +sanity_check_paths = { + 'files': ['bin/mafft'], + 'dirs': [], +} + +moduleclass = 'bio' From 8764cffa51c23b253321a8eefcf3d9b601b65885 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 4 May 2019 10:56:23 +0200 Subject: [PATCH 1433/5331] use GCCcore toolchain --- ...2018b.eb => INTEGRATE-0.2.6-GCCcore-8.2.0.eb} | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/i/INTEGRATE/{INTEGRATE-0.2.6-foss-2018b.eb => INTEGRATE-0.2.6-GCCcore-8.2.0.eb} (57%) diff --git a/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-foss-2018b.eb b/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb similarity index 57% rename from easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-foss-2018b.eb rename to easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb index bbf7927089a..bdd715d4087 100644 --- a/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-foss-2018b.eb +++ b/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb @@ -3,19 +3,21 @@ easyblock = 'CMakeMake' name = 'INTEGRATE' version = '0.2.6' -homepage = "https://sourceforge.net/p/integrate-fusion/wiki/Home/" -description = """\ - INTEGRATE is a tool calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq - and WGS data. It is highly sensitive and accurate by applying a fast split-read mapping algorithm based on - Burrow-Wheeler transform. """ +homepage = 'https://sourceforge.net/p/integrate-fusion/wiki/Home/' +description = """ INTEGRATE is a tool calling gene fusions with exact fusion junctions and genomic breakpoints + by combining RNA-Seq and WGS data. It is highly sensitive and accurate by applying a fast split-read + mapping algorithm based on Burrow-Wheeler transform. """ -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['https://download.sourceforge.net/integrate-fusion/'] sources = ['%(name)s.%(version)s.tar.gz'] checksums = ['b65b14432b7184900d1f777f96fa73f4d0dffda4418936e8334613d6aa876e38'] -builddependencies = [('CMake', '3.12.1')] +builddependencies = [ + ('CMake', '3.13.3'), + ('binutils', '2.31.1'), +] separate_build_dir = True From 09626e60e920b7ee17a7fae725077edd4c846f13 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 May 2019 12:26:37 +0200 Subject: [PATCH 1434/5331] adding easyconfigs: Ruby-2.6.3-GCCcore-8.2.0.eb --- .../r/Ruby/Ruby-2.6.3-GCCcore-8.2.0.eb | 133 ++++++++++++++++++ 1 file changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.6.3-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.6.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.6.3-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..65168a24994 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.6.3-GCCcore-8.2.0.eb @@ -0,0 +1,133 @@ +name = 'Ruby' +version = '2.6.3' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['577fd3795f22b8d91c1d4e6733637b0394d4082db659fccf224c774a2b1c82fb'] + +builddependencies = [('binutils', '2.31.1')] + +exts_default_options = { + 'source_urls': ['http://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_list = [ + ('ffi', '1.10.0', { + 'checksums': ['17001940b28a961c94251a39f0ae00b32c2d0850479b5978c971759591fc1749'], + }), + ('childprocess', '1.0.1', { + 'checksums': ['7fe65b8d220967e8b47d8027274db40667641829f12ce9c6145022949c564fb4'], + }), + ('json', '2.2.0', { + 'checksums': ['9dd1437156773f72c096058ec837faac1b00077121a3fd574e68f895ea3aa96b'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.14.0', { + 'checksums': ['d6d949ff429354faa55e244b6ad792a3f80946699d443e08b07325b380bb459e'], + }), + ('arr-pm', '0.0.10', { + 'checksums': ['0fa2d425a84eeeaf8f95268568e826723b41aeefa14511d1f0ed1368c30bdd1f'], + }), + ('clamp', '1.3.0', { + 'checksums': ['1c466e93c14ed78078a428990f113b30f256189ec76f682f759e5aa2a181acfb'], + }), + ('multipart-post', '2.0.0', { + 'checksums': ['3dc44e50d3df3d42da2b86272c568fd7b75c928d8af3cc5f9834e2e5d9586026'], + }), + ('faraday', '0.15.4', { + 'checksums': ['00e6ffd6f1bccd9dc9e3b993a0004e69680559422206ce4cbb81fd2d0ba8e268'], + }), + ('faraday_middleware', '0.13.1', { + 'checksums': ['b94e3e7845f78db0eacdfc7e0185f0310765ccd70a46b6ce6478aa858ace23a9'], + }), + ('highline', '2.0.2', { + 'checksums': ['999780b892b3bb835cdaafbd0933f65ff85b72ccd1326890629b23e9a8ba1fbc'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.2.2', { + 'checksums': ['c8cc9446bcc51034103c1259ad70b91dc9f5297d13460b2c0cce7e5a93e8d451'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.13.1', { + 'checksums': ['db8613c039b9501e6b2fb85efe4feabb02f55c3365bae52bba35381b89c780e6'], + }), + ('public_suffix', '3.0.3', { + 'checksums': ['d4f4addffbd1ad3e7b5bb2e258a761ccef5670c23c29b0476b2299bcca220623'], + }), + ('addressable', '2.4.0', { + 'checksums': ['7abfff765571b0a73549c9a9d2f7e143979cd0c252f7fa4c81e7102a973ef656'], + }), + ('gh', '0.15.1', { + 'checksums': ['ef733f81c17846f217f5ad9616105e9adc337775d41de1cc330133ad25708d3c'], + }), + ('launchy', '2.4.3', { + 'checksums': ['42f52ce12c6fe079bac8a804c66522a0eefe176b845a62df829defe0e37214a4'], + }), + ('ethon', '0.12.0', { + 'checksums': ['e99d3095e89f82c5a7e63d9261ddf4a21f28ae5d12a9d3abaa6920cce6cbef3d'], + }), + ('typhoeus', '1.3.1', { + 'checksums': ['257e7163d50bed15e52c3c25bde890ea3ad854f3bd2e3fd16ce0b216c342d132'], + }), + ('websocket', '1.2.8', { + 'checksums': ['1d8155c1cdaab8e8e72587a60e08423c9dd84ee44e4e827358ce3d4c2ccb2138'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.3', { + 'checksums': ['ea7bf591567e391ef262a7c29edaf87c6205204afb5bb39dfa8f08f2e51282a3'], + }), + ('rspec-support', '3.8.0', { + 'checksums': ['0918cc4165bb7626e518cef41046ddab90d0435868b0fb85dc90e61e733b755c'], + }), + ('rspec-mocks', '3.8.0', { + 'checksums': ['d73b926d641676025ba086b4854f70b8a70d6cb763d50e9d278b792c1902c51b'], + }), + ('rspec-expectations', '3.8.3', { + 'checksums': ['de192f5c3f9f2916857eaee42964b062bcfdd1b822d5063506751eb77cd18fb0'], + }), + ('rspec-core', '3.8.0', { + 'checksums': ['97d0b30c5687075417ac6f837c44a95e4a825007d0017fccec7a5cbcec2a3adc'], + }), + ('rspec', '3.8.0', { + 'checksums': ['83f519611bb674d456e87397fea7c5b15b1af8bdc77ce929673ae3b4b656f796'], + }), + ('rack', '2.0.7', { + 'checksums': ['5158fb64313c17fb2535c8e5def3de7e8b38baf2ab9e4c90155ebed5a9db207d'], + }), + ('rack-protection', '2.0.5', { + 'checksums': ['53cb7ad3f8119fac5a3d2be13e288f29fa15e29058421339beb1d75c043e2694'], + }), + ('tilt', '2.0.9', { + 'checksums': ['9fd77f52eb8dbeae741a7110c08fd9777679bb25dd8873fc9e19384e19984431'], + }), + ('mustermann', '1.0.3', { + 'checksums': ['219ecbefebccb10778273bbd64ae468e5da30ac55f346b93700b786feb7ccc53'], + }), + ('sinatra', '2.0.5', { + 'checksums': ['3e9f56189bc6d40eb8c3ef9ee1b5ec905d23c63521823011d8be96e08a7d5abd'], + }), + ('rack-test', '1.1.0', { + 'checksums': ['154161f40f162b1c009a655b7b0c5de3a3102cc6d7d2e94b64e1f46ace800866'], + }), + ('bundler', '2.0.1', { + 'checksums': ['c7e38039993c9c2edc27397aef4a3370a4b35c7fae3d93e434e501c4bd7656ea'], + }), +] + +moduleclass = 'lang' From f2c758289dc0a439c29650a8f94994632ca6daf5 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Sat, 4 May 2019 12:42:09 +0200 Subject: [PATCH 1435/5331] adding easyconfigs: MPFR-4.0.2-GCCcore-8.2.0.eb --- .../m/MPFR/MPFR-4.0.2-GCCcore-8.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-4.0.2-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.0.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.0.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..84200357eb5 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.0.2-GCCcore-8.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '4.0.2' + +homepage = 'http://www.mpfr.org' + +description = """ + The MPFR library is a C library for multiple-precision floating-point + computations with correct rounding. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' From 7bd44c1ea0b265a39c320bdda67f6862aa174b34 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 4 May 2019 16:48:40 +0200 Subject: [PATCH 1436/5331] Update checksum for VMD 1.9.3 --- .../easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb | 2 +- .../easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb | 2 +- .../easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb index e5dd9e0f5b8..9a938ca483e 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb @@ -30,7 +30,7 @@ patches = [ 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', ] checksums = [ - '0538f35273668df2e38cdeb170293bf3b9178d6033170b38638fec285160e287', # vmd-1.9.3.src.tar.gz + '7bc614e18bed32f5caabeee8ad75b825dead0252f3ecbaa2e4fb4a5624bbddd1', # vmd-1.9.3.src.tar.gz '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb index cd9946233a7..cb9a9fefedf 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb @@ -30,7 +30,7 @@ patches = [ 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', ] checksums = [ - '0538f35273668df2e38cdeb170293bf3b9178d6033170b38638fec285160e287', # vmd-1.9.3.src.tar.gz + '7bc614e18bed32f5caabeee8ad75b825dead0252f3ecbaa2e4fb4a5624bbddd1', # vmd-1.9.3.src.tar.gz '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb index ced6067a4ba..a8cb7ae1abe 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb @@ -30,7 +30,7 @@ patches = [ 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', ] checksums = [ - '0538f35273668df2e38cdeb170293bf3b9178d6033170b38638fec285160e287', # vmd-1.9.3.src.tar.gz + '7bc614e18bed32f5caabeee8ad75b825dead0252f3ecbaa2e4fb4a5624bbddd1', # vmd-1.9.3.src.tar.gz '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb index d1bd8e4e417..9b39079c0b7 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb @@ -30,7 +30,7 @@ patches = [ 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', ] checksums = [ - '0538f35273668df2e38cdeb170293bf3b9178d6033170b38638fec285160e287', # vmd-1.9.3.src.tar.gz + '7bc614e18bed32f5caabeee8ad75b825dead0252f3ecbaa2e4fb4a5624bbddd1', # vmd-1.9.3.src.tar.gz '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch From 82e333349364aac6f9dfde314571f36ce3b71d93 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 4 May 2019 16:52:10 +0200 Subject: [PATCH 1437/5331] Add missing dependency for Ruby, fix Python and Ruby detection. Add missing modextrapath. --- .../w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb index 79efbd5f30a..c6c41bc17c2 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.24.1-GCC-8.2.0-2.31.1.eb @@ -32,6 +32,7 @@ osdependencies = [ builddependencies = [ ('CMake', '3.13.3'), + ('Python', '3.7.2'), ('Perl', '5.28.1'), ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), ] @@ -47,13 +48,18 @@ dependencies = [ ('libtasn1', '4.13'), ('GStreamer', '1.16.0'), ('OpenJPEG', '2.3.1'), + ('Ruby', '2.6.3'), ] -configopts = "-DPORT=GTK " +configopts = "-DPORT=GTK -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python -DRUBY_EXECUTABLE=$EBROOTRUBY/bin/ruby " sanity_check_paths = { 'files': ['bin/WebKitWebDriver', 'lib/libwebkit2gtk-4.0.%s' % SHLIB_EXT], 'dirs': ['include/webkitgtk-4.0/webkit2', 'libexec/webkit2gtk-4.0'], } +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', +} + moduleclass = 'lib' From 16b6a81618f85e5f94513fd6ac966aa72f125ae6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 May 2019 09:31:17 +0200 Subject: [PATCH 1438/5331] fix source URLs for libcerf 1.7 --- .../easyconfigs/l/libcerf/libcerf-1.7-GCCcore-7.3.0.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.7-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.7-GCCcore-7.3.0.eb index 3754226407c..27260a3e9ea 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-1.7-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.7-GCCcore-7.3.0.eb @@ -14,12 +14,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://apps.jcns.fz-juelich.de/src/libcerf/', - 'http://apps.jcns.fz-juelich.de/src/libcerf/old', -] -sources = [SOURCE_TGZ] -checksums = ['01ddaacaab1e3b120d7480ce518bef02cb658f9728184375f0670a6eb6753da0'] +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['9c5bdd138860eefea72518fef4ab43fde491dccea3cfc450a7a612af7cf55d29'] builddependencies = [ ('binutils', '2.30'), From dbf3c21e5521717c6e7d84f608b5042a39d9a7f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 May 2019 09:34:44 +0200 Subject: [PATCH 1439/5331] use https:// in source URLs for Ruby 2.6.3 --- easybuild/easyconfigs/r/Ruby/Ruby-2.6.3-GCCcore-8.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.6.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.6.3-GCCcore-8.2.0.eb index 65168a24994..c9e1a23a522 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.6.3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.6.3-GCCcore-8.2.0.eb @@ -8,14 +8,14 @@ description = """Ruby is a dynamic, open source programming language with toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['http://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['577fd3795f22b8d91c1d4e6733637b0394d4082db659fccf224c774a2b1c82fb'] builddependencies = [('binutils', '2.31.1')] exts_default_options = { - 'source_urls': ['http://rubygems.org/downloads/'], + 'source_urls': ['https://rubygems.org/downloads/'], 'source_tmpl': '%(name)s-%(version)s.gem', } From a0090903e3f3f57f9157c360164e8e96ec445fca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 May 2019 10:31:36 +0200 Subject: [PATCH 1440/5331] use https for homepage/source_urls involved GCC 9.1.0-2.32 --- easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb | 2 +- easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb | 4 ++-- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb index 01768c26d5c..b46a869bd63 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Bison' version = '3.3.2' -homepage = 'http://www.gnu.org/software/bison' +homepage = 'https://www.gnu.org/software/bison' description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb index 9dcc984d3a2..1efeca34ea5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb @@ -1,7 +1,7 @@ name = 'binutils' version = '2.32' -homepage = 'http://directory.fsf.org/project/binutils/' +homepage = 'https://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '9.1.0'} diff --git a/easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb b/easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb index e295ebfc924..e68c767c1d9 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb @@ -6,7 +6,7 @@ version = '9.1.0' binutilsver = '2.32' versionsuffix = '-%s' % binutilsver -homepage = 'http://gcc.gnu.org/' +homepage = 'https://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb index b145edd8135..eb7c39ad3f0 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'EB_GCC' name = 'GCCcore' version = '9.1.0' -homepage = 'http://gcc.gnu.org/' +homepage = 'https://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb index 46d56136336..7cb0d843963 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'M4' version = '1.4.18' -homepage = 'http://www.gnu.org/software/m4/m4.html' +homepage = 'https://www.gnu.org/software/m4/m4.html' description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb index d78aa50d923..25ecfcd4a9e 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'zlib' version = '1.2.11' -homepage = 'http://www.zlib.net/' +homepage = 'https://www.zlib.net/' description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.""" @@ -11,7 +11,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum toolchain = {'name': 'GCCcore', 'version': '9.1.0'} toolchainopts = {'pic': True} -source_urls = ['http://zlib.net/fossils'] +source_urls = ['https://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] From 1b6542f50a1840d14d0809d5944a471ce239fcba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 May 2019 10:48:23 +0200 Subject: [PATCH 1441/5331] {vis}[GCCcore/8.2.0] PyQt5 v5.12.1 w/ Python 3.7.2 --- ...PyQt5-5.12.1-GCCcore-8.2.0-Python-3.7.2.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..0d30a23d92c --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,67 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.31.1')] +dependencies = [ + ('Python', '3.7.2'), + ('Qt5', '5.12.3'), +] + +default_easyblock = 'ConfigureMakePythonPackage' + +pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +sip_configopts = "configure.py --bindir %%(installdir)s/bin --incdir %%(installdir)s/include --destdir %s" % pylibdir +# required for PyQt5, cfr. http://pyqt.sourceforge.net/Docs/PyQt5/installation.html#downloading-sip +# and http://pyqt.sourceforge.net/Docs/sip4/using.html#ref-private-sip +sip_configopts += " --sip-module PyQt5.sip" + +pyqt5_configopts = "configure.py --confirm-license --verbose --destdir=%s " % pylibdir +pyqt5_configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages --bindir=%(installdir)s/bin" +pyqt5_configopts += " --designer-plugindir=%(installdir)s/plugins/designer" +pyqt5_configopts += " --qml-plugindir=%(installdir)s/plugins/PyQt5" +pyqt5_configopts += " --no-sip-files --no-stubs " + +sipver = '4.19.16' +components = [ + ('SIP', sipver, { + 'source_urls': ['https://www.riverbankcomputing.com/static/Downloads/sip/%s' % sipver], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['184c790d58e9527fc6bdac2bbf8638f3d1b41dea922cad8eb83172b4ba70c620'], + 'start_dir': 'sip-%s' % sipver, + 'configopts': sip_configopts, + 'options': {'modulename': 'PyQt5.sip'}, + }), + (name, version, { + 'source_urls': ['https://www.riverbankcomputing.com/static/Downloads/PyQt5/%(version)s/'], + 'sources': ['%(name)s_gpl-%(version)s.tar.gz'], + 'checksums': ['3718ce847d824090fd5f95ff3f13847ee75c2507368d4cbaeb48338f506e59bf'], + 'start_dir': 'PyQt5_gpl-%(version)s', + 'preconfigopts': "export PATH=%(installdir)s/bin:$PATH && ", + 'configopts': pyqt5_configopts, + 'options': {'modulename': 'PyQt5.QtCore'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h', 'lib/python%(pyshortver)s/site-packages/sipconfig.py', + 'lib/python%(pyshortver)s/site-packages/sipdistutils.py', + 'lib/python%%(pyshortver)s/site-packages/PyQt5/sip.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_PLUGIN_PATH': 'plugins', +} + +moduleclass = 'vis' From 54f358f0f284fc9035537c289eeab248229fc91c Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 5 May 2019 14:29:15 +0200 Subject: [PATCH 1442/5331] Clean out commented leftovers --- easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb | 1 - .../easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb index c78bb632dff..b4c0b12882f 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019a-Python-3.7.2.eb @@ -67,7 +67,6 @@ configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)sm.%s " configopts += "-DVTK_Group_MPI:BOOL=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" -# preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb index 9dc8eba2c6f..3d0d5c71397 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-intel-2019a-Python-3.7.2.eb @@ -67,7 +67,6 @@ configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)sm.%s " configopts += "-DVTK_Group_MPI:BOOL=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" -# preinstallopts = "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages/ && " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} From 34aa4f05b91ef8f4557332b96ccae9165be96690 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 5 May 2019 15:29:52 +0200 Subject: [PATCH 1443/5331] VMD can now be downloaded directly without registration. Update source_urls and adjust checksum again. --- .../easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb | 4 ++-- .../easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb | 4 ++-- .../easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb | 4 ++-- .../easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb index 9a938ca483e..17114b9a6af 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-foss-2017b-Python-2.7.14.eb @@ -14,8 +14,8 @@ toolchain = {'name': 'foss', 'version': '2017b'} unpack_stride_cmd = 'tar -C vmd-%(version)s/lib/stride -xf %s' -# downloading requires registration, so only stride's URL here source_urls = [ + 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', 'http://webclu.bio.wzw.tum.de/stride/' ] sources = [ @@ -30,7 +30,7 @@ patches = [ 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', ] checksums = [ - '7bc614e18bed32f5caabeee8ad75b825dead0252f3ecbaa2e4fb4a5624bbddd1', # vmd-1.9.3.src.tar.gz + '5bdc314dc836d620fe510ed4b6c3dbe3cf66525b61680ffec4e2563cf495f128', # vmd-1.9.3.src.tar.gz '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb index cb9a9fefedf..f8b3b942b6a 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2016b-Python-2.7.12.eb @@ -14,8 +14,8 @@ toolchain = {'name': 'intel', 'version': '2016b'} unpack_stride_cmd = 'tar -C vmd-%(version)s/lib/stride -xf %s' -# downloading requires registration, so only stride's URL here source_urls = [ + 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', 'http://webclu.bio.wzw.tum.de/stride/' ] sources = [ @@ -30,7 +30,7 @@ patches = [ 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', ] checksums = [ - '7bc614e18bed32f5caabeee8ad75b825dead0252f3ecbaa2e4fb4a5624bbddd1', # vmd-1.9.3.src.tar.gz + '5bdc314dc836d620fe510ed4b6c3dbe3cf66525b61680ffec4e2563cf495f128', # vmd-1.9.3.src.tar.gz '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb index a8cb7ae1abe..4efe4d3a347 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018a-Python-2.7.14.eb @@ -14,8 +14,8 @@ toolchain = {'name': 'intel', 'version': '2018a'} unpack_stride_cmd = 'tar -C vmd-%(version)s/lib/stride -xf %s' -# downloading requires registration, so only stride's URL here source_urls = [ + 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', 'http://webclu.bio.wzw.tum.de/stride/' ] sources = [ @@ -30,7 +30,7 @@ patches = [ 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', ] checksums = [ - '7bc614e18bed32f5caabeee8ad75b825dead0252f3ecbaa2e4fb4a5624bbddd1', # vmd-1.9.3.src.tar.gz + '5bdc314dc836d620fe510ed4b6c3dbe3cf66525b61680ffec4e2563cf495f128', # vmd-1.9.3.src.tar.gz '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb index 9b39079c0b7..b401ca3a908 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.3-intel-2018b-Python-2.7.15.eb @@ -14,8 +14,8 @@ toolchain = {'name': 'intel', 'version': '2018b'} unpack_stride_cmd = 'tar -C vmd-%(version)s/lib/stride -xf %s' -# downloading requires registration, so only stride's URL here source_urls = [ + 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', 'http://webclu.bio.wzw.tum.de/stride/' ] sources = [ @@ -30,7 +30,7 @@ patches = [ 'VMD-%(version)s_stride_MAX_AT_IN_RES.patch', ] checksums = [ - '7bc614e18bed32f5caabeee8ad75b825dead0252f3ecbaa2e4fb4a5624bbddd1', # vmd-1.9.3.src.tar.gz + '5bdc314dc836d620fe510ed4b6c3dbe3cf66525b61680ffec4e2563cf495f128', # vmd-1.9.3.src.tar.gz '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz 'b203eb1af21b643d3dfb18a38af17fbd96719048a750d22e4aefbb1b00cb3765', # VMD-1.9.3_configure.patch 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch From 215d795dd22096dfbb36186bc9e16f73f55d6109 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 May 2019 15:33:57 +0200 Subject: [PATCH 1444/5331] adding easyconfigs: py-cpuinfo-5.0.0.eb --- .../p/py-cpuinfo/py-cpuinfo-5.0.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb new file mode 100644 index 00000000000..0e9903cb023 --- /dev/null +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'py-cpuinfo' +version = '5.0.0' + +homepage = 'https://github.com/workhorsy/py-cpuinfo' +description = "py-cpuinfo gets CPU info with pure Python." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2cf6426f776625b21d1db8397d3297ef7acfa59018f02a8779123f3190f18500'] + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +options = {'modulename': 'cpuinfo'} + +sanity_check_paths = { + 'files': ['bin/cpuinfo'], + 'dirs': ['lib/python%s/site-packages' % pyshortver], +} + +sanity_check_commands = [ + "cpuinfo", + "python -m cpuinfo", +] + +moduleclass = 'tools' From 9aae685eedddd9a3d8bed42163b82b37ad7e136d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 5 May 2019 15:36:49 +0200 Subject: [PATCH 1445/5331] $GI_TYPELIB_PATH must be set for GTK+ --- easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb index c1776bac900..77b3673ae83 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb @@ -41,6 +41,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } From 71854fdb96f1d50f78d8dda55394852be6a513ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Sun, 5 May 2019 16:07:36 +0200 Subject: [PATCH 1446/5331] switch to GCCcore toolchain --- .../{ncdu-1.14-foss-2018b.eb => ncdu-1.14-GCCcore-7.3.0.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/n/ncdu/{ncdu-1.14-foss-2018b.eb => ncdu-1.14-GCCcore-7.3.0.eb} (90%) diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.14-foss-2018b.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.14-GCCcore-7.3.0.eb similarity index 90% rename from easybuild/easyconfigs/n/ncdu/ncdu-1.14-foss-2018b.eb rename to easybuild/easyconfigs/n/ncdu/ncdu-1.14-GCCcore-7.3.0.eb index c4373a97550..03e0b54f8d9 100644 --- a/easybuild/easyconfigs/n/ncdu/ncdu-1.14-foss-2018b.eb +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.14-GCCcore-7.3.0.eb @@ -11,12 +11,14 @@ description = """Ncdu is a disk usage analyzer with an ncurses interface. It is desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed.""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = ['https://dev.yorhel.nl/download/'] sources = [SOURCE_TAR_GZ] checksums = ['c694783aab21e27e64baad314b7c1ff34541bfa219fe9645ef6780f1c5558c44'] +builddependencies = [('binutils', '2.30')] + dependencies = [('ncurses', '6.1')] sanity_check_paths = { From 7a8dba64d114cee77fc3b82c27ce3d9f7e6d4bf9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Sun, 5 May 2019 16:20:00 +0200 Subject: [PATCH 1447/5331] revert adding cURL for versions below 1.7 --- easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb | 1 - easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb | 1 - easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb | 1 - easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb | 1 - easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb | 1 - easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb | 1 - easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb | 1 - easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-GCC-6.4.0-2.28.eb | 1 - easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-foss-2017a.eb | 1 - .../SAMtools/SAMtools-1.6-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 1 - easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-intel-2017b.eb | 1 - 11 files changed, 11 deletions(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb index cc748b0e581..984114fed31 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-foss-2016b.eb @@ -33,7 +33,6 @@ dependencies = [ ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ('XZ', '5.2.2'), - ('cURL', '7.49.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb index 1efba02c096..1eafb1aad7e 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-goolf-1.4.10.eb @@ -36,7 +36,6 @@ dependencies = [ ('zlib', '1.2.7'), ('bzip2', '1.0.6'), ('XZ', '5.2.2'), - ('cURL', '7.29.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb index 12ec373a875..d4d93bf4d5f 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2016b.eb @@ -33,7 +33,6 @@ dependencies = [ ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ('XZ', '5.2.2'), - ('cURL', '7.49.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb index 9e43b582181..593be9f574d 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4-intel-2017a.eb @@ -33,7 +33,6 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), - ('cURL', '7.53.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb index ab0003de7fb..ca5e5ba8406 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.4.1-intel-2017a.eb @@ -33,7 +33,6 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), - ('cURL', '7.53.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb index 77ddfe2035c..30006e4f3c0 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-foss-2016b.eb @@ -33,7 +33,6 @@ dependencies = [ ('zlib', '1.2.8'), ('bzip2', '1.0.6'), ('XZ', '5.2.2'), - ('cURL', '7.49.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb index 416549cb221..8946ef723cd 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.5-intel-2017a.eb @@ -33,7 +33,6 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), - ('cURL', '7.53.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-GCC-6.4.0-2.28.eb index 770f9ce3971..f8cedd5875a 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-GCC-6.4.0-2.28.eb @@ -33,7 +33,6 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), - ('cURL', '7.58.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-foss-2017a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-foss-2017a.eb index 1933a2350e8..7c9997f8bc1 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-foss-2017a.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-foss-2017a.eb @@ -33,7 +33,6 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), - ('cURL', '7.53.1'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index 093b740aa3e..6ec0fbd7093 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -33,7 +33,6 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), - ('cURL', '7.58.0'), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-intel-2017b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-intel-2017b.eb index 48029ca2f9f..a0bf05f899a 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-intel-2017b.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.6-intel-2017b.eb @@ -33,7 +33,6 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('XZ', '5.2.3'), - ('cURL', '7.56.0'), ] moduleclass = 'bio' From 8c4ae17925d8c84a54b4de1c09465a1d0544da06 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 5 May 2019 22:35:30 +0200 Subject: [PATCH 1448/5331] fix style --- .../easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb index bdd715d4087..c7cb191adc1 100644 --- a/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb @@ -34,7 +34,7 @@ postinstallcmds = [ sanity_check_paths = { 'files': ['bin/Integrate'], - 'dirs': [''], + 'dirs': [], } moduleclass = 'bio' From 33247af420d72220099671a47a0f4580558f8e4a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 6 May 2019 07:30:16 +0200 Subject: [PATCH 1449/5331] Add GI_TYPELIB_PATH to the rest of the active GTK+ easyconfigs. --- easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb | 1 + easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb | 1 + 12 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb index 01b9324df53..8f98f42b866 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.28-intel-2016a.eb @@ -29,6 +29,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb index c2a9dc97ec0..f3e8bdf2f31 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-foss-2016a.eb @@ -29,6 +29,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb index 903aa877564..5703658508f 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.30-intel-2016a.eb @@ -29,6 +29,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb index 20478335c2f..45ad00ae23c 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-foss-2016b.eb @@ -29,6 +29,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb index c4dfb4aa1f2..b2eff3d30ae 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2016b.eb @@ -29,6 +29,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb index da29a06a743..05643f884d4 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.31-intel-2017a.eb @@ -31,6 +31,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb index 7c78377569b..2681fd72f0a 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2017b.eb @@ -30,6 +30,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb index 522c274bd99..184830d5437 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018a.eb @@ -31,6 +31,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb index 790f906aa10..943ff5dd70f 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-foss-2018b.eb @@ -33,6 +33,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb index 4fdea8f3c39..3755e9d6410 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2017b.eb @@ -30,6 +30,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb index 2998eb97abf..9387ef58059 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.32-intel-2018a.eb @@ -31,6 +31,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb index 797e04d0dbd..a416c0bf4cf 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb @@ -40,6 +40,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } From 89e2736313a8e0be6649cfb8096b5f6a316e9c2e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 6 May 2019 09:16:53 +0200 Subject: [PATCH 1450/5331] Move code around to follow style guide. --- .../easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb | 9 ++------- .../h/h5py/h5py-2.9.0-fosscuda-2019a.eb | 9 ++------- .../easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb | 15 +++++---------- .../h/h5py/h5py-2.9.0-intelcuda-2019a.eb | 15 +++++---------- 4 files changed, 14 insertions(+), 34 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb index e510a14f5e2..b919c5b0719 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-foss-2019a.eb @@ -15,9 +15,6 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - multi_deps = {'Python': ['3.7.2', '2.7.15']} builddependencies = [('pkgconfig', '1.5.1', '-python')] @@ -30,9 +27,7 @@ dependencies = [ use_pip = False download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} +# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb index fd4cb0d3487..01a2c967563 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-fosscuda-2019a.eb @@ -15,9 +15,6 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - multi_deps = {'Python': ['3.7.2', '2.7.15']} builddependencies = [('pkgconfig', '1.5.1', '-python')] @@ -30,9 +27,7 @@ dependencies = [ use_pip = False download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} +# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb index eda050deb44..10fe86a9292 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intel-2019a.eb @@ -15,12 +15,6 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] -# required because we're building Python packages using Intel compilers on top of Python built with GCC -check_ldshared = True - -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - multi_deps = {'Python': ['3.7.2', '2.7.15']} builddependencies = [('pkgconfig', '1.5.1', '-python')] @@ -33,9 +27,10 @@ dependencies = [ use_pip = False download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb index 8fa44e84f3c..8c65086fa06 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.9.0-intelcuda-2019a.eb @@ -15,12 +15,6 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['9d41ca62daf36d6b6515ab8765e4c8c4388ee18e2a665701fef2b41563821002'] -# required because we're building Python packages using Intel compilers on top of Python built with GCC -check_ldshared = True - -# to really use mpi enabled hdf5 we now seem to need a configure step -prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' - multi_deps = {'Python': ['3.7.2', '2.7.15']} builddependencies = [('pkgconfig', '1.5.1', '-python')] @@ -33,9 +27,10 @@ dependencies = [ use_pip = False download_dep_fail = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' moduleclass = 'data' From c0e54247c4d99b50c62340f5e1915d7aa9f252d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 May 2019 10:59:32 +0200 Subject: [PATCH 1451/5331] don't use pip for py-cpuinfo since we're using system Python --- easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb index 0e9903cb023..b4dc3e676e0 100644 --- a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb @@ -15,6 +15,9 @@ checksums = ['2cf6426f776625b21d1db8397d3297ef7acfa59018f02a8779123f3190f18500'] allow_system_deps = [('Python', SYS_PYTHON_VERSION)] pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +# don't use pip since we're not sure whether or not it's installed on the system... +use_pip = False + options = {'modulename': 'cpuinfo'} sanity_check_paths = { From fd8de5ad99ea5cd36f7804fec3edabeb10b31111 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 6 May 2019 11:45:04 +0200 Subject: [PATCH 1452/5331] make suggested style change --- .../Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb index b852cffa7b7..c411bea9f27 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb @@ -35,7 +35,9 @@ configopts = '-DCYCLES_CUDA_BINARIES_ARCH="sm_30;sm_35;sm_37;sm_50;sm_52;sm_60;s # the CUPTI directory contains old GL headers, which interfere with Blender # see: https://github.com/easybuilders/easybuild-easyblocks/issues/1492 # see: https://github.com/easybuilders/easybuild-easyblocks/pull/1306/files -buildopts = "CPATH=${CPATH/${EBROOTCUDA}'/extras/CUPTI/include:'/}" +# FOO=${FOO/bar/} results in $FOO value with 'bar' removed +# quotes are required here because value to remove includes slashes (/) +buildopts = 'CPATH=${CPATH/"$EBROOTCUDA/extras/CUPTI/include:"/}' # use Intel software rasterizer by default (no GPU hardware acceleration) modextravars = {'GALLIUM_DRIVER': 'swr'} From 47330408a357e3712a285c4efd740cceb8a00133 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 6 May 2019 14:55:32 +0200 Subject: [PATCH 1453/5331] Perl: add Parallel::ForkManager --- .../easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb | 9 +++++++-- .../easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb | 7 ++++++- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb index 8919ccf4b33..5c03b81587d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ osdependencies = ['openssl', ('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # !! order of extensions is important !! -# extensions updated on June 26th 2018 +# extensions updated on May 6th 2018 exts_list = [ ('Config::General', '2.63', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', @@ -990,10 +990,10 @@ exts_list = [ 'checksums': ['18790b0cc5f0a51468495c3847b16738f785a2d460403595001e0b932e5db676'], }), ('Scalar::List::Utils', '1.50', { + 'modulename': 'List::Util', 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], 'checksums': ['06aab9c693380190e53be09be7daed20c5d6278f71956989c24cca7782013675'], - 'modulename': 'List::Util', }), ('Data::Section::Simple', '0.07', { 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', @@ -1470,6 +1470,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], }), + ('Parallel::ForkManager', '2.02', { + 'source_tmpl': 'Parallel-ForkManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Y/YA/YANICK/'], + 'checksums': ['c1b2970a8bb666c3de7caac4a8f4dbcc043ab819bbc337692ec7bf27adae4404'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb index 38fa62b45e3..b34b6420e0d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb @@ -22,7 +22,7 @@ dependencies = [ osdependencies = ['openssl', ('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # !! order of extensions is important !! -# extensions updated on March 13th 2019 +# extensions updated on May 6th 2018 exts_list = [ ('Config::General', '2.63', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', @@ -1470,6 +1470,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA/'], 'checksums': ['9b60767fe40752ef7a9d3f13f19060a63389a5c23acc3e9827e19b75500f81f3'], }), + ('Parallel::ForkManager', '2.02', { + 'source_tmpl': 'Parallel-ForkManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Y/YA/YANICK/'], + 'checksums': ['c1b2970a8bb666c3de7caac4a8f4dbcc043ab819bbc337692ec7bf27adae4404'], + }), ] moduleclass = 'lang' From 427bb71f93d423b001aeba4f238bf423f5a06506 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 6 May 2019 16:25:22 +0200 Subject: [PATCH 1454/5331] adding easyconfigs: CGAL-4.11.3-foss-2019a-Python-3.7.2.eb, CGAL-4.11.3-intel-2019a-Python-3.7.2.eb --- .../CGAL-4.11.3-foss-2019a-Python-3.7.2.eb | 37 +++++++++++++++++++ .../CGAL-4.11.3-intel-2019a-Python-3.7.2.eb | 37 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-foss-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..c685addb572 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,37 @@ +name = 'CGAL' +version = '4.11.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['3ed80bc87f00eb3c72357f5842907f828f8ab8fc66053351aab76aa10566981a'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.7.2'), + ('Boost', '1.70.0'), + ('MPFR', '4.0.2'), + ('GMP', '6.1.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.12.3'), +] + +builddependencies = [ + ('CMake', '3.13.3'), + ('Eigen', '3.3.7'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..aa55046cc05 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,37 @@ +name = 'CGAL' +version = '4.11.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['3ed80bc87f00eb3c72357f5842907f828f8ab8fc66053351aab76aa10566981a'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.7.2'), + ('Boost', '1.70.0'), + ('MPFR', '4.0.2'), + ('GMP', '6.1.2'), + ('libGLU', '9.0.0'), + ('Qt5', '5.12.3'), +] + +builddependencies = [ + ('CMake', '3.13.3'), + ('Eigen', '3.3.7'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' From 6f56f77aaa6235d7d2f0ebb988ec415a869a7e38 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Wed, 24 Apr 2019 16:14:58 +0200 Subject: [PATCH 1455/5331] adding easyconfigs: QuantumESPRESSO-6.4.1-intel-2019a.eb, ELPA-2018.11.001-intel-2019a.eb --- .../e/ELPA/ELPA-2018.11.001-intel-2019a.eb | 51 +++++++++++++++++++ .../QuantumESPRESSO-6.4.1-intel-2019a.eb | 40 +++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb new file mode 100644 index 00000000000..02f8c215b7a --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb @@ -0,0 +1,51 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'ELPA' +version = '2018.11.001' + +homepage = 'http://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cc27fe8ba46ce6e6faa8aea02c8c9983052f8e73a00cfea38abf7613cb1e1b16'] + +builddependencies = [ + ('Autotools', '20180311'), +] + +common_configopts = 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' +common_configopts += 'LIBS="$LIBSCALAPACK" ' + +configopts = [ + common_configopts + '--enable-openmp ', + common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. +] + +buildopts = ' V=1 ' + +postinstallcmds = [ + # The include files and Fortran module files are identical with and + # without openmp. + 'ln -s elpa-%(version)s/elpa %(installdir)s/include', + 'ln -s elpa-%(version)s/modules %(installdir)s/include', +] + +sanity_check_paths = { + 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', + 'lib/libelpa_openmp.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb new file mode 100644 index 00000000000..677b8eb828f --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.4.1-intel-2019a.eb @@ -0,0 +1,40 @@ +name = 'QuantumESPRESSO' +version = '6.4.1' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s_release_pack.tgz', + {'filename': 'wannier90-3.0.0.tar.gz', 'download_filename': 'v3.0.0.tar.gz'}, +] +checksums = [ + 'a9b19cf620656d89a83c1abdf87fbfd66a7d011e6153fa6db2dc207bf25f138a', # qe-6.4.1_release_pack.tgz + 'f196e441dcd7b67159a1d09d2d7de2893b011a9f03aab6b30c4703ecbf20fe5b', # wannier90-3.0.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.10.5'), + ('ELPA', '2018.11.001'), + ('libxc', '4.3.4'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built +buildopts = 'all gwl xspectra couple epw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' From ff5642b785bbfb2180daaba94234e1f191f86018 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 May 2019 18:51:47 +0200 Subject: [PATCH 1456/5331] adding easyconfigs: Molcas-8.2-centos-mkl-par.eb, Molcas-8.2-centos-par.eb --- .../m/Molcas/Molcas-8.2-centos-mkl-par.eb | 48 +++++++++++++++++++ .../m/Molcas/Molcas-8.2-centos-par.eb | 48 +++++++++++++++++++ 2 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-mkl-par.eb create mode 100644 easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-par.eb diff --git a/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-mkl-par.eb b/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-mkl-par.eb new file mode 100644 index 00000000000..5bcbc9e8202 --- /dev/null +++ b/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-mkl-par.eb @@ -0,0 +1,48 @@ +easyblock = 'PackedBinary' + +name = 'Molcas' +version = '8.2' +versionsuffix = '-centos-mkl-par' + +homepage = 'http://www.molcas.org' +description = """Molcas is an ab initio quantum chemistry software package +developed by scientists to be used by scientists. The basic philosophy is is to +be able to treat general electronic structures for molecules consisting of +atoms from most of the periodic table. As such, the primary focus of the +package is on multiconfigurational methods with applications typically +connected to the treatment of highly degenerate states.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download requires registration, see http://www.molcas.org/download.html +sources = ['%(namelower)s%(version_major)s%(version_minor)s%(versionsuffix)s.tar.gz'] +checksums = ['54497a1b3e482802c05d0320c2e4fd57fb0f0c6f47b950517ae46e24d4da3b87'] + +# The Molcas installation procedure creates a binary in a separate directory, +# but that binary depends on being able to find the originally extracted files. +# Because we don't want to rely on root privileges, and we do want to use +# EasyBuild paths, this means we need to extract Molcas to a subdirectory of +# the proposed installation directory. +unpack_options = "--transform='s,^%(namelower)s-%(version)s%(versionsuffix)s,%(namelower)s_files,'" + +buildininstalldir = True +skipsteps = ['install'] + +molcas_subdir = 'molcas%(version_major)s%(version_minor)s%(versionsuffix)s' + +# For the same reason as the tarball needs an extraction prefix, we need to +# finish up the installation by taking the Molcas driver and moving it to an +# EasyBuild style binary directory. +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin', + 'cp %%(installdir)s/%s/sbin/molcas.driver %%(installdir)s/bin/molcas' % molcas_subdir, +] + +modextravars = {'MOLCAS': '%%(installdir)s/%s' % molcas_subdir} + +sanity_check_paths = { + 'files': ['bin/molcas'], + 'dirs': [molcas_subdir], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-par.eb b/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-par.eb new file mode 100644 index 00000000000..14ca91925d8 --- /dev/null +++ b/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-par.eb @@ -0,0 +1,48 @@ +easyblock = 'PackedBinary' + +name = 'Molcas' +version = '8.2' +versionsuffix = '-centos-par' + +homepage = 'http://www.molcas.org' +description = """Molcas is an ab initio quantum chemistry software package +developed by scientists to be used by scientists. The basic philosophy is is to +be able to treat general electronic structures for molecules consisting of +atoms from most of the periodic table. As such, the primary focus of the +package is on multiconfigurational methods with applications typically +connected to the treatment of highly degenerate states.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download requires registration, see http://www.molcas.org/download.html +sources = ['%(namelower)s%(version_major)s%(version_minor)s%(versionsuffix)s.tar.gz'] +checksums = ['f968333625a2e549cd6ab6c564c7b20587f3fe3b4c80305c1c39d3105d131e79'] + +# The Molcas installation procedure creates a binary in a separate directory, +# but that binary depends on being able to find the originally extracted files. +# Because we don't want to rely on root privileges, and we do want to use +# EasyBuild paths, this means we need to extract Molcas to a subdirectory of +# the proposed installation directory. +unpack_options = "--transform='s,^%(namelower)s-%(version)s%(versionsuffix)s,%(namelower)s_files,'" + +buildininstalldir = True +skipsteps = ['install'] + +molcas_subdir = 'molcas%(version_major)s%(version_minor)s%(versionsuffix)s' + +# For the same reason as the tarball needs an extraction prefix, we need to +# finish up the installation by taking the Molcas driver and moving it to an +# EasyBuild style binary directory. +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin', + 'cp %%(installdir)s/%s/sbin/molcas.driver %%(installdir)s/bin/molcas' % molcas_subdir, +] + +modextravars = {'MOLCAS': '%%(installdir)s/%s' % molcas_subdir} + +sanity_check_paths = { + 'files': ['bin/molcas'], + 'dirs': [molcas_subdir], +} + +moduleclass = 'chem' From f63ae8301eb149f74a0dcdbbbd97711caf56bc3c Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 6 May 2019 18:56:05 +0200 Subject: [PATCH 1457/5331] Added Eigen-3.3.7-GCCcore-8.2.0.eb --- .../e/Eigen/Eigen-3.3.7-GCCcore-8.2.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-8.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..5418fdb8f4c --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-8.2.0.eb @@ -0,0 +1,22 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'Eigen' +version = '3.3.7' + +homepage = 'http://%(namelower)s.tuxfamily.org/index.php?title=Main_Page' + +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, so no need for a non-dummy toolchain +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] +checksums = ['9f13cf90dedbe3e52a19f43000d71fdf72e986beb9a5436dddcd61ff9d77a3ce'] + +builddependencies = [ + ('CMake', '3.13.3'), +] + +moduleclass = 'math' From 729adb2077a4b4a42158b8bc1cb3463f0e79678b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 May 2019 19:02:38 +0200 Subject: [PATCH 1458/5331] {tools}[intel/2019a] simpy v3.0.11 w/ Python 3.7.2 + 2.7.15 --- .../s/simpy/simpy-3.0.11-intel-2019a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2019a.eb diff --git a/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2019a.eb b/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2019a.eb new file mode 100644 index 00000000000..c69ea372378 --- /dev/null +++ b/easybuild/easyconfigs/s/simpy/simpy-3.0.11-intel-2019a.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'simpy' +version = '3.0.11' + +homepage = 'https://simpy.readthedocs.io' +description = "SimPy is a process-based discrete-event simulation framework based on standard Python." + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d09625b9b01f34242ae100fe6bdb6c9508da181a08419ab00cc2bd47c7ec0f43'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [('SciPy-bundle', '2019.03')] + +download_dep_fail = True +use_pip = True + +moduleclass = 'tools' From e44b519fdf773a809e1b2f25acd536eb6efc5bf3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 May 2019 20:25:33 +0200 Subject: [PATCH 1459/5331] temporarily only test with Python 2.6 + Lmod --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 1ba3bbcf630..74ffd8c1f40 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,9 +4,9 @@ matrix: fast_finish: true include: - python: 2.6 - env: LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Tcl + # env: LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Tcl # also test default configuration with Python 2.7 - - python: 2.7 + #- python: 2.7 env: LMOD_VERSION=6.6.3 addons: apt: From e82ed001a49ea27541f5c206dc2383f963f40220 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 May 2019 20:53:05 +0200 Subject: [PATCH 1460/5331] restore Travis configuration to test with both Pyhton 2.6 & 2.7 with Lmod/Tmod --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 74ffd8c1f40..1ba3bbcf630 100644 --- a/.travis.yml +++ b/.travis.yml @@ -4,9 +4,9 @@ matrix: fast_finish: true include: - python: 2.6 - # env: LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Tcl + env: LMOD_VERSION=6.6.3 EASYBUILD_MODULE_SYNTAX=Tcl # also test default configuration with Python 2.7 - #- python: 2.7 + - python: 2.7 env: LMOD_VERSION=6.6.3 addons: apt: From 6a77caad7be3c922e6bdb77171bd25981feb80e5 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 6 May 2019 21:45:08 +0200 Subject: [PATCH 1461/5331] Updated dependencies for Eigen and deleted Eigen-GCCcore.eb --- .../CGAL-4.11.3-foss-2019a-Python-3.7.2.eb | 2 +- .../CGAL-4.11.3-intel-2019a-Python-3.7.2.eb | 2 +- .../e/Eigen/Eigen-3.3.7-GCCcore-8.2.0.eb | 22 ------------------- 3 files changed, 2 insertions(+), 24 deletions(-) delete mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-foss-2019a-Python-3.7.2.eb index c685addb572..fbcbb92ff85 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-foss-2019a-Python-3.7.2.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.13.3'), - ('Eigen', '3.3.7'), + ('Eigen', '3.3.7', '', True), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-intel-2019a-Python-3.7.2.eb index aa55046cc05..baaa8b50a03 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-intel-2019a-Python-3.7.2.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.13.3'), - ('Eigen', '3.3.7'), + ('Eigen', '3.3.7', '', True), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-8.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-8.2.0.eb deleted file mode 100644 index 5418fdb8f4c..00000000000 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7-GCCcore-8.2.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -name = 'Eigen' -version = '3.3.7' - -homepage = 'http://%(namelower)s.tuxfamily.org/index.php?title=Main_Page' - -description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, - and related algorithms.""" - -# only includes header files, so no need for a non-dummy toolchain -toolchain = {'name': 'GCCcore', 'version': '8.2.0'} - -source_urls = [BITBUCKET_SOURCE] -sources = ['%(version)s.tar.bz2'] -checksums = ['9f13cf90dedbe3e52a19f43000d71fdf72e986beb9a5436dddcd61ff9d77a3ce'] - -builddependencies = [ - ('CMake', '3.13.3'), -] - -moduleclass = 'math' From c697753cc30a610b19f93a23f5bf505b3f784920 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 7 May 2019 08:13:53 +0200 Subject: [PATCH 1462/5331] Use CMake instead of configuremake. --- .../p/protobuf/protobuf-3.7.1-GCCcore-8.2.0.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.7.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.7.1-GCCcore-8.2.0.eb index 69b0d0e7ee6..99107bb1b39 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-3.7.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.7.1-GCCcore-8.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'protobuf' version = '3.7.1' @@ -14,10 +14,12 @@ checksums = ['f1748989842b46fa208b2a6e4e2785133cfcc3e4d43c17fecb023733f0f5443f'] builddependencies = [ ('binutils', '2.31.1'), - ('Autotools', '20180311'), + ('CMake', '3.13.3'), ] -preconfigopts = "./autogen.sh && " +srcdir = 'cmake' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON ' sanity_check_paths = { 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], From 394d21c036536883c2fbc03530caa3e263e8ed27 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 May 2019 09:50:39 +0200 Subject: [PATCH 1463/5331] {vis}[intel/2019a] PyQtGraph v0.10.0 w/ Python 3.7.2 --- ...QtGraph-0.10.0-intel-2019a-Python-3.7.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..d3d1d417ab2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.10.0-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyQtGraph' +version = '0.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pyqtgraph.org/' +description = """PyQtGraph is a pure-python graphics and GUI library built on PyQt4/PySide and numpy.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.pyqtgraph.org/downloads/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c74597dd87c31987099bd0949a5207e5d58297bd8a663279562ca1cb334074fc'] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), # required for numpy + ('PyQt5', '5.12.1', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'vis' From 75d8f6f3bbe9c891a42945b05598f4320bc1141a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 May 2019 10:19:16 +0200 Subject: [PATCH 1464/5331] adding easyconfigs: Clang-8.0.0-GCC-8.2.0-2.31.1.eb --- .../c/Clang/Clang-8.0.0-GCC-8.2.0-2.31.1.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..78202ad0a35 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '8.0.0' + +homepage = 'http://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'cfe-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', +] +checksums = [ + '8872be1b12c61450cacc82b3d153eab02be2546ef34fa3580ed14137bb26224c', # llvm-8.0.0.src.tar.xz + '084c115aab0084e63b23eee8c233abb6739c399e29966eaeccfc6e088e0b736b', # cfe-8.0.0.src.tar.xz + 'b435c7474f459e71b2831f1a4e3f1d21203cb9c0172e94e9d9b69f50354f21b1', # compiler-rt-8.0.0.src.tar.xz + 'e3f5a3d6794ef8233af302c45ceb464b74cdc369c1ac735b6b381b21e4d89df4', # polly-8.0.0.src.tar.xz + 'f7b1705d2f16c4fc23d6531f67d2dd6fb78a077dd346b02fed64f4b8df65c9d5', # openmp-8.0.0.src.tar.xz +] + +dependencies = [ + ('GMP', '6.1.2'), +] + +builddependencies = [ + ('CMake', '3.13.3'), + ('Python', '2.7.15'), + ('libxml2', '2.9.8'), +] + +assertions = True +usepolly = True +skip_all_tests = True + +moduleclass = 'compiler' From cbfcd56c9786f182a18fc9143cef0ccafe316171 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 May 2019 10:53:19 +0200 Subject: [PATCH 1465/5331] adding easyconfigs: memory-profiler-0.55.0-intel-2019a.eb --- .../memory-profiler-0.55.0-intel-2019a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-intel-2019a.eb diff --git a/easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-intel-2019a.eb b/easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-intel-2019a.eb new file mode 100644 index 00000000000..d2820e6f231 --- /dev/null +++ b/easybuild/easyconfigs/m/memory-profiler/memory-profiler-0.55.0-intel-2019a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'memory-profiler' +version = '0.55.0' + +homepage = 'https://pypi.org/project/memory-profiler' +description = """memory-profiler is a Python module for monitoring memory consumption of a process + as well as line-by-line analysis of memory consumption for python programs.""" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_SOURCE] +sources = ['memory_profiler-%(version)s.tar.gz'] +checksums = ['5fa47b274c929dd2cbcd9190afb62fec110701251d2ac2d301caaf545c81afc1'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +use_pip = True +download_dep_fail = True + +fix_python_shebang_for = ['bin/mprof'] + +sanity_check_paths = { + 'files': ['bin/mprof'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["mprof run --help"] + +moduleclass = 'tools' From 12bf68b80099e8765e5315f46a1c296f565345c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 May 2019 11:39:28 +0200 Subject: [PATCH 1466/5331] adding easyconfigs: rapidtide-1.7.0-intel-2019a-Python-3.7.2.eb --- ...apidtide-1.7.0-intel-2019a-Python-3.7.2.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/r/rapidtide/rapidtide-1.7.0-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/r/rapidtide/rapidtide-1.7.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/r/rapidtide/rapidtide-1.7.0-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..316fc65f178 --- /dev/null +++ b/easybuild/easyconfigs/r/rapidtide/rapidtide-1.7.0-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'rapidtide' +version = '1.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://rapidtide.readthedocs.io' +description = """Rapidtide is a suite of python programs used to perform time delay analysis on functional imaging + data to find time lagged correlations between the voxelwise time series and other time series.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +dependencies = [ + ('Python', '3.7.2'), + ('matplotlib', '3.0.3', versionsuffix), + ('scikit-learn', '0.20.3'), + ('NiBabel', '2.4.0'), + ('numba', '0.43.1'), + ('pyFFTW', '0.11.1'), + ('PyQtGraph', '0.10.0', versionsuffix), + ('memory-profiler', '0.55.0'), +] + +use_pip = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +fix_python_shebang_for = ['bin/*'] + +exts_list = [ + ('patsy', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/patsy'], + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + ('statsmodels', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels'], + 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/bbfrederick/rapidtide/archive/'], + 'checksums': ['3c17f65baf13d588564467026f7d6d09c1c537a04ce4bf65f0faf37e708df23d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/rapidtide2', 'bin/showtc', 'bin/tidepool'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "rapidtide2 --help", + "tidepool --help", +] + +moduleclass = 'data' From 6fcf6b4cd6f153ee566d499b82a4ec377d9a2ded Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 7 May 2019 12:00:33 +0200 Subject: [PATCH 1467/5331] revert updated extensions date --- easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb index 5c03b81587d..7c4ceab58fe 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.0-GCCcore-7.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ osdependencies = ['openssl', ('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # !! order of extensions is important !! -# extensions updated on May 6th 2018 +# extensions updated on June 26th 2018 exts_list = [ ('Config::General', '2.63', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb index b34b6420e0d..e0c5f78f76e 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb @@ -22,7 +22,7 @@ dependencies = [ osdependencies = ['openssl', ('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # !! order of extensions is important !! -# extensions updated on May 6th 2018 +# extensions updated on June 26th 2018 exts_list = [ ('Config::General', '2.63', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', From cdf8c3b8eea938a6f546a2cad15e38285418d3a7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 7 May 2019 12:04:42 +0200 Subject: [PATCH 1468/5331] fix oops --- easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb index e0c5f78f76e..484bcef4725 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb @@ -22,7 +22,7 @@ dependencies = [ osdependencies = ['openssl', ('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # !! order of extensions is important !! -# extensions updated on June 26th 2018 +# extensions updated on March 13th 2019 exts_list = [ ('Config::General', '2.63', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', From a22d6ec8ed56d33c14df7c5470fed103439b2087 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 May 2019 13:25:55 +0200 Subject: [PATCH 1469/5331] change Clang 8.0 easyconfig to use GCCcore and add binutils as a runtime dependency --- ...0.0-GCC-8.2.0-2.31.1.eb => Clang-8.0.0-GCCcore-8.2.0.eb} | 4 +++- test/easyconfigs/easyconfigs.py | 6 ++++-- 2 files changed, 7 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/c/Clang/{Clang-8.0.0-GCC-8.2.0-2.31.1.eb => Clang-8.0.0-GCCcore-8.2.0.eb} (91%) diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb similarity index 91% rename from easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCC-8.2.0-2.31.1.eb rename to easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb index 78202ad0a35..4fa097341fb 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb @@ -17,7 +17,7 @@ description = """C, C++, Objective-C compiler, based on LLVM. Does not # Clang also depends on libstdc++ during runtime, but this dependency is # already specified as the toolchain. -toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} # Do not set optarch to True: it will cause the build to fail toolchainopts = {'optarch': False} @@ -38,6 +38,8 @@ checksums = [ ] dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.31.1'), ('GMP', '6.1.2'), ] diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9e9b14acd4c..7a308f89188 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -572,7 +572,7 @@ def template_easyconfig_test(self, spec): for old_url in old_urls: self.assertFalse(old_url in ec.rawtxt, "Old URL '%s' not found in %s" % (old_url, spec)) - # make sure binutils is included as a build dep if toolchain is GCCcore + # make sure binutils is included as a (build) dep if toolchain is GCCcore if ec['toolchain']['name'] == 'GCCcore': # with 'Tarball' easyblock: only unpacking, no building; Eigen is also just a tarball requires_binutils = ec['easyblock'] not in ['Tarball'] and ec['name'] not in ['Eigen'] @@ -587,7 +587,9 @@ def template_easyconfig_test(self, spec): requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) if requires_binutils: - dep_names = [d['name'] for d in ec.builddependencies()] + # dependencies() returns both build and runtime dependencies + # in some cases, binutils can also be a runtime dep (e.g. for Clang) + dep_names = [d['name'] for d in ec.dependencies()] self.assertTrue('binutils' in dep_names, "binutils is a build dep in %s: %s" % (spec, dep_names)) # make sure all patch files are available From 1304b589c084b05d8ff65349c76c370acb00b979 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Tue, 7 May 2019 12:34:41 +0100 Subject: [PATCH 1470/5331] Description shortened and some style changes. --- .../v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb index 0425b7f385c..036a1b09106 100644 --- a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.1-foss-2018b.eb @@ -9,16 +9,7 @@ version = '2.6.1' homepage = 'https://virtualgl.org/' description = """VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full -hardware acceleration. Some remote display software cannot be used with OpenGL -applications at all. Other remote display software forces OpenGL applications -to use a slow, software-only renderer, to the detriment of performance as well -as compatibility. The traditional method of displaying OpenGL applications to -an X server on a different machine (indirect rendering) supports hardware -acceleration, but this approach requires that all of the OpenGL commands and -3D data be sent over the network to be rendered. That is not a tenable -proposition unless the 3D data is relatively small and static, unless the -network is very fast, and unless the OpenGL application is specifically tuned -for a remote X-Windows environment.""" +hardware acceleration.""" toolchain = {'name': 'foss', 'version': '2018b'} @@ -26,12 +17,13 @@ source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['38d1d32efe97adaea6754f4559520454d4f0d2400964ebc59f8ac01f0146e23f'] +builddependencies = [('CMake', '3.12.1')] + dependencies = [ ('libjpeg-turbo', '2.0.0'), ('Mesa', '18.1.1'), ('libGLU', '9.0.0'), ] -builddependencies = [('CMake', '3.12.1')] binaries = [ 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', @@ -39,7 +31,6 @@ binaries = [ 'vglserver_config' ] - sanity_check_paths = { 'files': ['bin/%s' % x for x in binaries], 'dirs': ['lib64', 'share', 'include'], From 80e208e2c154125ebe6a14f4a5f615bb081d42e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 May 2019 15:19:01 +0200 Subject: [PATCH 1471/5331] replace LibUUID dependencies with util-linux (cfr. #6963) --- easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb | 2 +- .../l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb | 2 +- easybuild/easyconfigs/l/libdap/libdap-3.19.1-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/l/libdap/libdap-3.19.1-foss-2017b.eb | 2 +- easybuild/easyconfigs/l/libdap/libdap-3.19.1-intel-2017b.eb | 2 +- easybuild/easyconfigs/l/libdap/libdap-3.20.3-GCCcore-7.3.0.eb | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb index f4e5dff7759..74417523335 100644 --- a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb +++ b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb @@ -16,7 +16,7 @@ sources = ['R_%s.tar.gz' % version.replace('.', '_')] builddependencies = [ ('CMake', '3.8.1'), - ('LibUUID', '1.0.3'), + ('util-linux', '2.29.2'), ('gtest', '1.8.0'), ('Doxygen', '1.8.13'), ] diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb index 74988997940..2273111e3b5 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('cURL', '7.47.0'), ('libxml2', '2.9.3'), - ('LibUUID', '1.0.3'), + ('util-linux', '2.28'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb index 437ea556cf8..958dbffd395 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('cURL', '7.53.1'), ('libxml2', '2.9.4'), - ('LibUUID', '1.0.3'), + ('util-linux', '2.29.2'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.19.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.19.1-GCCcore-6.4.0.eb index dbafe5c30e4..2963524cda2 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.19.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.19.1-GCCcore-6.4.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('cURL', '7.58.0'), ('libxml2', '2.9.7'), - ('LibUUID', '1.0.3'), + ('util-linux', '2.31.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.19.1-foss-2017b.eb b/easybuild/easyconfigs/l/libdap/libdap-3.19.1-foss-2017b.eb index d8abaf42875..21718eef1f8 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.19.1-foss-2017b.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.19.1-foss-2017b.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('cURL', '7.56.0'), ('libxml2', '2.9.4'), - ('LibUUID', '1.0.3'), + ('util-linux', '2.31.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.19.1-intel-2017b.eb b/easybuild/easyconfigs/l/libdap/libdap-3.19.1-intel-2017b.eb index 117b975846b..f1a053dff69 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.19.1-intel-2017b.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.19.1-intel-2017b.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('cURL', '7.56.0'), ('libxml2', '2.9.4'), - ('LibUUID', '1.0.3'), + ('util-linux', '2.31.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.3-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.3-GCCcore-7.3.0.eb index 7b1ef6d5163..e64cd9dd2dd 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.20.3-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.3-GCCcore-7.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('cURL', '7.60.0'), ('libxml2', '2.9.8'), - ('LibUUID', '1.0.3'), + ('util-linux', '2.32'), ] sanity_check_paths = { From 10fc88c06c5ee0de644c34af9a894b45e43a02b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 May 2019 16:08:25 +0200 Subject: [PATCH 1472/5331] add missing checksums for davix/libdap --- easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb | 1 + .../l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb | 1 + easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb index 74417523335..4797c446ad4 100644 --- a/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb +++ b/easybuild/easyconfigs/d/davix/davix-0.6.6-intel-2017a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://github.com/cern-it-sdc-id/davix/archive/'] sources = ['R_%s.tar.gz' % version.replace('.', '_')] +checksums = ['f807615aef8e65a047f1d2c7920aefffadce62dbc96996070bcdea60c283cf8b'] builddependencies = [ ('CMake', '3.8.1'), diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb index 2273111e3b5..5219fb63915 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://www.opendap.org/pub/source/'] sources = [SOURCE_TAR_GZ] +checksums = ['a755c472d7c9e54bc3aa6c92a847a69466fbc6cdc56ee912f411802a725d57a4'] builddependencies = [ ('Bison', '3.0.4'), diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb index 958dbffd395..f74fcba9313 100644 --- a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb +++ b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-intel-2017a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://www.opendap.org/pub/source/'] sources = [SOURCE_TAR_GZ] +checksums = ['a755c472d7c9e54bc3aa6c92a847a69466fbc6cdc56ee912f411802a725d57a4'] builddependencies = [ ('Bison', '3.0.4'), From dfc9bb5e2a67964a46b77eef98fa8f193707cdcf Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Tue, 7 May 2019 15:47:42 +0100 Subject: [PATCH 1473/5331] adding easyconfigs: hunspell-1.7.0-GCCcore-8.2.0.eb --- .../hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..6b2ed7d32c5 --- /dev/null +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'hunspell' +version = '1.7.0' + +homepage = 'http://hunspell.github.io/' +description = """Hunspell is a spell checker and morphological analyzer library and program designed for languages + with rich morphology and complex word compounding or character encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/hunspell/hunspell/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.31.1'), +] + +preconfigopts = "autoreconf -vfi && " + +sanity_check_paths = { + 'files': ['bin/hunspell', 'lib/libhunspell-%(version_major_minor)s.a', + 'lib/libhunspell-%%(version_major_minor)s.%s' % SHLIB_EXT, 'lib/pkgconfig/hunspell.pc'], + 'dirs': ['include/hunspell'], +} + +moduleclass = 'tools' From b1871ce44ff51828fe810192470fe56cc189c1e1 Mon Sep 17 00:00:00 2001 From: Fenglai Liu Date: Tue, 7 May 2019 10:16:01 -0500 Subject: [PATCH 1474/5331] add GRACE_HOME env var to the 2018a eb file --- .../easyconfigs/g/Grace/Grace-5.1.25-foss-2018a-5build1.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2018a-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2018a-5build1.eb index 81e9cc49e49..7f69fb3a8e8 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2018a-5build1.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2018a-5build1.eb @@ -34,4 +34,8 @@ sanity_check_paths = { 'dirs': ['include', 'fonts', 'templates'], } +modextravars = { + 'GRACE_HOME': '%(installdir)s', +} + moduleclass = 'vis' From ba5db650a5067aef8954bba80a9d2dfefb40f51e Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 7 May 2019 17:18:36 +0200 Subject: [PATCH 1475/5331] Use CMake from GCCcore when installing Eigen3 --- easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb index 756bf0485c8..fddf82c8f50 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb @@ -15,8 +15,13 @@ source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] checksums = ['9f13cf90dedbe3e52a19f43000d71fdf72e986beb9a5436dddcd61ff9d77a3ce'] -# stick to latest CMake 3.9.x, since more recent CMake versions require a C++ compiler that supports C++11, -# which may not be available yet in older OSs (e.g. CentOS 6.x) -builddependencies = [('CMake', '3.9.6')] +# Any CMake > 2.8.5 will work. Reusing one from GCCcore from around the same time, because +# building CMake at core level is often difficult. +# Change the GCCcore version if you want to reuse a different CMake you already have installed. +builddependencies = [ + ('GCCcore', '7.3.0'), + ('binutils', '2.31.1'), + ('CMake', '3.12.1', '-GCCcore-7.3.0'), +] moduleclass = 'math' From 34cffd97f62c739fe06e05d15b7e4eb5ea518085 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 7 May 2019 17:56:04 +0200 Subject: [PATCH 1476/5331] Add explanations why deps are needed --- easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb index fddf82c8f50..9ff7967ddbf 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb @@ -19,8 +19,8 @@ checksums = ['9f13cf90dedbe3e52a19f43000d71fdf72e986beb9a5436dddcd61ff9d77a3ce'] # building CMake at core level is often difficult. # Change the GCCcore version if you want to reuse a different CMake you already have installed. builddependencies = [ - ('GCCcore', '7.3.0'), - ('binutils', '2.31.1'), + ('GCCcore', '7.3.0'), # Needed to access CMake when using HMNS + ('binutils', '2.31.1'), # Needed to pass CMakes compiler health check on old systems ('CMake', '3.12.1', '-GCCcore-7.3.0'), ] From c10fd7d6a43cac670a7a92eca27ccde02a7e5295 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 7 May 2019 18:10:11 +0200 Subject: [PATCH 1477/5331] Add same fixes to Eigen 3.3.4 and 3.3.5 --- easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb | 11 ++++++++--- easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb | 11 ++++++++--- 2 files changed, 16 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb index e364da87a9d..b00d99847c9 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb @@ -15,8 +15,13 @@ source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] checksums = ['dd254beb0bafc695d0f62ae1a222ff85b52dbaa3a16f76e781dce22d0d20a4a6'] -# stick to latest CMake 3.9.x, since more recent CMake versions require a C++ compiler that supports C++11, -# which may not be available yet in older OSs (e.g. CentOS 6.x) -builddependencies = [('CMake', '3.9.6')] +# Any CMake > 2.8.5 will work. Reusing one from GCCcore from around the same time, because +# building CMake at core level is often difficult. +# Change the GCCcore version if you want to reuse a different CMake you already have installed. +builddependencies = [ + ('GCCcore', '6.4.0'), # Needed to access CMake when using HMNS + ('binutils', '2.28'), # Needed to pass CMakes compiler health check on old systems + ('CMake', '3.11.1', '-GCCcore-6.4.0'), +] moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb index 2dd440247c8..549c7213223 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb @@ -15,8 +15,13 @@ source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] checksums = ['7352bff3ea299e4c7d7fbe31c504f8eb9149d7e685dec5a12fbaa26379f603e2'] -# stick to latest CMake 3.9.x, since more recent CMake versions require a C++ compiler that supports C++11, -# which may not be available yet in older OSs (e.g. CentOS 6.x) -builddependencies = [('CMake', '3.9.6')] +# Any CMake > 2.8.5 will work. Reusing one from GCCcore from around the same time, because +# building CMake at core level is often difficult. +# Change the GCCcore version if you want to reuse a different CMake you already have installed. +builddependencies = [ + ('GCCcore', '6.4.0'), # Needed to access CMake when using HMNS + ('binutils', '2.28'), # Needed to pass CMakes compiler health check on old systems + ('CMake', '3.11.1', '-GCCcore-6.4.0'), +] moduleclass = 'math' From 09418acfed3dce16cf293bd0ae2443722611b8c4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 7 May 2019 21:13:45 +0200 Subject: [PATCH 1478/5331] Update patch for disabling AVX512 DGEMM kernels on OpenBLAS 0.35 --- .../OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb | 4 +- ...AS-0.3.5_disable_AVX512_dgemm_kernel.patch | 42 +++++++++++++++++++ 2 files changed, 44 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb index dc9ad24d9c7..3cd0f050663 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb @@ -27,12 +27,12 @@ checksums = [ 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch - '1b43496a5bd71ee2c7d9b8adb6789a018da400050a6e3313839d5471c72d3b47', + '2338ed3188d1a111f82ad20db9f9bffe848a26eb40902e9c2f9e9b3099d7b739', ] skipsteps = ['configure'] -buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' +buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$FC"' installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch index abc64ee3f2e..d8f5a326ed1 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch @@ -6,6 +6,22 @@ Date: Wed Mar 13 22:10:28 2019 +0100 Due to as yet unresolved errors seen in #1955 and #2029 +commit 7ed8431527eb00f161de4dd309fd4d2b6c885b0c +Author: Martin Kroeker +Date: Sat May 4 22:54:41 2019 +0200 + + Disable the SkyLakeX DGEMMITCOPY kernel as well + + as a stopgap measure for https://github.com/numpy/numpy/issues/13401 as mentioned in #1955 + +commit b1561ecc6864428baa4f1336d47d23729b9636f2 +Author: Martin Kroeker +Date: Sun May 5 15:52:01 2019 +0200 + + Disable DGEMMINCOPY as well for now + + #1955 + diff --git a/kernel/x86_64/KERNEL.SKYLAKEX b/kernel/x86_64/KERNEL.SKYLAKEX index acc6356..5d0a300 100644 --- a/kernel/x86_64/KERNEL.SKYLAKEX @@ -19,3 +35,29 @@ index acc6356..5d0a300 100644 DGEMMINCOPY = dgemm_ncopy_8_skylakex.c DGEMMITCOPY = dgemm_tcopy_8_skylakex.c +diff --git a/kernel/x86_64/KERNEL.SKYLAKEX b/kernel/x86_64/KERNEL.SKYLAKEX +index 5d0a300..3c67890 100644 +--- a/kernel/x86_64/KERNEL.SKYLAKEX ++++ b/kernel/x86_64/KERNEL.SKYLAKEX +@@ -10,7 +10,7 @@ SGEMMOTCOPY = ../generic/gemm_tcopy_4.c + #DGEMMKERNEL = dgemm_kernel_4x8_skylakex.c + + DGEMMINCOPY = dgemm_ncopy_8_skylakex.c +-DGEMMITCOPY = dgemm_tcopy_8_skylakex.c ++#DGEMMITCOPY = dgemm_tcopy_8_skylakex.c + DGEMMONCOPY = dgemm_ncopy_8_skylakex.c + DGEMMOTCOPY = dgemm_tcopy_8_skylakex.c + +diff --git a/kernel/x86_64/KERNEL.SKYLAKEX b/kernel/x86_64/KERNEL.SKYLAKEX +index 3c67890..d61c516 100644 +--- a/kernel/x86_64/KERNEL.SKYLAKEX ++++ b/kernel/x86_64/KERNEL.SKYLAKEX +@@ -9,7 +9,7 @@ SGEMMOTCOPY = ../generic/gemm_tcopy_4.c + + #DGEMMKERNEL = dgemm_kernel_4x8_skylakex.c + +-DGEMMINCOPY = dgemm_ncopy_8_skylakex.c ++#DGEMMINCOPY = dgemm_ncopy_8_skylakex.c + #DGEMMITCOPY = dgemm_tcopy_8_skylakex.c + DGEMMONCOPY = dgemm_ncopy_8_skylakex.c + DGEMMOTCOPY = dgemm_tcopy_8_skylakex.c From feefe7120c162d702528c6fb7a2255ccca9c143c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 May 2019 22:28:38 +0200 Subject: [PATCH 1479/5331] add jemalloc dep for Salmon 0.12.0 + pkg-config as build dep --- .../easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb index ba1d6149389..7b184da8b27 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb @@ -15,15 +15,21 @@ source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['91ebd1efc5b0b4c12ec6babecf3c0b79f7102e42b8895ca07c8c8fea869fefa3'] -builddependencies = [('CMake', '3.12.1')] - -runtest = 'test' +builddependencies = [ + ('CMake', '3.12.1'), + ('pkg-config', '0.29.2'), +] dependencies = [ ('Boost', '1.67.0'), ('tbb', '2018_U5'), + ('jemalloc', '5.1.0'), ] +configopts = '-DJEMALLOC_ROOT=$EBROOTJEMALLOC' + +runtest = 'test' + sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': [] From aee1019af936a7ebe301c1ea0c17dad1994748f5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 May 2019 12:37:48 +0800 Subject: [PATCH 1480/5331] add patch --- ..._Solutions-8.20-fix-which-skip-alias.patch | 64 +++++++++++++++++++ .../FDTD_Solutions-8.20.1731.eb | 7 +- 2 files changed, 70 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20-fix-which-skip-alias.patch diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20-fix-which-skip-alias.patch b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20-fix-which-skip-alias.patch new file mode 100644 index 00000000000..916ff679062 --- /dev/null +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20-fix-which-skip-alias.patch @@ -0,0 +1,64 @@ +# Remove --skip-alias arg to "which", not understood by all versions of +# the command. +# +# Åke Sandgren, 2017-02-07 +diff -ru opt.orig/lumerical/fdtd/bin/fdtd-config.sh opt/lumerical/fdtd/bin/fdtd-config.sh +--- opt.orig/lumerical/fdtd/bin/fdtd-config.sh 2016-09-10 02:54:24.000000000 +0200 ++++ opt/lumerical/fdtd/bin/fdtd-config.sh 2017-01-31 16:46:08.038859599 +0100 +@@ -13,7 +13,7 @@ + echo "Add FDTD Solutions directory to path" + echo + +-BINDIR=`dirname $(readlink -f $(which --skip-alias $0))` ++BINDIR=`dirname $(readlink -f $(which $0))` + + if which CAD &> /dev/null; then + CURPATH=`which CAD |sed 's#/CAD##g'` +diff -ru opt.orig/lumerical/fdtd/bin/fdtd-mpi-status.sh opt/lumerical/fdtd/bin/fdtd-mpi-status.sh +--- opt.orig/lumerical/fdtd/bin/fdtd-mpi-status.sh 2016-09-10 02:54:25.000000000 +0200 ++++ opt/lumerical/fdtd/bin/fdtd-mpi-status.sh 2017-01-31 16:46:15.006792376 +0100 +@@ -20,7 +20,7 @@ + echo " 2) fdtd-engine-mpichp4 MPICH for TCP/IP networked clusters (ch_p4) - included with FDTD Solutions" + echo " 3) fdtd-engine-mpichshmem MPICH for shared memory systems (ch_shmem) - included with FDTD Solutions" + +-MPITESTDIR=`dirname $(readlink -f $(which --skip-alias $0))` ++MPITESTDIR=`dirname $(readlink -f $(which $0))` + + FDTD_PARS=(hpmpi impi infinipath mpich2 mpichp4 ompi scali ) + MPI_NAMES=("HP MPI" "Intel MPI" "Infinipath MPI" MPICH2 MPICH OpenMPI "Scali MPI") +diff -ru opt.orig/lumerical/fdtd/bin/fdtd-process-template.sh opt/lumerical/fdtd/bin/fdtd-process-template.sh +--- opt.orig/lumerical/fdtd/bin/fdtd-process-template.sh 2016-09-10 02:54:24.000000000 +0200 ++++ opt/lumerical/fdtd/bin/fdtd-process-template.sh 2017-01-31 16:46:22.358721449 +0100 +@@ -77,7 +77,7 @@ + FILENAME=`basename $1` + + #Run FDTD to get stats from project file +-SCRIPTDIR=`dirname $(readlink -f $(which --skip-alias $0))` ++SCRIPTDIR=`dirname $(readlink -f $(which $0))` + $SCRIPTDIR/fdtd-engine-mpich2nem -mr $1 > $1.tmp + + #Estimated memory +diff -ru opt.orig/lumerical/fdtd/bin/fdtd-run-local.sh opt/lumerical/fdtd/bin/fdtd-run-local.sh +--- opt.orig/lumerical/fdtd/bin/fdtd-run-local.sh 2016-09-10 02:54:24.000000000 +0200 ++++ opt/lumerical/fdtd/bin/fdtd-run-local.sh 2017-01-31 16:46:25.758688650 +0100 +@@ -20,7 +20,7 @@ + + #Locate the directory of this script so we can find + #utility scripts and templates relative to this path +-SCRIPTDIR=`dirname $(readlink -f $(which --skip-alias $0))` ++SCRIPTDIR=`dirname $(readlink -f $(which $0))` + + #Set path to mpiexec + MPIEXEC=$SCRIPTDIR/../mpich2/nemesis/bin/mpiexec +diff -ru opt.orig/lumerical/fdtd/bin/fdtd-run-pbs.sh opt/lumerical/fdtd/bin/fdtd-run-pbs.sh +--- opt.orig/lumerical/fdtd/bin/fdtd-run-pbs.sh 2016-09-10 02:54:24.000000000 +0200 ++++ opt/lumerical/fdtd/bin/fdtd-run-pbs.sh 2017-01-31 16:46:29.382653688 +0100 +@@ -26,7 +26,7 @@ + + #Locate the directory of this script so we can find + #utility scripts and templates relative to this path +-SCRIPTDIR=`dirname $(readlink -f $(which --skip-alias $0))` ++SCRIPTDIR=`dirname $(readlink -f $(which $0))` + + #The location of the template file to use when submitting jobs + #The line below can be changed to use your own template file diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb index 05deb18ba6c..820e48bc28f 100644 --- a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb @@ -8,6 +8,11 @@ of nanophotonic devices, processes and materials.""" toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCE_TAR_GZ] -checksums = ['e742bd5a7a64d04d6aa6ee99cbafd77fb63a0388951cd83431e4da4ce84f6a48'] +patches = ['%(name)s-%(version_major_minor)s-fix-which-skip-alias.patch'] +checksums = [ + 'e742bd5a7a64d04d6aa6ee99cbafd77fb63a0388951cd83431e4da4ce84f6a48', # FDTD_Solutions-8.20.1731.tar.gz + # FDTD_Solutions-8.20-fix-which-skip-alias.patch + '177f63815f1df533a35b211f39f5153cb6c6096925e682e7c689c80c7ed97351', +] moduleclass = 'cae' From eea52668f9a710bc8a8126a5e7c032982fdbf626 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 8 May 2019 07:46:47 +0200 Subject: [PATCH 1481/5331] Add info on which issues and PRs the patch relates to. --- .../o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb | 2 +- .../OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb index 3cd0f050663..dcdbeec6bd4 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb @@ -27,7 +27,7 @@ checksums = [ 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch - '2338ed3188d1a111f82ad20db9f9bffe848a26eb40902e9c2f9e9b3099d7b739', + '56d5034869ebd7b63c7af23eadd0935280d4d57ac3b0d35956c64015a3103da9', ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch index d8f5a326ed1..f9f35d3e9fd 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch @@ -1,3 +1,10 @@ +This relates to https://github.com/xianyi/OpenBLAS/issues/1955 and #2029 and was taken from +https://github.com/xianyi/OpenBLAS/pull/2061 (commit e608d4f7fe1a2085b22af206d0c8c2cc128c1e9a) +and +https://github.com/xianyi/OpenBLAS/pull/2111 (the other two commits) + +Åke Sandgren, 20190508 +===== commit e608d4f7fe1a2085b22af206d0c8c2cc128c1e9a Author: Martin Kroeker Date: Wed Mar 13 22:10:28 2019 +0100 From c103ed615acb34cc5a5b1261a814afa8a10bb760 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 May 2019 14:29:04 +0800 Subject: [PATCH 1482/5331] add checksum --- easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2018a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2018a.eb b/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2018a.eb index 8dc2d49d710..eed01eeb4cb 100644 --- a/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2018a.eb +++ b/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2018a.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'foss', 'version': '2018a'} source_urls = ['https://github.com/lh3/psmc/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['0954b3e28dda4ae350bdb9ebe9eeb3afb3a6d4448cf794dac3b4fde895c3489b'] buildopts = '&& cd utils && make' From 8d315d4e0a9f9d02669fb8ca5a0287018d76bbca Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 8 May 2019 08:44:03 +0200 Subject: [PATCH 1483/5331] FoX must not be external, see https://github.com/easybuilders/easybuild-easyblocks/blob/c8d825e2413cdaba68126e850b859a80517dd3d5/easybuild/easyblocks/q/quantumespresso.py#L220 --- .../q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb index 797a71243fb..5ba34f7a825 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb @@ -37,12 +37,8 @@ checksums = [ dependencies = [ ('HDF5', '1.10.1'), - ('FoX', '4.1.2'), - ] -# source checksums - buildopts = 'all gwl xspectra couple epw w90' # parallel build tends to fail From 26c31a75d229cab5c20bc2333b6d5c2c2ea64ed2 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 8 May 2019 09:21:46 +0200 Subject: [PATCH 1484/5331] adding easyconfigs: Lua-5.3.5-GCCcore-8.2.0.eb --- .../l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..2c3844e5629 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Lua' +version = '5.3.5' + +homepage = 'http://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0c2eed3f960446e1a3e4b9a1ca2f3ff893b6ce41942cf54d5dd59ab4b3b058ac'] + +builddependencies = [ + ('binutils', '2.31.1'), +] +dependencies = [ + ('ncurses', '6.1'), + ('libreadline', '8.0'), +] + +buildopts = 'linux' + +installopts = "linux INSTALL_TOP=%(installdir)s" + +skipsteps = ['configure'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'lang' From d4e19ec6163b8fdf8c533d997b1a278cd195e47f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 10:04:02 +0200 Subject: [PATCH 1485/5331] add missing download_dep_fail for py-cpuinfo --- easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb index b4dc3e676e0..ec72cdf71da 100644 --- a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb @@ -15,6 +15,7 @@ checksums = ['2cf6426f776625b21d1db8397d3297ef7acfa59018f02a8779123f3190f18500'] allow_system_deps = [('Python', SYS_PYTHON_VERSION)] pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) +download_dep_fail = True # don't use pip since we're not sure whether or not it's installed on the system... use_pip = False From 4f1e7c4e5181ee1bf63b528cb984aa1291a4b064 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 8 May 2019 10:21:30 +0200 Subject: [PATCH 1486/5331] Update homepage for HDF5 and QM-E. Add missing libxml2 dep for HDF5. --- easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-iomkl-2017b.eb | 3 ++- .../q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-iomkl-2017b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-iomkl-2017b.eb index c5207050471..bf3e0424af1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-iomkl-2017b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.1-iomkl-2017b.eb @@ -1,7 +1,7 @@ name = 'HDF5' version = '1.10.1' -homepage = 'https://support.hdfgroup.org/HDF5/' +homepage = 'https://portal.hdfgroup.org/display/support' description = """HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.""" @@ -15,6 +15,7 @@ checksums = ['048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172'] dependencies = [ ('zlib', '1.2.11'), ('Szip', '2.1.1'), + ('libxml2', '2.9.7'), ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb index 5ba34f7a825..45cc1c7cf09 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb @@ -1,7 +1,7 @@ name = 'QuantumESPRESSO' version = '6.2.1' -homepage = 'http://www.pwscf.org/' +homepage = 'https://www.quantum-espresso.org' description = """Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials From 7380a4ffdfec2d771512de4785171d9a77757775 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 8 May 2019 10:30:32 +0200 Subject: [PATCH 1487/5331] Update lua install according to Liinux from Scratch --- .../l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb | 7 +++- easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb | 39 +++++++++++++++++++ .../l/libreadline/libreadline-8.0.eb | 39 +++++++++++++++++++ 3 files changed, 83 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.0.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb index 2c3844e5629..c3eefd890eb 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb @@ -25,12 +25,15 @@ dependencies = [ ('libreadline', '8.0'), ] -buildopts = 'linux' +prebuildopts = "sed -i '/#define LUA_ROOT/s:/usr/local/:%(installdir)s/:' src/luaconf.h &&" +buildopts = 'MYCFLAGS="-DLUA_COMPAT_5_2 -DLUA_COMPAT_5_1" linux' -installopts = "linux INSTALL_TOP=%(installdir)s" +installopts = "linux INSTALL_TOP=%(installdir)s INSTALL_DATA='cp -d' " skipsteps = ['configure'] +runtest = 'test' + sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': [], diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb new file mode 100644 index 00000000000..e666a786cb1 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Lua' +version = '5.3.5' + +homepage = 'http://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0c2eed3f960446e1a3e4b9a1ca2f3ff893b6ce41942cf54d5dd59ab4b3b058ac'] + +dependencies = [ + ('ncurses', '6.1'), + ('libreadline', '8.0'), +] + +prebuildopts = "sed -i '/#define LUA_ROOT/s:/usr/local/:%(installdir)s/:' src/luaconf.h &&" +buildopts = 'MYCFLAGS="-DLUA_COMPAT_5_2 -DLUA_COMPAT_5_1" linux' + +installopts = "linux INSTALL_TOP=%(installdir)s INSTALL_DATA='cp -d' " + +skipsteps = ['configure'] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.0.eb new file mode 100644 index 00000000000..b95217dbd94 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.0' + +homepage = 'http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html' + +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'pic': True} + +source_urls = ['http://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['e339f51971478d369f8a053a330a190781acb9864cf4c541060f12078948e461'] + +dependencies = [ + ('ncurses', '6.1'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' From a356b9d1fe613203be674b0f748a879ce8e15d82 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 8 May 2019 11:15:04 +0200 Subject: [PATCH 1488/5331] split url in two lines to make travis happy --- easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb b/easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb index 8253f2426fc..e439135d325 100644 --- a/easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb +++ b/easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb @@ -15,7 +15,9 @@ description = """.NET Core is a free and open-source managed computer software f toolchain = {'name': 'dummy', 'version': ''} source_urls = [ - 'https://download.visualstudio.microsoft.com/download/pr/927cbf41-157f-488b-ac7d-32034defebc3/41b011418f795d5a76bf930ad57a055b/' + 'https://download.visualstudio.microsoft.com/download/pr/' + + '927cbf41-157f-488b-ac7d-32034defebc3/41b011418f795d5a76bf930ad57a055b/' + # url splitted in two lines to make travis happy (line too long) ] sources = ['aspnetcore-runtime-%(version)s-linux-x64.tar.gz'] checksums = ['88831762a54fec8f8d1408a31a1a6dd226ffaf72eac6373ac93ccac21ec4fa56'] From 36f6df05428838212e0bf8f3e91d799b515c65e0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 8 May 2019 11:36:46 +0200 Subject: [PATCH 1489/5331] Add checksums to FDTD_Solutions-8.16.982.eb --- .../f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb index c108d214693..b90f9315a5e 100644 --- a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb @@ -8,11 +8,18 @@ of nanophotonic devices, processes and materials.""" toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCE_TAR_GZ] - patches = [ '%(name)s-%(version_major_minor)s-fix-which-skip-alias.patch', '%(name)s-%(version_major_minor)s-fix-install-paths.patch', '%(name)s-%(version_major_minor)s-fix-interconnect-api-path.patch', ] +checksums = [ + 'b19011183f4968b84ff06f2f0bc434a09b65449a2ddb2953a4ec162997d44cb5', # FDTD_Solutions-8.16.982.tar.gz + # FDTD_Solutions-8.16-fix-which-skip-alias.patch + '177f63815f1df533a35b211f39f5153cb6c6096925e682e7c689c80c7ed97351', + '41335c67b36ce8862e7d625b321f8a3117c03dbad8d0eff30643a8218dbba27c', # FDTD_Solutions-8.16-fix-install-paths.patch + # FDTD_Solutions-8.16-fix-interconnect-api-path.patch + 'b9e9aa1ecf0e0fbb47e6cdfb0bab6e51163da1e3de0f32e04c7f66765d0ff178', +] moduleclass = 'cae' From dda192f2063a54baf2eec72cdcbb9f0fff82d85f Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Wed, 8 May 2019 11:02:10 +0100 Subject: [PATCH 1490/5331] Checksum added --- .../easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb index 6b2ed7d32c5..dc0045cd59e 100644 --- a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb @@ -1,3 +1,6 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + easyblock = 'ConfigureMake' name = 'hunspell' @@ -11,6 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['https://github.com/hunspell/hunspell/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['bb27b86eb910a8285407cf3ca33b62643a02798cf2eef468c0a74f6c3ee6bc8a'] builddependencies = [ ('Autotools', '20180311'), From ca8ab03de1bcc1d4fc16bc0b908a274ad8df7a97 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Wed, 8 May 2019 11:16:57 +0100 Subject: [PATCH 1491/5331] Style problem addressed --- .../easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb index dc0045cd59e..4ce61cab534 100644 --- a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-8.2.0.eb @@ -17,8 +17,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['bb27b86eb910a8285407cf3ca33b62643a02798cf2eef468c0a74f6c3ee6bc8a'] builddependencies = [ - ('Autotools', '20180311'), - ('binutils', '2.31.1'), + ('Autotools', '20180311'), + ('binutils', '2.31.1'), ] preconfigopts = "autoreconf -vfi && " From be8646c023533167579b98ecb9f8d4dc48b36fd9 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 8 May 2019 12:19:32 +0200 Subject: [PATCH 1492/5331] added easyconfig for GEMMA --- .../g/GEMMA/GEMMA-0.97-foss-2016b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb new file mode 100644 index 00000000000..8606dd48d2a --- /dev/null +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'GEMMA' +version = '0.97' + +homepage = 'https://github.com/genetics-statistics/GEMMA' +description = "Genome-wide Efficient Mixed Model Association" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/genetics-statistics/GEMMA/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9b22a61f01af27e60d483cb7bca73e397d8ca4719c741349a8551984c6c33976'] + +builddependencies = [ + ('Eigen', '3.3.4', '', True), +] + +dependencies = [ + ('GSL', '2.3'), + ('zlib', '1.2.8'), +] + +files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES.md", "scripts", "VERSION"] + +sanity_check_commands = ["cd %(builddir)s/%(name)s-%(version)s/ && ./run_tests.sh"] + +sanity_check_paths = { + 'files': ["bin/gemma"], + 'dirs': [] +} + +moduleclass = 'bio' From bb154c2db8211378769317fab6ebb608923f89b5 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 8 May 2019 12:39:35 +0200 Subject: [PATCH 1493/5331] added latest gemma release with foss/2018b --- .../g/GEMMA/GEMMA-0.98.1-foss-2018b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb new file mode 100644 index 00000000000..1c64661fdc7 --- /dev/null +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'GEMMA' +version = '0.98.1' + +homepage = 'https://github.com/genetics-statistics/GEMMA' +description = "Genome-wide Efficient Mixed Model Association" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/genetics-statistics/GEMMA/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6beeed4a9e727a96fdea9e86e39bbe9cbc9f0540ad3a1053814e95b0863a7e6b'] + +builddependencies = [ + ('Eigen', '3.3.4', '', True), +] + +dependencies = [ + ('GSL', '2.5'), + ('zlib', '1.2.11'), +] + +files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES.md", "scripts", "VERSION"] + +sanity_check_commands = ["cd %(builddir)s/%(name)s-%(version)s/ && ./run_tests.sh"] + +sanity_check_paths = { + 'files': ["bin/gemma"], + 'dirs': [] +} + +moduleclass = 'bio' From ce3f4235f4d5d2551ff498c29a88e3e0c325dba2 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 8 May 2019 12:41:52 +0200 Subject: [PATCH 1494/5331] fix tarball filename --- easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb index 1c64661fdc7..f1e422c404a 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb @@ -14,7 +14,7 @@ description = "Genome-wide Efficient Mixed Model Association" toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/genetics-statistics/GEMMA/archive/'] -sources = ['v%(version)s.tar.gz'] +sources = ['%(version)s.tar.gz'] checksums = ['6beeed4a9e727a96fdea9e86e39bbe9cbc9f0540ad3a1053814e95b0863a7e6b'] builddependencies = [ From 92be581afc85eaf9cfbf79f8a4cf3fae133100c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 14:04:05 +0200 Subject: [PATCH 1495/5331] clean up Lua 5.3.4 easyconfigs --- .../easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb | 25 ++++--------------- easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb | 25 ++++--------------- 2 files changed, 10 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb index 70ddc97853f..c0b4276001d 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb @@ -1,12 +1,7 @@ -easyblock = 'EB_Lua' +name = 'Lua' +version = '5.3.4' -buildopts = 'linux' -installopts = 'INSTALL_TOP=%(installdir)s' - -name = "Lua" -version = "5.3.4" - -homepage = "http://www.lua.org/" +homepage = 'http://www.lua.org/' description = """Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, @@ -18,16 +13,6 @@ toolchain = {'name': 'GCC', 'version': '7.2.0-2.29'} source_urls = ['https://www.lua.org/ftp/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['f681aa518233bc407e23acf0f5887c884f17436f000d453b2491a9f11a52400c'] -sanity_check_paths = { - 'files': ["bin/lua"], - 'dirs': [] -} - -modextravars = { - 'LUA_DIR': '%(installdir)s', -} - -runtest='test' - -moduleclass = "lang" +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb index 5560e9f8422..3f44002b69d 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb @@ -1,12 +1,7 @@ -easyblock = 'EB_Lua' +name = 'Lua' +version = '5.3.4' -buildopts = 'linux' -installopts = 'INSTALL_TOP=%(installdir)s' - -name = "Lua" -version = "5.3.4" - -homepage = "http://www.lua.org/" +homepage = 'http://www.lua.org/' description = """Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, @@ -18,16 +13,6 @@ toolchain = {'name': 'dummy', 'version': ''} source_urls = ['https://www.lua.org/ftp/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['f681aa518233bc407e23acf0f5887c884f17436f000d453b2491a9f11a52400c'] -sanity_check_paths = { - 'files': ["bin/lua"], - 'dirs': [] -} - -modextravars = { - 'LUA_DIR': '%(installdir)s', -} - -runtest='test' - -moduleclass = "lang" +moduleclass = 'lang' From 39f2af6b8fdf28f090bca6d99ea22dfbdc1a25ed Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 8 May 2019 14:17:00 +0200 Subject: [PATCH 1496/5331] Update to use new lua easyblock --- .../l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb | 17 +---------------- easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb | 16 ---------------- 2 files changed, 1 insertion(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb index c3eefd890eb..6746c5e906a 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-8.2.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'Lua' version = '5.3.5' @@ -20,23 +18,10 @@ checksums = ['0c2eed3f960446e1a3e4b9a1ca2f3ff893b6ce41942cf54d5dd59ab4b3b058ac'] builddependencies = [ ('binutils', '2.31.1'), ] + dependencies = [ ('ncurses', '6.1'), ('libreadline', '8.0'), ] -prebuildopts = "sed -i '/#define LUA_ROOT/s:/usr/local/:%(installdir)s/:' src/luaconf.h &&" -buildopts = 'MYCFLAGS="-DLUA_COMPAT_5_2 -DLUA_COMPAT_5_1" linux' - -installopts = "linux INSTALL_TOP=%(installdir)s INSTALL_DATA='cp -d' " - -skipsteps = ['configure'] - -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [], -} - moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb index e666a786cb1..825d95f267a 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'Lua' version = '5.3.5' @@ -22,18 +20,4 @@ dependencies = [ ('libreadline', '8.0'), ] -prebuildopts = "sed -i '/#define LUA_ROOT/s:/usr/local/:%(installdir)s/:' src/luaconf.h &&" -buildopts = 'MYCFLAGS="-DLUA_COMPAT_5_2 -DLUA_COMPAT_5_1" linux' - -installopts = "linux INSTALL_TOP=%(installdir)s INSTALL_DATA='cp -d' " - -skipsteps = ['configure'] - -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [], -} - moduleclass = 'lang' From b4c2e356ebc5a289aa690bb11079746d559af3df Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 14:22:00 +0200 Subject: [PATCH 1497/5331] use GCCcore rather than GCC toolchain for Lua + add missing ncurses/libreadline deps --- ...Lua-5.3.4-GCC-7.2.0.eb => Lua-5.3.4-GCCcore-7.2.0.eb} | 9 ++++++++- easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb | 5 +++++ 2 files changed, 13 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/l/Lua/{Lua-5.3.4-GCC-7.2.0.eb => Lua-5.3.4-GCCcore-7.2.0.eb} (80%) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCCcore-7.2.0.eb similarity index 80% rename from easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb rename to easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCCcore-7.2.0.eb index c0b4276001d..92adf9afec1 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCC-7.2.0.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4-GCCcore-7.2.0.eb @@ -9,10 +9,17 @@ description = """Lua is a powerful, fast, lightweight, embeddable scripting lang and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.""" -toolchain = {'name': 'GCC', 'version': '7.2.0-2.29'} +toolchain = {'name': 'GCCcore', 'version': '7.2.0'} source_urls = ['https://www.lua.org/ftp/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['f681aa518233bc407e23acf0f5887c884f17436f000d453b2491a9f11a52400c'] +builddependencies = [('binutils', '2.29')] + +dependencies = [ + ('ncurses', '6.1'), + ('libreadline', '7.0'), +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb index 3f44002b69d..421b6d5d18d 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb @@ -15,4 +15,9 @@ source_urls = ['https://www.lua.org/ftp/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['f681aa518233bc407e23acf0f5887c884f17436f000d453b2491a9f11a52400c'] +dependencies = [ + ('ncurses', '6.0'), + ('libreadline', '6.3'), +] + moduleclass = 'lang' From 1deb3de586714a46fc4ce975ca031dda9ff282a1 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 8 May 2019 08:34:51 -0400 Subject: [PATCH 1498/5331] Revert checksum change for boot extension back to original value. The orginal tarball on the R website was restored in the mean time... --- easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb index 51fbf775b80..3792661502d 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb @@ -462,7 +462,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], + 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb index 2e2c0888d0c..8160b831f0a 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb @@ -470,7 +470,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], + 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb index 69285fca419..6b1a391603b 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb @@ -489,7 +489,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], + 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb index f30b361b36b..221e6835916 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb @@ -489,7 +489,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], + 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb index 70aa7bbf4c7..779850e09b1 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb @@ -489,7 +489,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], + 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb index eae392cf887..ee5a16f71d1 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb @@ -552,7 +552,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], + 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index d17b5098e9d..37500630b71 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -559,7 +559,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], + 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 6d2e61ebf7d..545db9193f4 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -557,7 +557,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], + 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], From 8af53f3abf2729a1d02a9550d0ad228c16e947f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 14:53:13 +0200 Subject: [PATCH 1499/5331] bump to ncurses 6.1 + libreadline 8.0 for Lua 5.3.4 built with dummy toolchain --- easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb index 421b6d5d18d..c46350b406a 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb @@ -16,8 +16,8 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['f681aa518233bc407e23acf0f5887c884f17436f000d453b2491a9f11a52400c'] dependencies = [ - ('ncurses', '6.0'), - ('libreadline', '6.3'), + ('ncurses', '6.1'), + ('libreadline', '8.0'), ] moduleclass = 'lang' From 6fd47fbf4ab1cd02a7e9270fa7b9837c35307577 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 8 May 2019 09:53:02 -0400 Subject: [PATCH 1500/5331] Hello: change moduleclass from system to tools. --- easybuild/easyconfigs/h/Hello/Hello-2.10-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Hello/Hello-2.10-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/Hello/Hello-2.10-GCCcore-8.2.0.eb index 7cf260f10c2..5e3a475d011 100644 --- a/easybuild/easyconfigs/h/Hello/Hello-2.10-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/Hello/Hello-2.10-GCCcore-8.2.0.eb @@ -30,4 +30,4 @@ sanity_check_paths = { } sanity_check_commands = ['hello'] -moduleclass = 'system' +moduleclass = 'tools' From fcf1b3be4c5e30855b0b8e995ed8fcaa7f232272 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 16:16:09 +0200 Subject: [PATCH 1501/5331] fix MAJIQ easyconfig by fixing order of extensions + avoid numpy test hang --- .../MAJIQ-1.1.1-intel-2018a-Python-3.6.4.eb | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/m/MAJIQ/MAJIQ-1.1.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/m/MAJIQ/MAJIQ-1.1.1-intel-2018a-Python-3.6.4.eb index cdb7926f36b..11b1a3ee12d 100644 --- a/easybuild/easyconfigs/m/MAJIQ/MAJIQ-1.1.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/m/MAJIQ/MAJIQ-1.1.1-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'MAJIQ' commit = '9671da7' @@ -25,8 +25,7 @@ dependencies = [ ('h5py', '2.7.1', versionsuffix), ] - -exts_defaultclass = 'PythonPackage' +use_pip = True exts_list = [ ('numpy', '1.14.2', { @@ -37,16 +36,18 @@ exts_list = [ 'facc6f925c3099ac01a1f03758100772560a0b020fb9d70f210404be08006bcb', # numpy-1.14.2.zip 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch ], - 'use_pip': True, - }), - ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], - 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + # workaround for hanging numpy test, + # see https://software.intel.com/en-us/forums/intel-math-kernel-library/topic/760830 + 'pretestopts': "export KMP_INIT_AT_FORK=FALSE && ", }), ('MarkupSafe', '1.0', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['a6be69091dac236ea9c6bc7d012beab42010fa914c459791d627dad4910eb665'], }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), ('psutil', '5.4.3', { 'source_urls': ['https://pypi.python.org/packages/source/p/psutil/'], 'checksums': ['e2467e9312c2fa191687b89ff4bc2ad8843be4af6fb4dc95a7cc5f7d7a327b18'], @@ -69,7 +70,7 @@ exts_list = [ ] sanity_check_paths = { - 'files': [], + 'files': ['bin/majiq'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From d9f30c8b445450d8d259b0c1d9fc8401b7b4f2c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 16:20:53 +0200 Subject: [PATCH 1502/5331] use Autotools 20180311 with GCCcore/7.2.0 toolchain --- easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-7.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-7.2.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-7.2.0.eb index 2a2577c381e..4fcc35f1ab1 100644 --- a/easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.10-GCCcore-7.2.0.eb @@ -14,7 +14,7 @@ checksums = ['b3cb6bdedcef5607ce34a350cf0b182eb979f8f7bc31eae55a93a70a3f020d13'] builddependencies = [ ('binutils', '2.29'), - ('Autotools', '20180311'), + ('Autotools', '20170619'), ] preconfigopts = "sh bootstrap.sh && " From 110d633c10ab609ad332a79d9f38cdc0a8dbd627 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 17:09:09 +0200 Subject: [PATCH 1503/5331] switch to PythonBundle for cutadapt 1.18 + add missing required extension xopen --- .../cutadapt-1.18-intel-2018b-Python-3.6.6.eb | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb index e5515ceeae8..9be9efe8ad8 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-intel-2018b-Python-3.6.6.eb @@ -7,7 +7,7 @@ # Modufied by: Albert Bogdanowicz # Institute of Biochemistry and Biophysics PAS -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'cutadapt' version = '1.18' @@ -19,12 +19,19 @@ description = """Cutadapt finds and removes adapter sequences, primers, poly-A t toolchain = {'name': 'intel', 'version': '2018b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['17aabf9b19d09a426d96030a83ad003c97b26dba9d45bf5570d33088fcd533f9'] +dependencies = [('Python', '3.6.6')] -dependencies = [ - ('Python', '3.6.6'), +use_pip = True + +exts_list = [ + ('xopen', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], + 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], + 'checksums': ['17aabf9b19d09a426d96030a83ad003c97b26dba9d45bf5570d33088fcd533f9'], + }), ] sanity_check_paths = { From 2c2e138292d817bef083390a1344795ccb62dd39 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 17:30:41 +0200 Subject: [PATCH 1504/5331] fix checksums for boot/nlme in R 3.5.1 easyconfig using intel/2018b --- easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb index 4005df888c4..02f3f86d19a 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb @@ -395,7 +395,7 @@ exts_list = [ 'checksums': ['41366f777d8adb83d0bdbac1392a1ab118b36217ca648d3bb9db763aa7ff4686'], }), ('nlme', '3.1-137', { - 'checksums': ['01049bb9c53826ff4ec5ba7117d766b17a0108c85f80871a5adb0c0b58ef7e87'], + 'checksums': ['ac82a5d15233dfca2a1aaf9f3ceee018adfe2983344750023dd433ed49b07ba8'], }), ('mgcv', '1.8-24', { 'checksums': ['a9f8e9823f6d6a4a568d151f2fa619bb2811df73c013e9a105720d9b32b4740c'], @@ -557,7 +557,7 @@ exts_list = [ 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], }), ('boot', '1.3-20', { - 'checksums': ['f339ddb7138ad05fe3e19852caf7d369f9c1ab827a70045ff66223e032cd0e06'], + 'checksums': ['adcb90b72409705e3f9c69ea6c15673dcb649b464fed06723fe0930beac5212a'], }), ('mixtools', '1.1.0', { 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], From 5a747c1603f53623c1b9ac3e28b51f5966d900bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 17:50:28 +0200 Subject: [PATCH 1505/5331] switch to PythonBundle for cutadapt 2.1 + enable use_pip + add missing xopen/dnaio extensions --- .../cutadapt-2.1-foss-2018b-Python-3.6.6.eb | 25 +++++++++++++------ 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb index 536fd24f538..a48d2fa83b1 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.1-foss-2018b-Python-3.6.6.eb @@ -7,7 +7,7 @@ # Modufied by: Albert Bogdanowicz # Institute of Biochemistry and Biophysics PAS -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'cutadapt' version = '2.1' @@ -19,12 +19,23 @@ description = """Cutadapt finds and removes adapter sequences, primers, poly-A t toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['09fd222a27cc1eeb571633f2bd54442ea9d4ff668ef1f475fd9d5253a7d315ef'] - -dependencies = [ - ('Python', '3.6.6'), +dependencies = [('Python', '3.6.6')] + +use_pip = True + +exts_list = [ + ('xopen', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], + 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], + }), + ('dnaio', '0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/d/dnaio'], + 'checksums': ['47e4449affad0981978fe986684fc0d9c39736f05a157f6cf80e54dae0a92638'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/c/cutadapt'], + 'checksums': ['09fd222a27cc1eeb571633f2bd54442ea9d4ff668ef1f475fd9d5253a7d315ef'], + }), ] sanity_check_paths = { From 6c6cc21407deda62176d27cecc3f7f6d4eb8d67c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 8 May 2019 11:14:09 -0500 Subject: [PATCH 1506/5331] Remove unnecessary bz2file extension --- .../c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb | 4 ---- .../c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb | 4 ---- 2 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb index 8784bad6041..d3fed465492 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-foss-2017b-Python-3.6.3.eb @@ -26,10 +26,6 @@ dependencies = [ use_pip = True exts_list = [ - ('bz2file', '0.98', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], - 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], - }), ('xopen', '0.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb index ffd35630e41..e0e98c0a7c6 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.16-intel-2017b-Python-3.6.3.eb @@ -23,10 +23,6 @@ dependencies = [ use_pip = True exts_list = [ - ('bz2file', '0.98', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file'], - 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], - }), ('xopen', '0.5.1', { 'source_urls': ['https://pypi.python.org/packages/source/x/xopen'], 'checksums': ['80757c50816162001e8629524f907426f82e885c168705a276abc649739ef200'], From b257bdda3e7978b8bf05415a6b8e869c86540ac2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 18:19:20 +0200 Subject: [PATCH 1507/5331] use Boost.Python as a dep for PyCUDA, enable download_dep_fail and use_pip --- .../p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb index 50f46f90bca..e98942047c3 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb @@ -16,14 +16,15 @@ checksums = ['6b5a9384e38c603ee429f8a6bee424532db7b3505027ce22f7e18ad19564b563'] dependencies = [ ('Python', '2.7.14'), ('CUDA', '9.1.85', '', True), - ('Boost', '1.66.0', versionsuffix), + ('Boost.Python', '1.66.0', versionsuffix), ] +download_dep_fail = True +use_pip = True + prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " -options = {'modulename': '%(namelower)s'} - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 0afb5c2daf5f517cddba5b77213860d88ead1562 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 18:28:13 +0200 Subject: [PATCH 1508/5331] use %(version)s template in sources/patches --- easybuild/easyconfigs/n/NBO/NBO-7.0-intel-2017b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0-intel-2017b.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0-intel-2017b.eb index fb245f812df..c2784486357 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0-intel-2017b.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0-intel-2017b.eb @@ -13,8 +13,8 @@ toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers # NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx -sources = ['nbo7.0-src.tar'] -patches = ['NBO-7.0_make.patch'] +sources = ['nbo%(version)s-src.tar'] +patches = ['NBO-%(version)s_make.patch'] checksums = [ '45cc4b85c53f66328d0262b18150ec5557f252b244511148a858933469ecf88c', # nbo7.0-src.tar '832e2f29f728d15e114b81978d3308ab7b1b7c73deccadd2a562a5ecfd7f27f4', # NBO-7.0_make.patch From e82937de3647446796b057a4bd0ce474f99fed0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 18:50:35 +0200 Subject: [PATCH 1509/5331] remove checksum --- .../easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb index b8a2632a841..9caa766ffab 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb @@ -16,7 +16,6 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # tar cfvz Kent_tools-20190326.tar.gz Kent_tools # sources = [SOURCE_TAR_GZ] -checksums = ['ce9da071e4e31abdda5ecff882fa9799ef879a4fc9a7d43a0799cff2de965444'] postinstallcmds = [ "cp -a %(builddir)s/Kent_tools/blat/{blat,gfClient,gfServer} %(installdir)s/bin", From 353abde1ac5ef7a2bf417897002e3588af128bc1 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 8 May 2019 12:05:03 -0500 Subject: [PATCH 1510/5331] Single line patches --- easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb index c4e7a556d0d..e4db8220275 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb @@ -12,9 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] sources = [SOURCELOWER_TAR_BZ2] -patches = [ - 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', -] +patches = ['CP2K-2.4.0-fix_compile_date_lastsvn.patch'] checksums = [ 'af803558e0a6b9e9d9ce8a3ab955ba32bacd179922455424e061c82c9fefa34b', # cp2k-6.1.tar.bz2 '02475cbe24c8d4ba27037c826adf8a534cad634c3c4e02c21d743f5284516bda', # CP2K-2.4.0-fix_compile_date_lastsvn.patch From d3a1950b92da7f140fa4a0dd87f431adc1a4d5ad Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 8 May 2019 12:06:46 -0500 Subject: [PATCH 1511/5331] Re-order builddependencies --- easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb index e4db8220275..fcd091d97d2 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb @@ -18,6 +18,11 @@ checksums = [ '02475cbe24c8d4ba27037c826adf8a534cad634c3c4e02c21d743f5284516bda', # CP2K-2.4.0-fix_compile_date_lastsvn.patch ] +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.5'), +] + dependencies = [ ('Libint', '1.1.6'), ('libxc', '4.3.4'), @@ -26,11 +31,6 @@ dependencies = [ ('PLUMED', '2.5.1'), ] -builddependencies = [ - ('flex', '2.6.4'), - ('Bison', '3.0.5'), -] - # values to use here are +1 those used for building Libint # see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT extradflags = "-D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5" From b7cf5061a9b299142d255fd633612f760e84aecc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 20:10:46 +0200 Subject: [PATCH 1512/5331] fix homepage + description for cdsapi --- .../c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb index e51ff98eca1..b0f1c28f7ff 100644 --- a/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.1.4-foss-2018b-Python-3.6.6.eb @@ -4,8 +4,8 @@ name = 'cdsapi' version = '0.1.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://pypi.python.org/pypi/wheel' -description = """A built-package format for Python.""" +homepage = 'https://pypi.org/project/cdsapi' +description = "Climate Data Store API" toolchain = {'name': 'foss', 'version': '2018b'} From e89d78491998c89e01628f50a3fdd34485573d1c Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 8 May 2019 13:28:45 -0500 Subject: [PATCH 1513/5331] Removed FFTW redundant dependency --- easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb index fcd091d97d2..dbf0ed1ab6b 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-6.1-foss-2019a.eb @@ -27,7 +27,6 @@ dependencies = [ ('Libint', '1.1.6'), ('libxc', '4.3.4'), ('libxsmm', '1.10'), - ('FFTW', '3.3.8'), ('PLUMED', '2.5.1'), ] From b73bf32daab7cca10c5b2f2e6bd1f9704c4dd8e9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 8 May 2019 20:31:31 +0200 Subject: [PATCH 1514/5331] adding easyconfigs: GConf-3.2.6-GCCcore-8.2.0-Python-3.7.2.eb and patches: GConf-3.2.6_call-dbus_g_thread_init.patch, GConf-3.2.6_fix_wrong_return_value.patch, GConf-3.2.6_gconf-path-max-hurd.patch, GConf-3.2.6_readd_gconf_engine_key_is_writable.patch --- .../dbus-glib-0.110-GCCcore-8.2.0.eb | 33 +++++++++++ .../GConf-3.2.6-GCCcore-8.2.0-Python-3.7.2.eb | 59 +++++++++++++++++++ .../GConf-3.2.6_call-dbus_g_thread_init.patch | 21 +++++++ .../GConf-3.2.6_fix_wrong_return_value.patch | 26 ++++++++ .../GConf-3.2.6_gconf-path-max-hurd.patch | 33 +++++++++++ ...6_readd_gconf_engine_key_is_writable.patch | 47 +++++++++++++++ .../GLib-2.60.1-GCCcore-8.2.0-Python-3.7.2.eb | 45 ++++++++++++++ 7 files changed, 264 insertions(+) create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6_call-dbus_g_thread_init.patch create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6_fix_wrong_return_value.patch create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6_gconf-path-max-hurd.patch create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6_readd_gconf_engine_key_is_writable.patch create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..843c4b96c2d --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.110' + +homepage = 'http://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] +checksums = ['7ce4760cf66c69148f6bd6c92feaabb8812dee30846b24cd0f7395c436d7e825'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.60.1', '-Python-3.7.2'), + ('DBus', '1.13.8'), + ('expat', '2.2.6'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +parallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..b7487ccbb6e --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://projects.gnome.org/gconf/' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +patches = [ + '%(name)s-%(version)s_call-dbus_g_thread_init.patch', + '%(name)s-%(version)s_fix_wrong_return_value.patch', + '%(name)s-%(version)s_gconf-path-max-hurd.patch', + '%(name)s-%(version)s_readd_gconf_engine_key_is_writable.patch', +] +checksums = [ + '1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c', # GConf-3.2.6.tar.xz + 'ed55bff5bc239115ae27b8520a923ae0d5cab6cb15ca9921a8c23b939306489f', # GConf-3.2.6_call-dbus_g_thread_init.patch + 'f8f7745c3648953098eb56af0f64adc69d8c0b0e78c8db351746a2b4c58e8bb4', # GConf-3.2.6_fix_wrong_return_value.patch + 'ee5524c3cb985088bbe4884531ddc48ba22d2fced2a34865304c77e194a55bde', # GConf-3.2.6_gconf-path-max-hurd.patch + # GConf-3.2.6_readd_gconf_engine_key_is_writable.patch + 'b95dfc2f0474d9162fc686f26cd4d3da5c9b01a9c609dc0a4f2b2bd901d497f3', +] + +builddependencies = [ + ('binutils', '2.31.1'), + ('GObject-Introspection', '1.60.1', versionsuffix), +] + +dependencies = [ + ('Python', '3.7.2'), + ('GLib', '2.60.1', versionsuffix), + ('dbus-glib', '0.110'), + ('libxml2', '2.9.8'), + ('GTK+', '3.24.8'), + ('intltool', '0.51.0'), +] + +configopts = '--disable-orbit ' + +sanity_check_paths = { + 'files': ['bin/gconf%s' % x for x in['-merge-tree', 'tool-2']] + + ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] + + ['lib/libgconf-2.%s' % x for x in['a', 'so']], + 'dirs': ['include', 'share'] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6_call-dbus_g_thread_init.patch b/easybuild/easyconfigs/g/GConf/GConf-3.2.6_call-dbus_g_thread_init.patch new file mode 100644 index 00000000000..6b21af9b770 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6_call-dbus_g_thread_init.patch @@ -0,0 +1,21 @@ +Author: Chow Loong Jin +Description: Call dbus_g_thread_init before calling any dbus functions +Bug-Ubuntu: https://bugs.launchpad.net/bugs/1048341 +Index: gconf-3.2.6/gconf/gconf-dbus.c +=================================================================== +--- gconf-3.2.6.orig/gconf/gconf-dbus.c 2013-01-23 11:17:02.023020067 +0100 ++++ gconf-3.2.6/gconf/gconf-dbus.c 2013-01-23 11:17:02.019020067 +0100 +@@ -396,6 +396,13 @@ + return FALSE; + } + ++ /* Initialize DBus Glib for multithreading -- this fixes race conditions when ++ multi-threaded applications use gconf. Additionally, although the API ++ documentation says that dbus_g_thread_init() may only be called once, it is ++ actually really a wrapper for dbus_threads_init_default() which casn be ++ called as many times as necessary. */ ++ dbus_g_thread_init (); ++ + dbus_error_init (&error); + + global_conn = dbus_bus_get_private (DBUS_BUS_SESSION, &error); diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6_fix_wrong_return_value.patch b/easybuild/easyconfigs/g/GConf/GConf-3.2.6_fix_wrong_return_value.patch new file mode 100644 index 00000000000..2266743cd1c --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6_fix_wrong_return_value.patch @@ -0,0 +1,26 @@ +Description: fix wrong return value +Bug: http://bugzilla.gnome.org/show_bug.cgi?id=582865 +Bug-Debian: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=532119 + +Index: gconf-3.2.6/gconf/gconf-client.c +=================================================================== +--- gconf-3.2.6.orig/gconf/gconf-client.c 2013-01-23 11:17:01.879020062 +0100 ++++ gconf-3.2.6/gconf/gconf-client.c 2013-01-23 11:17:01.875020063 +0100 +@@ -2373,7 +2373,7 @@ + { + g_free (dir); + trace ("Negative cache hit on %s", key); +- return TRUE; ++ return FALSE; + } + else + { +@@ -2389,7 +2389,7 @@ + { + g_free (dir); + trace ("Non-existing dir for %s", key); +- return TRUE; ++ return FALSE; + } + not_cached = TRUE; + } diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6_gconf-path-max-hurd.patch b/easybuild/easyconfigs/g/GConf/GConf-3.2.6_gconf-path-max-hurd.patch new file mode 100644 index 00000000000..d8ba4a7e962 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6_gconf-path-max-hurd.patch @@ -0,0 +1,33 @@ +Taken from Debian package for 3.2.6 +Index: gconf-3.2.6/backends/markup-tree.c +=================================================================== +--- gconf-3.2.6.orig/backends/markup-tree.c 2013-01-23 11:17:01.995020067 +0100 ++++ gconf-3.2.6/backends/markup-tree.c 2013-01-23 11:17:01.991020067 +0100 +@@ -71,6 +71,11 @@ + } + #endif + ++/* PATH_MAX is not defined in limits.h on some platforms */ ++#ifndef PATH_MAX ++#define PATH_MAX 4096 ++#endif ++ + typedef struct + { + char *locale; +Index: gconf-3.2.6/backends/xml-dir.c +=================================================================== +--- gconf-3.2.6.orig/backends/xml-dir.c 2013-01-23 11:17:01.995020067 +0100 ++++ gconf-3.2.6/backends/xml-dir.c 2013-01-23 11:17:01.991020067 +0100 +@@ -36,6 +36,11 @@ + + #include "gconf/gconf-internals.h" + ++/* PATH_MAX is not defined in limits.h on some platforms */ ++#ifndef PATH_MAX ++#define PATH_MAX 4096 ++#endif ++ + /* This makes hash table safer when debugging */ + #ifndef GCONF_ENABLE_DEBUG + #define safe_g_hash_table_insert g_hash_table_insert diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6_readd_gconf_engine_key_is_writable.patch b/easybuild/easyconfigs/g/GConf/GConf-3.2.6_readd_gconf_engine_key_is_writable.patch new file mode 100644 index 00000000000..287a3ef697f --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6_readd_gconf_engine_key_is_writable.patch @@ -0,0 +1,47 @@ +From 7fc5106b58e9270e0d92b4c054a120628320b410 Mon Sep 17 00:00:00 2001 +From: Vincent Untz +Date: Tue, 21 Feb 2012 15:26:47 +0100 +Subject: [PATCH] gconf-dbus: Add gconf_engine_key_is_writable() + +This went missing in the dbus port, and so we broke ABI. +It's really the same code as in the corba code. + +https://bugzilla.gnome.org/show_bug.cgi?id=668948 +--- + gconf/gconf-dbus.c | 23 +++++++++++++++++++++++ + 1 files changed, 23 insertions(+), 0 deletions(-) + +Index: GConf-3.2.6/gconf/gconf-dbus.c +=================================================================== +--- GConf-3.2.6.orig/gconf/gconf-dbus.c 2013-06-06 02:39:13.243932775 +0200 ++++ GConf-3.2.6/gconf/gconf-dbus.c 2013-06-06 02:39:13.239932729 +0200 +@@ -2195,6 +2195,29 @@ + } + } + ++gboolean ++gconf_engine_key_is_writable (GConfEngine *conf, ++ const gchar *key, ++ GError **err) ++{ ++ gboolean is_writable = TRUE; ++ GConfValue *val; ++ ++ CHECK_OWNER_USE (conf); ++ ++ /* FIXME implement IDL to allow getting only writability ++ * (not that urgent since GConfClient caches this crap ++ * anyway) ++ */ ++ ++ val = gconf_engine_get_full(conf, key, NULL, TRUE, ++ NULL, &is_writable, err); ++ ++ gconf_value_free (val); ++ ++ return is_writable; ++} ++ + static void + cnxn_get_all_func (gpointer key, + gpointer value, diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0-Python-3.7.2.eb new file mode 100644 index 00000000000..c4113dc4c86 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0-Python-3.7.2.eb @@ -0,0 +1,45 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.60.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['89f884f5d5c6126140ec868cef184c42ce72902c13cd08f36e660371779b5560'] + +builddependencies = [ + ('Meson', '0.50.0', versionsuffix), + ('Ninja', '1.9.0'), + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('libffi', '3.2.1'), + ('gettext', '0.19.8.1'), + ('libxml2', '2.9.8'), + ('PCRE', '8.43'), + ('util-linux', '2.33'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +postinstallcmds = ["sed -i -e 's|#!.*python[0-9.]*$|#!/usr/bin/env python|' %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' From 814ac8a1887a1e31afc40c64cd73d9f2fe463d99 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 21:26:43 +0200 Subject: [PATCH 1515/5331] add back sed command to fix 'perl' shebang in CD-HIT easyconfigs --- .../easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb index 71c1e46e109..7ddb9fca6e6 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-foss-2018b.eb @@ -2,8 +2,8 @@ easyblock = 'MakeCp' -name = "CD-HIT" -version = "4.8.1" +name = 'CD-HIT' +version = '4.8.1' homepage = 'http://weizhong-lab.ucsd.edu/cd-hit/' description = """ CD-HIT is a very widely used program for clustering and @@ -22,13 +22,15 @@ dependencies = [('Perl', '5.28.0')] buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' # put here the list of generated executables when compiling -list_of_executables = ["cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd-hit-div", "cd-hit-454"] +list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] # this is the real EasyBuild line to copy all the executables and perl scripts to "bin" -files_to_copy = [(list_of_executables, "bin"), (["*.pl"], 'bin'), "README", "doc", "license.txt"] +files_to_copy = [(list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +postinstallcmds = ["sed -i 's@#!/usr/bin/perl@/usr/bin/env perl@' %(installdir)s/bin/*.pl"] sanity_check_paths = { - 'files': ["bin/%s" % x for x in list_of_executables], + 'files': ['bin/%s' % x for x in list_of_executables], 'dirs': [], } From a08b91a4fe0882f5e52853e9409b597945578ec2 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 8 May 2019 14:44:52 -0500 Subject: [PATCH 1516/5331] Added charmm vs CHARMM explanation header --- easybuild/easyconfigs/c/charmm/charmm-43b2-foss-2017b.eb | 6 +++++- easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/charmm/charmm-43b2-foss-2017b.eb b/easybuild/easyconfigs/c/charmm/charmm-43b2-foss-2017b.eb index 62ad10b31e1..082f30332f5 100644 --- a/easybuild/easyconfigs/c/charmm/charmm-43b2-foss-2017b.eb +++ b/easybuild/easyconfigs/c/charmm/charmm-43b2-foss-2017b.eb @@ -1,4 +1,7 @@ -# Authors:: Ward Poelmans +# This easyconfig files builds charmm, the free version of CHARMM +# charmm provides all the functionality of CHARMM except its performance enhancements +# See https://www.charmm.org for naming convention + easyblock = 'EB_CHARMM' name = 'charmm' @@ -22,6 +25,7 @@ checksums = [ ] # MKL activated automatically when the intel toolchain is used +# DOMDEC is not supported by (free) charmm build_options = "FULL COLFFT PIPF -CMPI" # Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce diff --git a/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb b/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb index 6a43c53d199..d305d95e55a 100644 --- a/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb +++ b/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb @@ -1,4 +1,7 @@ -# Authors:: Ward Poelmans +# This easyconfig files builds charmm, the free version of CHARMM +# charmm provides all the functionality of CHARMM except its performance enhancements +# See https://www.charmm.org for naming convention + easyblock = 'EB_CHARMM' name = 'charmm' @@ -25,6 +28,7 @@ checksums = [ prebuildopts = 'MPIIFORT=YES' # MKL activated automatically when the intel toolchain is used +# DOMDEC is not supported by (free) charmm build_options = "FULL COLFFT PIPF -CMPI" # Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce From f8bbf095bb1e5d849555e1ea83e46f9d0d550065 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 22:13:25 +0200 Subject: [PATCH 1517/5331] make installopts for hdf5r extension in R 3.5.1 easyconfigs consistent --- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 4 ++-- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 4 ++-- easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb | 3 ++- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index 0fadb700a08..961ccf48897 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -1951,13 +1951,13 @@ exts_list = [ 'checksums': ['58e36d3b8a67d01194c4e5099499657d017f77fc2081213633964b1d57a7e32f'], }), ('hdf5r', '1.0.0', { - 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', 'patches': ['hdf5r-1.0.0_fix-HDF5-1.10.2.patch'], - 'preinstallopts': "unset LIBS && ", 'checksums': [ '6a5fb0c4ac7129405e993ce461db908d51bc0ea2b717e8ca306c26902423d7e8', # hdf5r_1.0.0.tar.gz 'a01ffc5aa37dc3df375638c78ac02bb7e518eb0e41447a25e77a6da6f4e92608', # hdf5r-1.0.0_fix-HDF5-1.10.2.patch ], + 'preinstallopts': "unset LIBS && ", + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', }), ('DTRreg', '1.3', { 'checksums': ['835df542d0ec55368834bc4173dc4aa90f1c0ff146ab243d6e377bba309b8484'], diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 975f1235d76..d559576b570 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -1949,13 +1949,13 @@ exts_list = [ 'checksums': ['58e36d3b8a67d01194c4e5099499657d017f77fc2081213633964b1d57a7e32f'], }), ('hdf5r', '1.0.0', { - 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', 'patches': ['hdf5r-1.0.0_fix-HDF5-1.10.2.patch'], - 'preinstallopts': "unset LIBS && ", 'checksums': [ '6a5fb0c4ac7129405e993ce461db908d51bc0ea2b717e8ca306c26902423d7e8', # hdf5r_1.0.0.tar.gz 'a01ffc5aa37dc3df375638c78ac02bb7e518eb0e41447a25e77a6da6f4e92608', # hdf5r-1.0.0_fix-HDF5-1.10.2.patch ], + 'preinstallopts': "unset LIBS && ", + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', }), ('DTRreg', '1.3', { 'checksums': ['835df542d0ec55368834bc4173dc4aa90f1c0ff146ab243d6e377bba309b8484'], diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb index 02f3f86d19a..d4a14c89437 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb @@ -1978,11 +1978,12 @@ exts_list = [ }), ('hdf5r', '1.0.0', { 'patches': ['hdf5r-1.0.0_fix-HDF5-1.10.2.patch'], - 'preinstallopts': "unset LIBS && ", 'checksums': [ '6a5fb0c4ac7129405e993ce461db908d51bc0ea2b717e8ca306c26902423d7e8', # hdf5r_1.0.0.tar.gz 'a01ffc5aa37dc3df375638c78ac02bb7e518eb0e41447a25e77a6da6f4e92608', # hdf5r-1.0.0_fix-HDF5-1.10.2.patch ], + 'preinstallopts': "unset LIBS && ", + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', }), ('DTRreg', '1.3', { 'checksums': ['835df542d0ec55368834bc4173dc4aa90f1c0ff146ab243d6e377bba309b8484'], From 88b5b15dacb0a0d106718bd72efa693668810364 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 8 May 2019 22:13:27 +0200 Subject: [PATCH 1518/5331] update Theano version --- .../d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb index 6aba7c3a750..6fa95023492 100644 --- a/easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} dependencies = [ ('Python', '3.6.6'), - ('Theano', '1.0.3', versionsuffix), + ('Theano', '1.0.4', versionsuffix), ('h5py', '2.8.0', versionsuffix), ('protobuf-python', '3.6.0', versionsuffix), ('Pillow', '5.3.0', versionsuffix), From 64e1b50ad40ae0147235838dc863ad5e269ae421 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Wed, 8 May 2019 15:49:03 -0500 Subject: [PATCH 1519/5331] Use SHLIB_EXT template --- .../easyconfigs/x/Xerces-C++/Xerces-C++-3.2.0-GCCcore-7.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.0-GCCcore-7.3.0.eb index 68a5d3eaa3b..c2446c81679 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.0-GCCcore-7.3.0.eb @@ -35,7 +35,7 @@ osdependencies = [ sanity_check_paths = { 'files': ['bin/XInclude', 'include/xercesc/xinclude/XIncludeUtils.hpp', - 'lib/libxerces-c-3.2.so'], + 'lib/libxerces-c-3.2.%s' % SHLIB_EXT], 'dirs': ['bin', 'include', 'lib'] } From 2f53ed0393c7aefa04324defefb465c97bceb9ca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 May 2019 22:54:19 +0200 Subject: [PATCH 1520/5331] add missing -Python-* versionsuffix for INTEGRATE-Neo easyconfig (+ rename it) --- ...2018b.eb => INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/i/INTEGRATE-Neo/{INTEGRATE-Neo-1.2.1-foss-2018b.eb => INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb} (95%) diff --git a/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b.eb b/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb similarity index 95% rename from easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b.eb rename to easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb index 7d3dcd215b3..ac7bc4747bd 100644 --- a/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b.eb +++ b/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb @@ -4,6 +4,7 @@ name = 'INTEGRATE-Neo' # version = '20180220' version = '1.2.1' commit = '6b9f666' +versionsuffix = '-Python-%(pyver)s' homepage = '' description = """ INTEGRATE-Neo is a gene fusion neoantigen discovering tool using next-generation sequencing data. @@ -34,7 +35,7 @@ postinstallcmds = ["sed -i '1 i#!/usr/bin/env python' bin/*.py"] sanity_check_paths = { 'files': ['bin/integrate-neo.py', 'bin/fusionBedpeAnnotator', 'bin/fusionBedpeSubsetter'], - 'dirs': [''], + 'dirs': [], } moduleclass = 'bio' From df06336219bc9b79857960d696c91586963f93f3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 9 May 2019 10:29:22 +0800 Subject: [PATCH 1521/5331] add patch --- .../FDTD_Solutions-8.20-fix-pbs-template.patch | 15 +++++++++++++++ .../f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb | 6 +++++- 2 files changed, 20 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20-fix-pbs-template.patch diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20-fix-pbs-template.patch b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20-fix-pbs-template.patch new file mode 100644 index 00000000000..e1808474b44 --- /dev/null +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20-fix-pbs-template.patch @@ -0,0 +1,15 @@ +fix paths in pbs template +Author: Miguel Dias Costa +--- opt/lumerical/fdtd/templates/fdtd-pbs-template.sh.orig 2019-05-09 09:30:30.424131000 +0800 ++++ opt/lumerical/fdtd/templates/fdtd-pbs-template.sh 2019-05-09 09:33:28.842542991 +0800 +@@ -10,8 +10,8 @@ + NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE` + echo "Starting run at: `date`" + echo "Running on $NUM_PROCS processors." +-MY_PROG="/opt/lumerical/fdtd/bin/fdtd-engine-mpichp4" ++MY_PROG="$EBROOTFDTD_SOLUTIONS/bin/fdtd-engine-mpich2nem" + INPUT="" +-/opt/lumerical/fdtd/mpich/ch_p4/bin/mpirun -n $NUM_PROCS $MY_PROG -t 1 ./${INPUT} ++$EBROOTFDTD_SOLUTIONS/mpich2/nemesis/bin/mpiexec -n $NUM_PROCS $MY_PROG -t 1 ./${INPUT} + echo "Job finished at: `date`" + exit diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb index 820e48bc28f..719fbe2f436 100644 --- a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb @@ -8,11 +8,15 @@ of nanophotonic devices, processes and materials.""" toolchain = {'name': 'dummy', 'version': 'dummy'} sources = [SOURCE_TAR_GZ] -patches = ['%(name)s-%(version_major_minor)s-fix-which-skip-alias.patch'] +patches = [ + '%(name)s-%(version_major_minor)s-fix-which-skip-alias.patch', + '%(name)s-%(version_major_minor)s-fix-pbs-template.patch', +] checksums = [ 'e742bd5a7a64d04d6aa6ee99cbafd77fb63a0388951cd83431e4da4ce84f6a48', # FDTD_Solutions-8.20.1731.tar.gz # FDTD_Solutions-8.20-fix-which-skip-alias.patch '177f63815f1df533a35b211f39f5153cb6c6096925e682e7c689c80c7ed97351', + '31dda0e6ef4e05d1fea40e396556598a8d1c45ec5dc98868c6bb8ab7003ef330', # FDTD_Solutions-8.20-fix-pbs-template.patch ] moduleclass = 'cae' From ccd52bb1bf9aa2238f90920d9cffeab5e24663fb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 9 May 2019 08:44:11 +0200 Subject: [PATCH 1522/5331] Add patch to make FoX build for QM-E 6.2.1. Fixed in 6.3 versions. --- .../QuantumESPRESSO-6.2.1-iomkl-2017b.eb | 6 +++++- ...QuantumESPRESSO-6.2.1_fix_building_fox.patch | 17 +++++++++++++++++ 2 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1_fix_building_fox.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb index 45cc1c7cf09..2d5b3eb9707 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1-iomkl-2017b.eb @@ -27,12 +27,16 @@ sources = [ 'qe-%(version)s.tar.gz', 'wannier90-2.1.0.tar.gz', ] -patches = ['%(name)s-%(version)s_fix_missing_include_dir_in_COUPLE.patch'] +patches = [ + '%(name)s-%(version)s_fix_missing_include_dir_in_COUPLE.patch', + '%(name)s-%(version)s_fix_building_fox.patch', +] checksums = [ '6cdd4c8883b4a2262ac98ea452f845ed935294b3988a84b238d833558eb90f0c', # qe-6.2.1.tar.gz 'ee90108d4bc4aa6a1cf16d72abebcb3087cf6c1007d22dda269eb7e7076bddca', # wannier90-2.1.0.tar.gz # QuantumESPRESSO-6.2.1_fix_missing_include_dir_in_COUPLE.patch '44751fe9d1e6eede4ba331e7216e222960ff19ba9170aaa0cd4393924aa54fbc', + '37da474c68572e4ddcd492c64e3dead0c52b82b00340771e4859b2280e9a98e1', # QuantumESPRESSO-6.2.1_fix_building_fox.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1_fix_building_fox.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1_fix_building_fox.patch new file mode 100644 index 00000000000..c5caba54c72 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.2.1_fix_building_fox.patch @@ -0,0 +1,17 @@ +Building fox requires FCFLAGS and a cleared LIBS. +This is fixed in QM-E 6.3 + +Miguel Dias Costa, 20190509 +diff -ru qe-6.2.1.orig/install/extlibs_makefile qe-6.2.1/install/extlibs_makefile +--- qe-6.2.1.orig/install/extlibs_makefile 2017-12-11 17:52:53.000000000 +0100 ++++ qe-6.2.1/install/extlibs_makefile 2019-05-09 08:04:29.548203090 +0200 +@@ -80,7 +80,8 @@ + if test ! -d ../FoX; then \ + mkdir ../FoX; \ + (gzip -dc ../archive/fox.tgz | (cd ../FoX; tar -xvf -)); \ +- cd ../FoX/fox/; export FC=$(F90); ./configure --prefix=$(TOPDIR)/FoX ;\ ++ cd ../FoX/fox/; export FC=$(F90); export FCFLAGS="$(FOX_FLAGS)"; \ ++ unset LIBS; ./configure --prefix=$(TOPDIR)/FoX ;\ + $(MAKE) install; cd ../; rm -fr fox;fi + # ELPA + libelpa : libelpa_$(ELPA_LIBS_SWITCH) From a6e170a1181fcb8d92a52ee83bb6f9b4d64bfad1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 9 May 2019 08:51:34 +0200 Subject: [PATCH 1523/5331] Handle too long lines. --- .../w/wxWidgets/wxWidgets-3.0.4-GCC-8.2.0-2.31.1.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.0.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.0.4-GCC-8.2.0-2.31.1.eb index 4c0ce3cd20f..647d22a352b 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.0.4-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.0.4-GCC-8.2.0-2.31.1.eb @@ -37,7 +37,9 @@ dependencies = [ ('WebKitGTK+', '2.24.1'), ] -preconfigopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' +cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % cpath_ext configopts = '--enable-intl --enable-ipv6 ' # Options required by wxPython @@ -48,7 +50,7 @@ configopts += '--enable-mediactrl --enable-display --enable-geometry ' configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' configopts += '--enable-autoidman --with-sdl ' -prebuildopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' +prebuildopts = 'CPATH=$CPATH:%s ' % cpath_ext sanity_check_paths = { 'files': ['bin/wx-config', 'bin/wxrc'], From 1405dbca031b059dc1063087de5d3958cac7d432 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 9 May 2019 09:19:02 +0200 Subject: [PATCH 1524/5331] add protobuf easyconfig --- ...ython-3.6.0-fosscuda-2018b-Python-3.6.6.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.6.0-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.6.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.6.0-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..61cd573dfd0 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.6.0-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = ['https://github.com/google/protobuf/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6b399412cd68c7efe64d31824ad0db44f803aed91d0c6a9ea94272682c3da2df'] + +dependencies = [ + ('Python', '3.6.6'), + ('protobuf', version), +] + +start_dir = 'python' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' From a116891591eb4b18c6e2a169f2ea73d1f4771050 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 9 May 2019 09:26:49 +0200 Subject: [PATCH 1525/5331] drop opencv --- .../OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb deleted file mode 100644 index 0aa61fe1e65..00000000000 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,45 +0,0 @@ -name = 'OpenCV' -version = '4.0.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://opencv.org/' -description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision - and machine learning software library. OpenCV was built to provide - a common infrastructure for computer vision applications and to accelerate - the use of machine perception in the commercial products.""" - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = [ - 'https://github.com/opencv/opencv/archive/', - # the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake - 'https://raw.githubusercontent.com/opencv/opencv_3rdparty/32e315a5b106a7b89dbed51c28f8120a48b368b4/ippicv', -] -sources = [ - '%(version)s.zip', - {'filename': 'ippicv_2019_lnx_intel64_general_20180723.tgz', 'extract_cmd': "cp %s %(builddir)s"}, -] -checksums = [ - 'b79ccdc4797a959c5ab17249a8a302c066248ae070e4d7010e2d77a625fdb30a', # 4.0.1.zip - 'fc167cb60deb8924339a7050f3da168bb02e221b2d6b8c00139d1fa7eace0c7d', # ippicv_2019_lnx_intel64_general_20180723.tgz -] - -builddependencies = [ - ('CMake', '3.12.1'), -] - -dependencies = [ - ('Python', '3.6.6'), - ('zlib', '1.2.11'), - ('FFmpeg', '4.1'), - ('libjpeg-turbo', '2.0.0'), - ('libpng', '1.6.34'), - ('LibTIFF', '4.0.9'), - ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.5', '-Java-%(javaver)s', True), - ('GLib', '2.54.3'), - ('GTK+', '2.24.32'), -] - -moduleclass = 'vis' From 0fabff3a81d6c20a706eee0c01e88c3236ee15bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 May 2019 09:28:46 +0200 Subject: [PATCH 1526/5331] add missing ptyprocess extension in FlexiDot easyconfig + avoid use of funky character in 'sed' command which breaks parsing of the easyconfig file --- .../f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb index a8be3f507b4..de20e2f3b74 100644 --- a/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/f/FlexiDot/FlexiDot-1.06-foss-2018b-Python-2.7.15.eb @@ -56,12 +56,16 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/c/colour/'], 'checksums': ['af20120fefd2afede8b001fbef2ea9da70ad7d49fafdb6489025dae8745c3aee'], }), + ('ptyprocess', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), ] postinstallcmds = [ 'mv %(installdir)s/code/flexidot_v%(version)s.py %(installdir)s/bin/flexidot.py', 'chmod +x %(installdir)s/bin/flexidot.py', - "sed -i -e 's/\x0D$//' -e '1 s|^.*$|#!/usr/bin/env python|' %(installdir)s/bin/flexidot.py", + "sed -i -e '1 s|^.*$|#!/usr/bin/env python|' %(installdir)s/bin/flexidot.py", ] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From a059c134b130dfe5a8a754b97ee39d1c69837c15 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 9 May 2019 10:43:50 +0200 Subject: [PATCH 1527/5331] Make the requirement on Python clear for GLib. Fix python shebang. --- .../easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb index 4d4f3b8d4b2..562fbe1bc59 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb @@ -14,10 +14,18 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['89f884f5d5c6126140ec868cef184c42ce72902c13cd08f36e660371779b5560'] builddependencies = [ + # Python is required for using GLib to build, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.7.2'), ('Meson', '0.50.0', '-Python-3.7.2'), ('Ninja', '1.9.0'), ('binutils', '2.31.1'), - ('Python', '3.7.2'), ('pkg-config', '0.29.2'), ] @@ -34,7 +42,7 @@ preconfigopts = "export PYTHON=python && " configopts = "--buildtype=release --default-library=both " -postinstallcmds = ["sed -i -e 's|#!.*python|#!/usr/bin/env python|' %(installdir)s/bin/*"] +postinstallcmds = ["sed -i -e 's|#!.*python[0-9.]*$|#!/usr/bin/env python|' %(installdir)s/bin/*"] sanity_check_paths = { 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], From 1309db5d91067cf786ca8ee3cde25df0d0594dbc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 9 May 2019 10:57:39 +0200 Subject: [PATCH 1528/5331] Dont make Python specific version of GConf. Depends on #8277. --- .../dbus-glib-0.110-GCCcore-8.2.0.eb | 5 +-- ...-3.7.2.eb => GConf-3.2.6-GCCcore-8.2.0.eb} | 6 +-- .../GLib-2.60.1-GCCcore-8.2.0-Python-3.7.2.eb | 45 ------------------- 3 files changed, 4 insertions(+), 52 deletions(-) rename easybuild/easyconfigs/g/GConf/{GConf-3.2.6-GCCcore-8.2.0-Python-3.7.2.eb => GConf-3.2.6-GCCcore-8.2.0.eb} (92%) delete mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb index 843c4b96c2d..a1fea770ea9 100644 --- a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb @@ -15,10 +15,11 @@ checksums = ['7ce4760cf66c69148f6bd6c92feaabb8812dee30846b24cd0f7395c436d7e825'] builddependencies = [ ('binutils', '2.31.1'), ('pkg-config', '0.29.2'), + ('Python', '3.7.2'), # Python is needed for using GLib at build time. ] dependencies = [ - ('GLib', '2.60.1', '-Python-3.7.2'), + ('GLib', '2.60.1'), ('DBus', '1.13.8'), ('expat', '2.2.6'), ] @@ -28,6 +29,4 @@ sanity_check_paths = { 'dirs': ['include', 'share'] } -parallel = 1 - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb similarity index 92% rename from easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0-Python-3.7.2.eb rename to easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb index b7487ccbb6e..5b3bce5e3a0 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-8.2.0.eb @@ -2,7 +2,6 @@ easyblock = 'ConfigureMake' name = 'GConf' version = '3.2.6' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://projects.gnome.org/gconf/' description = """GConf is a system for storing application preferences. @@ -30,12 +29,11 @@ checksums = [ builddependencies = [ ('binutils', '2.31.1'), - ('GObject-Introspection', '1.60.1', versionsuffix), + ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), ] dependencies = [ - ('Python', '3.7.2'), - ('GLib', '2.60.1', versionsuffix), + ('GLib', '2.60.1'), ('dbus-glib', '0.110'), ('libxml2', '2.9.8'), ('GTK+', '3.24.8'), diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0-Python-3.7.2.eb deleted file mode 100644 index c4113dc4c86..00000000000 --- a/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0-Python-3.7.2.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'GLib' -version = '2.60.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://www.gtk.org/' -description = """GLib is one of the base libraries of the GTK+ project""" - -toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -toolchainopts = {'pic': True} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['89f884f5d5c6126140ec868cef184c42ce72902c13cd08f36e660371779b5560'] - -builddependencies = [ - ('Meson', '0.50.0', versionsuffix), - ('Ninja', '1.9.0'), - ('binutils', '2.31.1'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '3.7.2'), - ('libffi', '3.2.1'), - ('gettext', '0.19.8.1'), - ('libxml2', '2.9.8'), - ('PCRE', '8.43'), - ('util-linux', '2.33'), -] - -# avoid using hardcoded path to Python binary in build step -preconfigopts = "export PYTHON=python && " - -configopts = "--buildtype=release --default-library=both " - -postinstallcmds = ["sed -i -e 's|#!.*python[0-9.]*$|#!/usr/bin/env python|' %(installdir)s/bin/*"] - -sanity_check_paths = { - 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include'], -} - -moduleclass = 'vis' From fbae991b9a4806f72bcedadfd105ea22497b40b4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 9 May 2019 11:42:49 +0200 Subject: [PATCH 1529/5331] Adjust comment text slightly. --- easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb index 562fbe1bc59..4435efb771a 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.60.1-GCCcore-8.2.0.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['89f884f5d5c6126140ec868cef184c42ce72902c13cd08f36e660371779b5560'] builddependencies = [ - # Python is required for using GLib to build, at least when + # Python is required for building against GLib, at least when # gdbus-codegen or one of the other python scripts are used. # Since Meson 0.50 and later are Python >=3.5 only we can't build # Python specific versions of GLib that uses Python 2.x From f56016d616d38fbfe498e38e76700d3cc4bdb628 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Thu, 9 May 2019 10:55:13 +0100 Subject: [PATCH 1530/5331] adding easyconfigs: Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb --- ...m_Galore-0.6.1-foss-2018b-Python-2.7.15.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..96d93d982ce --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,41 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'Tarball' + +name = 'Trim_Galore' +version = '0.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """Trim Galore is a wrapper around Cutadapt and FastQC to +consistently apply adapter and quality trimming to FastQ files, with extra +functionality for RRBS data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] + +checksums = ['658578c29d007fe66f9ab49608442be703a6fcf535db06eb82659c7edccb62b0'] + +dependencies = [ + ('Python', '2.7.15'), + ('Perl', '5.28.0'), + ('FastQC', '0.11.8', '-Java-1.8', True), + ('cutadapt', '1.18', versionsuffix) +] + +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s", +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' From 5e5e2de93c14c8cb58613c2d86b52584bc2b1931 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 May 2019 11:57:11 +0200 Subject: [PATCH 1531/5331] fix hanging 'make test' by unsetting jemalloc's $LD_PRELOAD --- easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb index 7b184da8b27..518ddfc0068 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb @@ -28,6 +28,7 @@ dependencies = [ configopts = '-DJEMALLOC_ROOT=$EBROOTJEMALLOC' +pretestopts = "unset LD_PRELOAD && " runtest = 'test' sanity_check_paths = { From 0006a7ff29f112682572a3872d6cf8dc1c1b67f3 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Thu, 9 May 2019 11:16:32 +0100 Subject: [PATCH 1532/5331] Python version corrected --- ...im_Galore-0.6.1-foss-2018b-Python-3.6.6.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..07037434493 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,42 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'Tarball' + +name = 'Trim_Galore' +version = '0.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """Trim Galore is a wrapper around Cutadapt and FastQC to +consistently apply adapter and quality trimming to FastQ files, with extra +functionality for RRBS data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] + +checksums = ['658578c29d007fe66f9ab49608442be703a6fcf535db06eb82659c7edccb62b0'] + +dependencies = [ + ('Python', '3.6.6'), # multi-core support requires Python 3.x + pigz + ('pigz', '2.4'), + ('Perl', '5.28.0'), + ('FastQC', '0.11.8', '-Java-1.8', True), + ('cutadapt', '1.18', versionsuffix) +] + +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s", +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' From c4f09973cb802f078d14cb9671f605ee2c26c2b7 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Thu, 9 May 2019 11:21:58 +0100 Subject: [PATCH 1533/5331] adding easyconfigs: Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb --- ...m_Galore-0.6.2-foss-2018b-Python-2.7.15.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..cf2e0c9f7dc --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,41 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'Tarball' + +name = 'Trim_Galore' +version = '0.6.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """Trim Galore is a wrapper around Cutadapt and FastQC to +consistently apply adapter and quality trimming to FastQ files, with extra +functionality for RRBS data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] + +checksums = ['c50b841bdc294a6cdc6a27fb7bfbed1973541d20a68a4708584b817c58b3f376'] + +dependencies = [ + ('Python', '2.7.15'), + ('Perl', '5.28.0'), + ('FastQC', '0.11.8', '-Java-1.8', True), + ('cutadapt', '1.18', versionsuffix) +] + +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s", +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' From bc0bc7668138df7b3baa163b2c522791cdbf2597 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 9 May 2019 12:27:07 +0200 Subject: [PATCH 1534/5331] Adjusted comment about Python+GLib slightly. --- .../easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb index a1fea770ea9..0a0aad3fee6 100644 --- a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.110-GCCcore-8.2.0.eb @@ -15,7 +15,7 @@ checksums = ['7ce4760cf66c69148f6bd6c92feaabb8812dee30846b24cd0f7395c436d7e825'] builddependencies = [ ('binutils', '2.31.1'), ('pkg-config', '0.29.2'), - ('Python', '3.7.2'), # Python is needed for using GLib at build time. + ('Python', '3.7.2'), # Python is needed for building against GLib. ] dependencies = [ From 171b4abd8ce1c9c2cffbb912a2f8421b0dba2496 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Thu, 9 May 2019 11:28:27 +0100 Subject: [PATCH 1535/5331] adding easyconfigs: Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb --- ...im_Galore-0.6.2-foss-2018b-Python-3.6.6.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..b4fc90cc570 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,42 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'Tarball' + +name = 'Trim_Galore' +version = '0.6.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """Trim Galore is a wrapper around Cutadapt and FastQC to +consistently apply adapter and quality trimming to FastQ files, with extra +functionality for RRBS data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] + +checksums = ['c50b841bdc294a6cdc6a27fb7bfbed1973541d20a68a4708584b817c58b3f376'] + +dependencies = [ + ('Python', '3.6.6'), # multi-core support requires Python 3.x + pigz + ('pigz', '2.4'), + ('Perl', '5.28.0'), + ('FastQC', '0.11.8', '-Java-1.8', True), + ('cutadapt', '1.18', versionsuffix) +] + +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s", +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' From b95f313244171770feef6d14c53b98e83b0e68c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 May 2019 13:02:50 +0200 Subject: [PATCH 1536/5331] jemalloc is just a build dep for Salmon --- easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb index 518ddfc0068..b292160c293 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb @@ -18,16 +18,17 @@ checksums = ['91ebd1efc5b0b4c12ec6babecf3c0b79f7102e42b8895ca07c8c8fea869fefa3'] builddependencies = [ ('CMake', '3.12.1'), ('pkg-config', '0.29.2'), + ('jemalloc', '5.1.0'), ] dependencies = [ ('Boost', '1.67.0'), ('tbb', '2018_U5'), - ('jemalloc', '5.1.0'), ] configopts = '-DJEMALLOC_ROOT=$EBROOTJEMALLOC' +# need to unset the $LD_PRELOAD set be jemalloc to avoid hanging 'make test' pretestopts = "unset LD_PRELOAD && " runtest = 'test' From 4e085fbabf954bdbdbca453a34e5b620fdadd789 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 May 2019 14:13:58 +0200 Subject: [PATCH 1537/5331] clarify unset $LD_PRELOAD for 'make test' --- easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb index b292160c293..30fbf155374 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb @@ -29,6 +29,8 @@ dependencies = [ configopts = '-DJEMALLOC_ROOT=$EBROOTJEMALLOC' # need to unset the $LD_PRELOAD set be jemalloc to avoid hanging 'make test' +# since jemalloc is statically linked in Salmon (and hence only a build dep), +# this only affects the tests pretestopts = "unset LD_PRELOAD && " runtest = 'test' From e15967df398d11e33a7f092faf43e960ccdef930 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 9 May 2019 15:47:28 +0200 Subject: [PATCH 1538/5331] Add `pkg-config` as build dependency --- easybuild/easyconfigs/d/DBus/DBus-1.13.6-GCCcore-6.4.0.eb | 1 + easybuild/easyconfigs/d/DBus/DBus-1.13.6-GCCcore-7.3.0.eb | 1 + easybuild/easyconfigs/d/DBus/DBus-1.13.8-GCCcore-8.2.0.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.6-GCCcore-6.4.0.eb index 1098a72486c..6601c58b83d 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.13.6-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.6-GCCcore-6.4.0.eb @@ -22,6 +22,7 @@ checksums = ['b533693232d36d608a09f70c15440c1816319bac3055433300d88019166c1ae4'] builddependencies = [ ('binutils', '2.28'), + ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.6-GCCcore-7.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.6-GCCcore-7.3.0.eb index 87066c3efd8..5205747c39a 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.13.6-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.6-GCCcore-7.3.0.eb @@ -22,6 +22,7 @@ checksums = ['b533693232d36d608a09f70c15440c1816319bac3055433300d88019166c1ae4'] builddependencies = [ ('binutils', '2.30'), + ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.8-GCCcore-8.2.0.eb index 2e4a146618e..6f4b0c0ea72 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.13.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.8-GCCcore-8.2.0.eb @@ -22,6 +22,7 @@ checksums = ['82a89f64e1b55e459725186467770995f33cac5eb8a050b5d8cbeb338078c4f6'] builddependencies = [ ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), ] dependencies = [ From b399cafd2c3416134c6029cba2cb72b476c3a4e4 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Thu, 9 May 2019 15:59:21 +0200 Subject: [PATCH 1539/5331] CGAL updated to v4.14 + some cleanup of *.eb files --- ....2.eb => CGAL-4.14-foss-2019a-Python-3.7.2.eb} | 15 ++++++++------- ...2.eb => CGAL-4.14-intel-2019a-Python-3.7.2.eb} | 15 ++++++++------- 2 files changed, 16 insertions(+), 14 deletions(-) rename easybuild/easyconfigs/c/CGAL/{CGAL-4.11.3-foss-2019a-Python-3.7.2.eb => CGAL-4.14-foss-2019a-Python-3.7.2.eb} (90%) rename easybuild/easyconfigs/c/CGAL/{CGAL-4.11.3-intel-2019a-Python-3.7.2.eb => CGAL-4.14-intel-2019a-Python-3.7.2.eb} (90%) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb similarity index 90% rename from easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-foss-2019a-Python-3.7.2.eb rename to easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb index fbcbb92ff85..4d717d55089 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb @@ -1,5 +1,5 @@ name = 'CGAL' -version = '4.11.3' +version = '4.14' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.cgal.org/' @@ -11,7 +11,12 @@ toolchainopts = {'strict': True} source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] sources = [SOURCE_TAR_XZ] -checksums = ['3ed80bc87f00eb3c72357f5842907f828f8ab8fc66053351aab76aa10566981a'] +checksums = ['59464b1eaee892f2223ba570a7642892c999e29524ab102a6efd7c29c94a29f7'] + +builddependencies = [ + ('CMake', '3.13.3'), + ('Eigen', '3.3.7', '', True), +] dependencies = [ ('zlib', '1.2.11'), @@ -19,15 +24,11 @@ dependencies = [ ('Boost', '1.70.0'), ('MPFR', '4.0.2'), ('GMP', '6.1.2'), + ('Mesa', '19.0.1'), ('libGLU', '9.0.0'), ('Qt5', '5.12.3'), ] -builddependencies = [ - ('CMake', '3.13.3'), - ('Eigen', '3.3.7', '', True), -] - configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb similarity index 90% rename from easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-intel-2019a-Python-3.7.2.eb rename to easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb index baaa8b50a03..7af7769dea5 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.3-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb @@ -1,5 +1,5 @@ name = 'CGAL' -version = '4.11.3' +version = '4.14' versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.cgal.org/' @@ -11,7 +11,12 @@ toolchainopts = {'strict': True} source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] sources = [SOURCE_TAR_XZ] -checksums = ['3ed80bc87f00eb3c72357f5842907f828f8ab8fc66053351aab76aa10566981a'] +checksums = ['59464b1eaee892f2223ba570a7642892c999e29524ab102a6efd7c29c94a29f7'] + +builddependencies = [ + ('CMake', '3.13.3'), + ('Eigen', '3.3.7', '', True), +] dependencies = [ ('zlib', '1.2.11'), @@ -19,15 +24,11 @@ dependencies = [ ('Boost', '1.70.0'), ('MPFR', '4.0.2'), ('GMP', '6.1.2'), + ('Mesa', '19.0.1'), ('libGLU', '9.0.0'), ('Qt5', '5.12.3'), ] -builddependencies = [ - ('CMake', '3.13.3'), - ('Eigen', '3.3.7', '', True), -] - configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT From 07abacea7da4aa590173e61f6f978d6c3d5f208a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Thu, 9 May 2019 16:53:48 +0200 Subject: [PATCH 1540/5331] add download_dep_fail and use_pip --- .../libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb index eaac3c29bf7..27271071651 100644 --- a/easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/l/libxml2.Python/libxml2.Python-2.9.8-foss-2018b-Python-2.7.15.eb @@ -36,6 +36,9 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +download_dep_fail = True +use_pip = True + options = {'modulename': 'libxml2'} modextrapaths = { From e9a865aae1588db73572ada0d3d48858d4a2e24b Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Thu, 9 May 2019 17:48:15 +0200 Subject: [PATCH 1541/5331] adding easyconfigs: Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb --- ...Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb new file mode 100644 index 00000000000..469dfe1d84d --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb @@ -0,0 +1,70 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '8.0.0' + +cudaver = '10.1.105' +versionsuffix = '-CUDA-%s' % (cudaver) + +homepage = 'http://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'cfe-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', +] +checksums = [ + '8872be1b12c61450cacc82b3d153eab02be2546ef34fa3580ed14137bb26224c', # llvm-8.0.0.src.tar.xz + '084c115aab0084e63b23eee8c233abb6739c399e29966eaeccfc6e088e0b736b', # cfe-8.0.0.src.tar.xz + 'b435c7474f459e71b2831f1a4e3f1d21203cb9c0172e94e9d9b69f50354f21b1', # compiler-rt-8.0.0.src.tar.xz + 'e3f5a3d6794ef8233af302c45ceb464b74cdc369c1ac735b6b381b21e4d89df4', # polly-8.0.0.src.tar.xz + 'f7b1705d2f16c4fc23d6531f67d2dd6fb78a077dd346b02fed64f4b8df65c9d5', # openmp-8.0.0.src.tar.xz + '9caec8ec922e32ffa130f0fb08e4c5a242d7e68ce757631e425e9eba2e1a6e37', # lld-8.0.0.src.tar.xz + 'c2902675e7c84324fb2c1e45489220f250ede016cc3117186785d9dc291f9de2', # libcxx-8.0.0.src.tar.xz + 'c2d6de9629f7c072ac20ada776374e9e3168142f20a46cdb9d6df973922b07cd', # libcxxabi-8.0.0.src.tar.xz +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.31.1'), + ('GMP', '6.1.2'), + ('CUDA', cudaver, '', True), +] + +builddependencies = [ + ('CMake', '3.13.3'), + ('Python', '2.7.15'), + ('libxml2', '2.9.8'), +] + +assertions = True +usepolly = True +build_lld = True +libcxx = True + +skip_all_tests = True + +moduleclass = 'compiler' From 7768748aaffa7ef4bca52a612ec9d85057208608 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 9 May 2019 19:05:23 +0200 Subject: [PATCH 1542/5331] Fix too long lines --- .../wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb | 4 +++- .../wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb index acb423f97f0..829dbd725c7 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-2.7.15.eb @@ -42,6 +42,8 @@ dependencies = [ ('wxWidgets', '3.0.4'), ] -preinstallopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' +cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preinstallopts = 'CPATH=$CPATH:%s ' % cpath_ext moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb index 075fdd92430..f8f502b1653 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.0.4-GCC-8.2.0-2.31.1-Python-3.7.2.eb @@ -42,6 +42,8 @@ dependencies = [ ('wxWidgets', '3.0.4'), ] -preinstallopts = 'CPATH=$CPATH:$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include ' +cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preinstallopts = 'CPATH=$CPATH:%s ' % cpath_ext moduleclass = 'vis' From 894c1172cd6c593416f4e5f0360f6eaa7713ecd8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 May 2019 21:11:44 +0200 Subject: [PATCH 1543/5331] prevent LUSCUS from installing it's configuration into $HOME/.luscus --- .../easyconfigs/l/LUSCUS/LUSCUS-0.8.6-foss-2018b.eb | 10 ++++++++-- .../l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb | 10 ++++++++-- .../l/LUSCUS/LUSCUS-0.8.6_config-dir.patch | 13 +++++++++++++ 3 files changed, 29 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6_config-dir.patch diff --git a/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-foss-2018b.eb b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-foss-2018b.eb index 86bae2768d2..49294fc816b 100644 --- a/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-foss-2018b.eb +++ b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-foss-2018b.eb @@ -10,10 +10,14 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = [SOURCEFORGE_SOURCE] sources = ['luscus_%(version)s.tar.gz'] -patches = ['LUSCUS-%(version)s_fix-X11-link.patch'] +patches = [ + 'LUSCUS-%(version)s_fix-X11-link.patch', + 'LUSCUS-%(version)s_config-dir.patch', +] checksums = [ 'e1bf08de586b6e1c88c22b3d1d9b00a49c227fded7d6dc17023d3e9a84c573a3', # luscus_0.8.6.tar.gz 'b4831c00ecb2311738ed236bbbe5307522d9fca90544967186cab342065b8fc7', # LUSCUS-0.8.6_fix-X11-link.patch + 'f2abb45185a8b0e2bfb766ee035d8e250a3f9b1cb5261da60e3514504de7a490', # LUSCUS-0.8.6_config-dir.patch ] builddependencies = [ @@ -29,7 +33,9 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/luscus'], - 'dirs': [], + 'dirs': ['config'], } +modextravars = {'LUSCUS_DIR': '%(installdir)s/config'} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb index b896b140f17..c61f7f5928b 100644 --- a/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb +++ b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6-intel-2018a.eb @@ -10,10 +10,14 @@ toolchain = {'name': 'intel', 'version': '2018a'} source_urls = [SOURCEFORGE_SOURCE] sources = ['luscus_%(version)s.tar.gz'] -patches = ['LUSCUS-%(version)s_fix-X11-link.patch'] +patches = [ + 'LUSCUS-%(version)s_fix-X11-link.patch', + 'LUSCUS-%(version)s_config-dir.patch', +] checksums = [ 'e1bf08de586b6e1c88c22b3d1d9b00a49c227fded7d6dc17023d3e9a84c573a3', # luscus_0.8.6.tar.gz 'b4831c00ecb2311738ed236bbbe5307522d9fca90544967186cab342065b8fc7', # LUSCUS-0.8.6_fix-X11-link.patch + 'f2abb45185a8b0e2bfb766ee035d8e250a3f9b1cb5261da60e3514504de7a490', # LUSCUS-0.8.6_config-dir.patch ] builddependencies = [ @@ -29,7 +33,9 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/luscus'], - 'dirs': [], + 'dirs': ['config'], } +modextravars = {'LUSCUS_DIR': '%(installdir)s/config'} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6_config-dir.patch b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6_config-dir.patch new file mode 100644 index 00000000000..45f21045287 --- /dev/null +++ b/easybuild/easyconfigs/l/LUSCUS/LUSCUS-0.8.6_config-dir.patch @@ -0,0 +1,13 @@ +change hardcoded $HOME/.luscus path to config subdir of installation ($LUSCUS_DIR should be set to point there) +author: Kenneth Hoste (HPC-UGent) +--- luscus_0.8.6/CMakeLists.txt.orig 2019-05-09 20:54:35.712120873 +0200 ++++ luscus_0.8.6/CMakeLists.txt 2019-05-09 20:55:06.922437408 +0200 +@@ -31,7 +31,7 @@ + set(CONFIG_DIR "/etc/luscus") + # message(status " CMAKE_PREFIX_PATH NOT DEFINED!") # DEBUG + else () +- set(CONFIG_DIR "$ENV{HOME}/.luscus") ++ set(CONFIG_DIR "${CMAKE_INSTALL_PREFIX}/config") + # message(status " CMAKE_PREFIX_PATH DEFINED!") # DEBUG + endif () + set(TMP_CONFIG_DIR ${CMAKE_CURRENT_BINARY_DIR}/luscusrc) From e0af4012f18f497e787c5b1a599a9d7b6f0e2a8a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 May 2019 08:00:37 +0200 Subject: [PATCH 1544/5331] Add missing $GI_TYPELIB_PATH to Pango module. Everything that uses GObject-Introspection should have this set. --- easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb index 9ea5c5a16db..4eb831877d5 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.43.0-GCCcore-8.2.0.eb @@ -39,6 +39,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } From 48562952568c85d48bc80a7d04afab2ababff718 Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Fri, 10 May 2019 09:27:37 +0200 Subject: [PATCH 1545/5331] adding easyconfigs: gimkl-2018b.eb, gimpi-2018b.eb, imkl-2018.3.222-gimpi-2018b.eb, impi-2018.3.222-GCC-7.3.0-2.30.eb --- easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb | 20 ++++++++++ easybuild/easyconfigs/g/gimpi/gimpi-2018b.eb | 18 +++++++++ .../i/imkl/imkl-2018.3.222-gimpi-2018b.eb | 39 +++++++++++++++++++ .../i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb | 31 +++++++++++++++ 4 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb create mode 100644 easybuild/easyconfigs/g/gimpi/gimpi-2018b.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb diff --git a/easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb b/easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb new file mode 100644 index 00000000000..70f138e1522 --- /dev/null +++ b/easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gimkl' +version = '2018b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp = ('GCC', '7.3.0-2.30') + +dependencies = [ + comp, +# impi/2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30 8) imkl/2018.3.222-iimpi-2018b + ('impi', '2018.3.222', '', comp), + ('imkl', '2018.3.222', '', ('gimpi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gimpi/gimpi-2018b.eb b/easybuild/easyconfigs/g/gimpi/gimpi-2018b.eb new file mode 100644 index 00000000000..ac6227f8a6e --- /dev/null +++ b/easybuild/easyconfigs/g/gimpi/gimpi-2018b.eb @@ -0,0 +1,18 @@ +easyblock = "Toolchain" + +name = 'gimpi' +version = '2018b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +comp = ('GCC', '7.3.0-2.30') + +dependencies = [ + comp, + ('impi', '2018.3.222', '', comp), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb new file mode 100644 index 00000000000..ff57ee108c3 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2018.3.222-gimpi-2018b.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2018.3.222' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'gimpi', 'version': '2018b'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['108d59c0927e58ce8c314db6c2b48ee331c3798f7102725f425d6884eb6ed241'] + +dontcreateinstalldir = 'True' + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..592479f3090 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2018.3.222-GCC-7.3.0-2.30.eb @@ -0,0 +1,31 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'impi' +version = '2018.3.222' + +homepage = 'http://software.intel.com/en-us/intel-mpi-library/' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} + +source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13063/'] +sources = ['l_mpi_%(version)s.tgz'] +checksums = ['5021d14b344fc794e89f146e4d53d70184d7048610895d7a6a1e8ac0cf258999'] + +dontcreateinstalldir = 'True' + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = 'True' + +postinstallcmds = [ + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpich.so', + 'ln -s %(installdir)s/lib64/libmpigc4.so %(installdir)s/lib64/libmpichcxx.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libfmpich.so', + 'ln -s %(installdir)s/lib64/libmpigf.so %(installdir)s/lib64/libmpichf90.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libmpl.so', + 'ln -s %(installdir)s/lib64/libmpi.so %(installdir)s/lib64/libopa.so' +] + +moduleclass = 'mpi' From f912ab0a97f7140a2cdadcb8ab71aec5bd0a96cb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 May 2019 09:30:32 +0200 Subject: [PATCH 1546/5331] Dropping the no longer used FoX 4.1.2 --- .../f/FoX/FoX-4.1.2-iomkl-2017b.eb | 26 ------------------- 1 file changed, 26 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FoX/FoX-4.1.2-iomkl-2017b.eb diff --git a/easybuild/easyconfigs/f/FoX/FoX-4.1.2-iomkl-2017b.eb b/easybuild/easyconfigs/f/FoX/FoX-4.1.2-iomkl-2017b.eb deleted file mode 100644 index 794db15bcf3..00000000000 --- a/easybuild/easyconfigs/f/FoX/FoX-4.1.2-iomkl-2017b.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'FoX' -version = '4.1.2' - -homepage = 'http://homepages.see.leeds.ac.uk/~earawa/FoX/' -description = """FoX is an XML library written in Fortran 95. -It allows software developers to read, write and modify XML documents from Fortran applications without the -complications of dealing with multi-language development.""" - -toolchain = {'name': 'iomkl', 'version': '2017b'} - -source_urls = ['http://homepages.see.leeds.ac.uk/~earawa/FoX/source/'] -sources = [SOURCE_TAR_GZ] -checksums = ['3b749138229e7808d0009a97e2ac47815ad5278df6879a9cc64351a7921ba06f'] - -sanity_check_paths = { - 'files': ['lib/libFoX_%s.a' % x for x in ['common', 'dom', 'fsys', 'sax', 'utils', 'wcml', 'wkml', 'wxml']], - 'dirs': ['finclude', 'lib', 'bin'] -} - -modextrapaths = { - 'CPATH': ['finclude'], -} - -moduleclass = 'lib' From 47559d2951c53b4e4e2902a568b18888efd2d15a Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Fri, 10 May 2019 09:32:44 +0200 Subject: [PATCH 1547/5331] drop wrong comment line --- easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb b/easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb index 70f138e1522..470b66fd9e6 100644 --- a/easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb +++ b/easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb @@ -12,7 +12,6 @@ comp = ('GCC', '7.3.0-2.30') dependencies = [ comp, -# impi/2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30 8) imkl/2018.3.222-iimpi-2018b ('impi', '2018.3.222', '', comp), ('imkl', '2018.3.222', '', ('gimpi', version)), ] From 9f862f80f0563d6d1686b0c8d3d683908db69036 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 May 2019 09:40:43 +0200 Subject: [PATCH 1548/5331] adding easyconfigs: gnuplot-5.2.6-GCCcore-8.2.0.eb and patches: gnuplot-5.2.6_fix_missing_dep_for_gobject_to_cairopdf.patch --- .../g/gnuplot/gnuplot-5.2.6-GCCcore-8.2.0.eb | 60 +++++++++++++++++++ ..._missing_dep_for_gobject_to_cairopdf.patch | 25 ++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6_fix_missing_dep_for_gobject_to_cairopdf.patch diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..68300314d31 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6-GCCcore-8.2.0.eb @@ -0,0 +1,60 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.2.6' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +patches = ['gnuplot-5.2.6_fix_missing_dep_for_gobject_to_cairopdf.patch'] +checksums = [ + '35dd8f013139e31b3028fac280ee12d4b1346d9bb5c501586d1b5a04ae7a94ee', # gnuplot-5.2.6.tar.gz + # gnuplot-5.2.6_fix_missing_dep_for_gobject_to_cairopdf.patch + '9ed75b3eac403d94d19fd9124bee9de08b35f499490b867e82c89e660df5333b', +] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), + ('Autotools', '20180311'), +] + +dependencies = [ + ('ncurses', '6.1'), + ('cairo', '1.16.0'), + ('libjpeg-turbo', '2.0.2'), + ('libpng', '1.6.36'), + ('libgd', '2.2.5'), + ('Pango', '1.43.0'), + ('libcerf', '1.11'), + ('X11', '20190311'), + ('Qt5', '5.12.3'), +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6_fix_missing_dep_for_gobject_to_cairopdf.patch b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6_fix_missing_dep_for_gobject_to_cairopdf.patch new file mode 100644 index 00000000000..64949d3ba27 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.2.6_fix_missing_dep_for_gobject_to_cairopdf.patch @@ -0,0 +1,25 @@ +The code in wxterminal depends on gobject. +The check for it is missing resulting in the link lacking -lgobject-2.0 + +Åke Sandgren, 20190510 +diff -ru gnuplot-5.2.6.orig/configure.ac gnuplot-5.2.6/configure.ac +--- gnuplot-5.2.6.orig/configure.ac 2018-12-24 22:06:00.000000000 +0100 ++++ gnuplot-5.2.6/configure.ac 2019-05-10 09:24:37.484483274 +0200 +@@ -1071,7 +1071,7 @@ + if test "${with_cairo}" = yes ; then + dnl cairo terminals + PKG_CHECK_MODULES_NOFAIL(CAIROPDF,dnl +- [cairo >= 1.2 cairo-pdf >= 1.2 pango >= 1.22 pangocairo >= 1.10 glib-2.0 >= 2.28]) ++ [cairo >= 1.2 cairo-pdf >= 1.2 pango >= 1.22 pangocairo >= 1.10 glib-2.0 >= 2.28 gobject-2.0 >= 2.38]) + if test $pkg_failed != no; then + AC_MSG_WARN([The cairo terminals will not be compiled.]) + with_cairo=no +@@ -1392,7 +1392,7 @@ + if test "$with_cairo" = yes; then + AC_MSG_RESULT([ cairo-based pdf and png terminals: yes ]) + else +- AC_MSG_RESULT([ cairo-based terminals: no (requires cairo>=1.2, pango>=1.22, glib>=2.28)]) ++ AC_MSG_RESULT([ cairo-based terminals: no (requires cairo>=1.2, pango>=1.22, glib>=2.28, gobject-2.0 >= 2.38)]) + fi + + if test "$with_lua" = yes; then From 3676424b5b76d8fe2f6bdd11e05a253276a207d6 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Fri, 10 May 2019 09:12:23 +0100 Subject: [PATCH 1549/5331] adding easyconfigs: HDF5-1.8.12-foss-2018b.eb --- .../h/HDF5/HDF5-1.8.12-foss-2018b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb new file mode 100644 index 00000000000..aeb80c3c5ae --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb @@ -0,0 +1,31 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +name = 'HDF5' +version = '1.8.12' + +homepage = 'https://support.hdfgroup.org/HDF5/' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + 'b5cccea850096962b5fd9e96f22c4f47d2379224bb41130d9bc038bb6c37dfcb', # HDF5-tarball + '44e04cace87c54f75e8eb5b710679104f6703d88d10d6f3e5130b8cd90c69aa1', # configure_libtool.patch +] + +patches = [ + 'configure_libtool.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From 90cba2e666d554321106fd74848113f05e7698e4 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Fri, 10 May 2019 09:15:23 +0100 Subject: [PATCH 1550/5331] adding easyconfigs: HDF5-1.8.13-foss-2018b.eb --- .../h/HDF5/HDF5-1.8.13-foss-2018b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2018b.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2018b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2018b.eb new file mode 100644 index 00000000000..eb564213be5 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2018b.eb @@ -0,0 +1,31 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +name = 'HDF5' +version = '1.8.13' + +homepage = 'https://support.hdfgroup.org/HDF5/' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '82f6b38eec103b4fccfbf14892786e0c27a8135d3252d8601cf5bf20066d38c1', # HDF5 tarball + '44e04cace87c54f75e8eb5b710679104f6703d88d10d6f3e5130b8cd90c69aa1', # configure_libtool.patch +] + +patches = [ + 'configure_libtool.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From a843252bda8c1bf245c2ca0107d5b77f72f03ce2 Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Fri, 10 May 2019 10:30:06 +0200 Subject: [PATCH 1551/5331] add HPL --- .../easyconfigs/h/HPL/HPL-2.2-gimkl-2018b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.2-gimkl-2018b.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-gimkl-2018b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-gimkl-2018b.eb new file mode 100644 index 00000000000..ee756eac672 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-gimkl-2018b.eb @@ -0,0 +1,22 @@ +name = 'HPL' +version = '2.2' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gimkl', 'version': '2018b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] +checksums = [ + 'ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440', # hpl-2.2.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' From 57b0b028f1ff481fa767ef0f0e5d03bfe6de9f5e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 May 2019 10:38:17 +0200 Subject: [PATCH 1552/5331] Add $GI_TYPELIB_PATH to all Pango easyconfigs with active toolchains. --- easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb | 1 + 16 files changed, 16 insertions(+) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb index 80529d5bda3..804cc904a06 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb @@ -25,6 +25,7 @@ dependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb index 3dc38160e5d..df0d37de4c7 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb @@ -25,6 +25,7 @@ dependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb index dadefa491a9..7a6e824e2c2 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb @@ -35,6 +35,7 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb index 8bb5a7c7ca1..35fe9dce66a 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb @@ -35,6 +35,7 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb index 3821abfbdaa..0a7f75f9998 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb @@ -29,6 +29,7 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb index 05fa4ad00df..91f70c3f43f 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb @@ -29,6 +29,7 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb index 040a66af794..4b6cb5c3ad1 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb @@ -29,6 +29,7 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb index ba54cd87da5..b5ba4b52c9d 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb @@ -28,6 +28,7 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb index db886f06371..10c2e1747e2 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb @@ -28,6 +28,7 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb index 5119a1130e4..f3ca35e5332 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb @@ -28,6 +28,7 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb index fec5414da16..a6f9c6c49ce 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-foss-2017b.eb @@ -35,6 +35,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb index fc8461d94e5..8536226c275 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.0-intel-2017b.eb @@ -35,6 +35,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb index e7d14c0cac6..c463e6d8d75 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-foss-2018a.eb @@ -36,6 +36,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb index 6a945a99651..ef6c66c151d 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.41.1-intel-2018a.eb @@ -36,6 +36,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb index 90c6d08cc5a..e3f0cb0bc42 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-foss-2018b.eb @@ -36,6 +36,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb index f1ab48733b4..37db73c862f 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.42.4-fosscuda-2018b.eb @@ -36,6 +36,7 @@ sanity_check_paths = { } modextrapaths = { + 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', } From a4ff0b572c6fb314808624d2c7876f61b70ea661 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 10:48:41 +0200 Subject: [PATCH 1553/5331] Remove Qt5-related easyconfigs that have been superseded --- .../l/libGLU/libGLU-9.0.0-GCCcore-6.4.0.eb | 30 -------- ...-1.0.7-GCCcore-6.4.0-Python-2.7.14-bare.eb | 33 --------- .../m/Mesa/Mesa-17.3.6-GCCcore-6.4.0.eb | 74 ------------------- .../q/Qt5/Qt5-5.10.1-GCCcore-6.4.0.eb | 34 --------- ...39.1.0-GCCcore-6.4.0-Python-2.7.14-bare.eb | 33 --------- 5 files changed, 204 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-6.4.0.eb delete mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-6.4.0-Python-2.7.14-bare.eb delete mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-GCCcore-6.4.0.eb delete mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-GCCcore-6.4.0.eb delete mode 100644 easybuild/easyconfigs/s/setuptools/setuptools-39.1.0-GCCcore-6.4.0-Python-2.7.14-bare.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-6.4.0.eb deleted file mode 100644 index 135a591a322..00000000000 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.0-GCCcore-6.4.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libGLU' -version = '9.0.0' - -homepage = 'ftp://ftp.freedesktop.org/pub/mesa/glu/' -description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -source_urls = ['ftp://ftp.freedesktop.org/pub/mesa/glu/'] -sources = ['glu-%(version)s.tar.bz2'] -checksums = ['1f7ad0d379a722fcbd303aa5650c6d7d5544fde83196b42a73d1193568a4df12'] - -dependencies = [ - ('Mesa', '17.3.6'), -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), -] - -sanity_check_paths = { - 'files': ['lib/libGLU.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-6.4.0-Python-2.7.14-bare.eb b/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-6.4.0-Python-2.7.14-bare.eb deleted file mode 100644 index 45ff68131ce..00000000000 --- a/easybuild/easyconfigs/m/Mako/Mako-1.0.7-GCCcore-6.4.0-Python-2.7.14-bare.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Mako' -version = '1.0.7' -versionsuffix = '-Python-%(pyver)s-bare' - -homepage = 'http://www.makotemplates.org' -description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = [ - '4e02fde57bd4abb5ec400181e4c314f56ac3e49ba4fb8b0d50bba18cb27d25ae', # Mako-1.0.7.tar.gz -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), -] - -dependencies = [ - ('Python', '2.7.14', '-bare'), - ('setuptools', '39.1.0', '-Python-2.7.14-bare'), -] - -sanity_check_paths = { - 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-GCCcore-6.4.0.eb deleted file mode 100644 index 9a0af02523b..00000000000 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-GCCcore-6.4.0.eb +++ /dev/null @@ -1,74 +0,0 @@ -# Automatically converted from Mesa-17.2.4-intel-2017b.eb -# Original message: -# the purpose of the easyconfig is to build a Mesa for software rendering, -# not hardware rendering. This means you want at least SSE4.2. We build: -# - llvmpipe: the high-performance Gallium LLVM driver -# - swr: Intel's OpenSWR -# it will try to use the llvmpipe by default. It you want swr, do: -# GALLIUM_DRIVER=swr - -easyblock = 'ConfigureMake' - -name = 'Mesa' -version = '17.3.6' - -homepage = 'http://www.mesa3d.org/' -description = """Mesa is an open-source implementation of the OpenGL specification - - a system for rendering interactive 3D graphics.""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -# swr detects and builds parts specific for AVX and AVX2. If we use -# -xHost, this always gets overwritten and will fail. -toolchainopts = {'optarch': False} - -source_urls = [ - 'https://mesa.freedesktop.org/archive/', - 'https://mesa.freedesktop.org/archive/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', -] -sources = [SOURCELOWER_TAR_XZ] -patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] -checksums = [ - 'e5915680d44ac9d05defdec529db7459ac9edd441c9845266eff2e2d3e57fbf8', # mesa-17.3.6.tar.xz - '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-17.3.6_fix-strip-llvm-flags.patch -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), - ('flex', '2.6.4'), - ('Bison', '3.0.4'), - ('Autotools', '20170619'), - ('pkg-config', '0.29.2'), - ('Mako', '1.0.7', '-Python-2.7.14-bare'), - ('libxml2', '2.9.7'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('nettle', '3.4'), - ('libdrm', '2.4.91'), - ('LLVM', '5.0.1'), - ('X11', '20180131'), -] - -# GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" -configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" -configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " - -buildopts = 'V=1' - -sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, - 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, - 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', - 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], - 'dirs': [] -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-GCCcore-6.4.0.eb deleted file mode 100644 index b5f1ad5b5a5..00000000000 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-GCCcore-6.4.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'EB_Qt' - -name = 'Qt5' -version = '5.10.1' - -homepage = 'http://qt.io/' -description = "Qt is a comprehensive cross-platform C++ application framework." - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = [ - 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', - 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/' -] -sources = ['qt-everywhere-src-%(version)s.tar.xz'] -checksums = ['05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a'] - -dependencies = [ - ('GLib', '2.54.3'), - ('libpng', '1.6.34'), - ('X11', '20180131'), - ('libGLU', '9.0.0'), -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), - ('pkg-config', '0.29.2'), -] - -# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) -configopts = '-skip qtgamepad' - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-39.1.0-GCCcore-6.4.0-Python-2.7.14-bare.eb b/easybuild/easyconfigs/s/setuptools/setuptools-39.1.0-GCCcore-6.4.0-Python-2.7.14-bare.eb deleted file mode 100644 index ac33003e7ae..00000000000 --- a/easybuild/easyconfigs/s/setuptools/setuptools-39.1.0-GCCcore-6.4.0-Python-2.7.14-bare.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'setuptools' -version = '39.1.0' -versionsuffix = '-Python-%(pyver)s-bare' - -homepage = 'http://pypi.python.org/pypi/setuptools/' -description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_ZIP] -checksums = [ - 'c5484e13b89927b44fd15897f7ce19dded8e7f035466a4fa7b946c0bdd86edd7', # setuptools-39.1.0.zip -] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), -] - -dependencies = [ - ('Python', '2.7.14', '-bare'), -] - -sanity_check_paths = { - 'files': ['bin/easy_install', - 'lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg'], - 'dirs': [], -} - -moduleclass = 'devel' From 6f6e109ff31e482f873fbfda633a7731406707a6 Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Fri, 10 May 2019 10:52:15 +0200 Subject: [PATCH 1554/5331] add openmp --- easybuild/easyconfigs/h/HPL/HPL-2.2-gimkl-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.2-gimkl-2018b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.2-gimkl-2018b.eb index ee756eac672..d234f76a1a5 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.2-gimkl-2018b.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.2-gimkl-2018b.eb @@ -7,7 +7,7 @@ description = """HPL is a software package that solves a (random) dense linear s implementation of the High Performance Computing Linpack Benchmark.""" toolchain = {'name': 'gimkl', 'version': '2018b'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'openmp': True} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] From 2c4b2f11536e743332e2e71658ef7b2a723ae4d7 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Fri, 10 May 2019 11:41:26 +0100 Subject: [PATCH 1555/5331] zlib-EB file added --- .../z/zlib/zlib-1.2.8-GCCcore-7.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-7.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..7e9a1629cf5 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-7.3.0.eb @@ -0,0 +1,28 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +checksums = ['36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d'] + +builddependencies = [('binutils', '2.30')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From d1647367a6b5d061eb2688f4b5c81c5427370239 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 May 2019 13:22:20 +0200 Subject: [PATCH 1556/5331] Add missing checksums. --- easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb | 1 + easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb | 1 + 5 files changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb index 804cc904a06..a69bff0ec36 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['13072ad9e49372d6d7ba7bb3b9b025faef04de3552b745e92d7880eb15d6ee7e'] glibver = '2.47.5' dependencies = [ diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb index df0d37de4c7..f9db731af7c 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['13072ad9e49372d6d7ba7bb3b9b025faef04de3552b745e92d7880eb15d6ee7e'] glibver = '2.47.5' dependencies = [ diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb index b5ba4b52c9d..f806f291d7f 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['abba8b5ce728520c3a0f1535eab19eac3c14aeef7faa5aded90017ceac2711d3'] dependencies = [ ('X11', '20160819'), diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb index 10c2e1747e2..ec003df5386 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['abba8b5ce728520c3a0f1535eab19eac3c14aeef7faa5aded90017ceac2711d3'] dependencies = [ ('X11', '20160819'), diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb index f3ca35e5332..81ecf8512a3 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] +checksums = ['24748140456c42360b07b2c77a1a2e1216d07c056632079557cd4e815b9d01c9'] dependencies = [ ('X11', '20170314'), From c6df816c22d3b0c5374a436ab7161231248014f2 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 10:54:55 +0200 Subject: [PATCH 1557/5331] Bump SIONlib to v1.7.4 for GCCcore 8.2.0 --- ...tools.eb => SIONlib-1.7.4-GCCcore-8.2.0-tools.eb} | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/s/SIONlib/{SIONlib-1.7.2-GCCcore-6.4.0-tools.eb => SIONlib-1.7.4-GCCcore-8.2.0-tools.eb} (85%) diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.2-GCCcore-6.4.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.4-GCCcore-8.2.0-tools.eb similarity index 85% rename from easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.2-GCCcore-6.4.0-tools.eb rename to easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.4-GCCcore-8.2.0-tools.eb index 3faf89a4302..d0200cf6e9f 100644 --- a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.2-GCCcore-6.4.0-tools.eb +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.4-GCCcore-8.2.0-tools.eb @@ -1,16 +1,16 @@ ## # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # -# Copyright:: Copyright 2016-2018 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer -# Modified 2017 by Andreas Henkel +# Modified 2017 by Andreas Henkel # License:: 3-clause BSD ## easyblock = 'ConfigureMake' name = 'SIONlib' -version = '1.7.2' +version = '1.7.4' # Provide a stripped-down version with renamed symbols for tools, # see description for further details versionsuffix = '-tools' @@ -27,17 +27,17 @@ description = """ a tool requiring a different SIONlib version. """ -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['http://apps.fz-juelich.de/jsc/sionlib/download.php?version=%(version)sl'] sources = ['sionlib-%(version)sl.tar.gz'] checksums = [ - '7d94fc9a285f407e4e80b49fa618a6d68c7c78dacf3ce45512bbffbbd96500ed', # sionlib-1.7.2l.tar.gz + '3dcb61ea6c2bfa765c44c2407aba7d4f91f39b93549e81a60b26782feab51dfe', # sionlib-1.7.4l.tar.gz ] builddependencies = [ # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), + ('binutils', '2.31.1'), ] configopts = '--disable-cxx --disable-fortran --disable-ompi' From 63b6c487789ab3d546f15a1c03724ba7630ed6d7 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 10:57:51 +0200 Subject: [PATCH 1558/5331] Build OTF2 with GCCcore 8.2.0 and bump SIONlib dependency --- ....1-GCCcore-6.4.0.eb => OTF2-2.1.1-GCCcore-8.2.0.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/o/OTF2/{OTF2-2.1.1-GCCcore-6.4.0.eb => OTF2-2.1.1-GCCcore-8.2.0.eb} (83%) diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-8.2.0.eb similarity index 83% rename from easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-8.2.0.eb index 82e53e6dcc0..89e1cd3074e 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-8.2.0.eb @@ -1,6 +1,6 @@ ## # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# Copyright:: Copyright 2013-2018 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer # License:: 3-clause BSD @@ -22,9 +22,9 @@ description = """ """ -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/otf2/'] sources = [SOURCELOWER_TAR_GZ] checksums = [ '01591b42e76f396869ffc84672f4eaa90ee8ec2a8939755d9c0b5b8ecdcf47d3', # otf2-2.1.1.tar.gz @@ -32,9 +32,9 @@ checksums = [ builddependencies = [ # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), + ('binutils', '2.31.1'), # SIONlib container support (optional): - ('SIONlib', '1.7.2', '-tools'), + ('SIONlib', '1.7.4', '-tools'), ] configopts = '--enable-shared' From 82f9e9209d93c03835fa5cc1addbfd0d1c7849fe Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 11:03:22 +0200 Subject: [PATCH 1559/5331] Build PDT with GCCcore 8.2.0 --- ...{PDT-3.25-GCCcore-6.4.0.eb => PDT-3.25-GCCcore-8.2.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/PDT/{PDT-3.25-GCCcore-6.4.0.eb => PDT-3.25-GCCcore-8.2.0.eb} (88%) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.2.0.eb similarity index 88% rename from easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.2.0.eb index 2942a9934d1..06de279ba5f 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-8.2.0.eb @@ -1,7 +1,7 @@ ## # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # -# Copyright:: Copyright 2013-2018 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer # License:: 3-clause BSD @@ -23,7 +23,7 @@ description = """ supporting common PDB operations. """ -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['http://tau.uoregon.edu/pdt_releases/'] sources = ['pdtoolkit-%(version)s.tar.gz'] @@ -33,7 +33,7 @@ checksums = [ builddependencies = [ # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), + ('binutils', '2.31.1'), ] moduleclass = 'perf' From 47e3c30ae39bf76a865d0eb9babb66d418b11c72 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 11:08:21 +0200 Subject: [PATCH 1560/5331] Bump OPARI2 to v2.0.4 and use GCCcore 8.2.0 --- ...CCcore-6.4.0.eb => OPARI2-2.0.4-GCCcore-8.2.0.eb} | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/o/OPARI2/{OPARI2-2.0.3-GCCcore-6.4.0.eb => OPARI2-2.0.4-GCCcore-8.2.0.eb} (74%) diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.4-GCCcore-8.2.0.eb similarity index 74% rename from easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.4-GCCcore-8.2.0.eb index b1d0a5dbcdc..9a735e64042 100644 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.4-GCCcore-8.2.0.eb @@ -1,7 +1,7 @@ ## # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # -# Copyright:: Copyright 2013-2018 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer # License:: 3-clause BSD @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'OPARI2' -version = '2.0.3' +version = '2.0.4' homepage = 'http://www.score-p.org' description = """ @@ -23,17 +23,17 @@ description = """ to the POMP2 measurement interface. """ -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] +source_urls = ['http://www.vi-hps.org/cms/upload/packages/opari2/'] sources = [SOURCELOWER_TAR_GZ] checksums = [ - '7e2efcfbc99152ee6e31454ef4fb747f77165691539d5d2c1df2abc4612de86c', # opari2-2.0.3.tar.gz + 'f69e324792f66780b473daf2b3c81f58ee8188adc72b6fe0dacf43d4c1a0a131', # opari2-2.0.4.tar.gz ] builddependencies = [ # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), + ('binutils', '2.31.1'), ] sanity_check_paths = { From 08f723a9e1985b2a3e6218a6500bfa6808ca8a7e Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 11:11:32 +0200 Subject: [PATCH 1561/5331] Bump CubeWriter to v4.4.2 and use GCCcore 8.2.0 --- ...core-6.4.0.eb => CubeWriter-4.4.2-GCCcore-8.2.0.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/c/CubeWriter/{CubeWriter-4.4-GCCcore-6.4.0.eb => CubeWriter-4.4.2-GCCcore-8.2.0.eb} (85%) diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.2-GCCcore-8.2.0.eb similarity index 85% rename from easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.2-GCCcore-8.2.0.eb index 31c04d8f44e..17f0df4e6db 100644 --- a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.2-GCCcore-8.2.0.eb @@ -1,7 +1,7 @@ ## # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # -# Copyright:: Copyright 2018 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer # License:: 3-clause BSD # @@ -12,7 +12,7 @@ easyblock = 'EB_Score_minus_P' name = 'CubeWriter' -version = '4.4' +version = '4.4.2' homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' description = """ @@ -26,17 +26,17 @@ description = """ This module provides the Cube high-performance C writer library component. """ -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] sources = ['cubew-%(version)s.tar.gz'] checksums = [ - 'b1d6fecb546bc645ced430ea3fc166e85835f3b997d4e5f0dece71919fc95a99', # cubew-4.4.tar.gz + '31a71e9a05e6523de2b86b4026821bbb75fb411eb5b18ae38b27c1f44158014a', # cubew-4.4.2.tar.gz ] builddependencies = [ # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), + ('binutils', '2.31.1'), ('pkg-config', '0.29.2'), ] From 907bfe3f424ef4818b575eb8d0d52b8fe8b4671d Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 11:16:23 +0200 Subject: [PATCH 1562/5331] Bump CubeLib to v4.4.3 and use GCCcore 8.2.0 --- ...GCCcore-6.4.0.eb => CubeLib-4.4.3-GCCcore-8.2.0.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/c/CubeLib/{CubeLib-4.4-GCCcore-6.4.0.eb => CubeLib-4.4.3-GCCcore-8.2.0.eb} (85%) diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4.3-GCCcore-8.2.0.eb similarity index 85% rename from easybuild/easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/c/CubeLib/CubeLib-4.4.3-GCCcore-8.2.0.eb index cd5e804916a..61861e220be 100644 --- a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4.3-GCCcore-8.2.0.eb @@ -1,7 +1,7 @@ ## # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # -# Copyright:: Copyright 2018 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer # License:: 3-clause BSD # @@ -12,7 +12,7 @@ easyblock = 'EB_Score_minus_P' name = 'CubeLib' -version = '4.4' +version = '4.4.3' homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' description = """ @@ -27,17 +27,17 @@ description = """ command-line tools. """ -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] sources = [SOURCELOWER_TAR_GZ] checksums = [ - '77548e1732fa5e82b13cc8465c8a21349bf42b45a382217d2e70d18576741d5c', # cubelib-4.4.tar.gz + 'bcd4fa81a5ba37194e590a5d7c3e6c44b448f5e156a175837b77c21206847a8d', # cubelib-4.4.3.tar.gz ] builddependencies = [ # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), + ('binutils', '2.31.1'), ('pkg-config', '0.29.2'), ] From 59664cb1c51b5f2ba7209f264f0f99de8bfcb924 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 11:22:42 +0200 Subject: [PATCH 1563/5331] Bump CubeGUI to v4.4.3 using CubeLib v4.4.3 and GCCcore 8.2.0 --- ...ore-6.4.0.eb => CubeGUI-4.4.3-GCCcore-8.2.0.eb} | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/c/CubeGUI/{CubeGUI-4.4-GCCcore-6.4.0.eb => CubeGUI-4.4.3-GCCcore-8.2.0.eb} (82%) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4.3-GCCcore-8.2.0.eb similarity index 82% rename from easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4.3-GCCcore-8.2.0.eb index 391ad730c4a..bcae9c3a646 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4.3-GCCcore-8.2.0.eb @@ -1,7 +1,7 @@ ## # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # -# Copyright:: Copyright 2018 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer # License:: 3-clause BSD # @@ -12,7 +12,7 @@ easyblock = 'EB_Score_minus_P' name = 'CubeGUI' -version = '4.4' +version = '4.4.3' homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' description = """ @@ -26,22 +26,22 @@ description = """ This module provides the Cube graphical report explorer. """ -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] sources = [SOURCELOWER_TAR_GZ] checksums = [ - '0620bae3ac357d0486ce7f5f97e448eeb2494c9a31865b679380ee08c6750e70', # cubegui-4.4.tar.gz + 'bf4b0f2ff68507ff82ba24eb4895aed961710dae16d783c222a12f152440cf36', # cubegui-4.4.3.tar.gz ] builddependencies = [ # use same binutils version that was used when building GCCcore - ('binutils', '2.28'), - ('CubeLib', '4.4'), + ('binutils', '2.31.1'), + ('CubeLib', '4.4.3'), ] dependencies = [ - ('Qt5', '5.10.1'), + ('Qt5', '5.12.3'), ] sanity_check_paths = { From d46dd53f6cc60a548c88fd5c7e852b01278e350b Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 11:29:39 +0200 Subject: [PATCH 1564/5331] Rework Cube convenience bundle --- ...Ccore-6.4.0.eb => Cube-20190321-GCCcore-8.2.0.eb} | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/c/Cube/{Cube-4.4-GCCcore-6.4.0.eb => Cube-20190321-GCCcore-8.2.0.eb} (84%) diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/Cube/Cube-20190321-GCCcore-8.2.0.eb similarity index 84% rename from easybuild/easyconfigs/c/Cube/Cube-4.4-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/c/Cube/Cube-20190321-GCCcore-8.2.0.eb index 5e0a4c3961a..c86e8e8a3cf 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-20190321-GCCcore-8.2.0.eb @@ -1,7 +1,7 @@ ## # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild # -# Copyright:: Copyright 2018 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany # Authors:: Markus Geimer # License:: 3-clause BSD # @@ -12,7 +12,7 @@ easyblock = 'Bundle' name = 'Cube' -version = '4.4' +version = '20190321' homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' description = """ @@ -28,15 +28,15 @@ description = """ command-line tools, and the graphical report explorer. """ -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} # Pure bundle -- no need to specify 'binutils' used when building GCCcore # toolchain as build dependency dependencies = [ - ('CubeWriter', '4.4'), - ('CubeLib', '4.4'), - ('CubeGUI', '4.4'), + ('CubeWriter', '4.4.2'), + ('CubeLib', '4.4.3'), + ('CubeGUI', '4.4.3'), ] moduleclass = 'perf' From 350e8d1f5a04ceb44ed53106b40852e83d381649 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 13:20:34 +0200 Subject: [PATCH 1565/5331] Add PAPI for GCCcore 8.2.0 --- .../p/PAPI/PAPI-5.7.0-GCCcore-8.2.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-5.7.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.7.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.7.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..3215fa7af4b --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.7.0-GCCcore-8.2.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.7.0' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d1a3bb848e292c805bc9f29e09c27870e2ff4cda6c2fba3b7da8b4bba6547589'] + +builddependencies = [ + ('binutils', '2.31.1'), +] + +start_dir = 'src' + +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' From 77ef3310119df6c826a359a4538ba8e8c7602dce Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 13:33:44 +0200 Subject: [PATCH 1566/5331] Bump Score-P to v5.0 and update dependencies --- .../s/Score-P/Score-P-5.0-gompi-2019a.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-5.0-gompi-2019a.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-5.0-gompi-2019a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-5.0-gompi-2019a.eb new file mode 100644 index 00000000000..f87087b32cc --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-5.0-gompi-2019a.eb @@ -0,0 +1,62 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Score-P' +version = '5.0' + +homepage = 'http://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2019a'} + +source_urls = ['http://www.vi-hps.org/cms/upload/packages/scorep/'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = [ + '0651614eacfc92ffbe5264a3efebd0803527ae6e8b11f7df99a56a02c37633e1', # scorep-5.0.tar.gz +] + +builddependencies = [ + ('CubeLib', '4.4.3'), + ('CubeWriter', '4.4.2'), + # Unwinding/sampling support (optional): + ('libunwind', '1.3.1'), +] + +dependencies = [ + # binutils is implicitly available via GCC toolchain + # ('binutils', '2.31.1'), + ('OPARI2', '2.0.4'), + ('OTF2', '2.1.1'), + # Hardware counter support (optional): + ('PAPI', '5.7.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/scorep', 'include/scorep/SCOREP_User.h', + ('lib/libscorep_adapter_mpi_event.a', 'lib64/libscorep_adapter_mpi_event.a'), + ('lib/libscorep_adapter_mpi_event.%s' % SHLIB_EXT, 'lib64/libscorep_adapter_mpi_event.%s' % SHLIB_EXT)], + 'dirs': [], +} + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 82c2d98e16d0f5eff8840eb303bd208b7c012579 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 13:33:58 +0200 Subject: [PATCH 1567/5331] Bump Scalasca to v2.5 and update dependencies --- ...i-2018a.eb => Scalasca-2.5-gompi-2019a.eb} | 16 ++--- .../s/Score-P/Score-P-4.0-gompi-2018a.eb | 62 ------------------- 2 files changed, 8 insertions(+), 70 deletions(-) rename easybuild/easyconfigs/s/Scalasca/{Scalasca-2.4-gompi-2018a.eb => Scalasca-2.5-gompi-2019a.eb} (79%) delete mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-4.0-gompi-2018a.eb diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.4-gompi-2018a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.5-gompi-2019a.eb similarity index 79% rename from easybuild/easyconfigs/s/Scalasca/Scalasca-2.4-gompi-2018a.eb rename to easybuild/easyconfigs/s/Scalasca/Scalasca-2.5-gompi-2019a.eb index 016bd7a4273..668ba474f36 100644 --- a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.4-gompi-2018a.eb +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.5-gompi-2019a.eb @@ -1,6 +1,6 @@ ## # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# Copyright:: Copyright 2013-2018 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr # Markus Geimer # License:: 3-clause BSD @@ -12,7 +12,7 @@ easyblock = 'EB_Score_minus_P' name = 'Scalasca' -version = '2.4' +version = '2.5' homepage = 'http://www.scalasca.org/' description = """ @@ -23,23 +23,23 @@ description = """ in exploring their causes. """ -toolchain = {'name': 'gompi', 'version': '2018a'} +toolchain = {'name': 'gompi', 'version': '2019a'} source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] sources = [SOURCELOWER_TAR_GZ] checksums = [ - '4a895868258030f700a635eac93d36764f60c8c63673c7db419ea4bcc6b0b760', # scalasca-2.4.tar.gz + '7dfa01e383bfb8a4fd3771c9ea98ff43772e415009d9f3c5f63b9e05f2dde0f6', # scalasca-2.5.tar.gz ] builddependencies = [ - ('CubeWriter', '4.4'), + ('CubeWriter', '4.4.2'), ] dependencies = [ - ('CubeGUI', '4.4'), - ('CubeLib', '4.4'), + ('CubeGUI', '4.4.3'), + ('CubeLib', '4.4.3'), ('OTF2', '2.1.1'), - ('Score-P', '4.0'), + ('Score-P', '5.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-4.0-gompi-2018a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-4.0-gompi-2018a.eb deleted file mode 100644 index 3e5c793655c..00000000000 --- a/easybuild/easyconfigs/s/Score-P/Score-P-4.0-gompi-2018a.eb +++ /dev/null @@ -1,62 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# Copyright:: Copyright 2013-2018 Juelich Supercomputing Centre, Germany -# Authors:: Bernd Mohr -# Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_Score_minus_P' - -name = 'Score-P' -version = '4.0' - -homepage = 'http://www.score-p.org' -description = """ - The Score-P measurement infrastructure is a highly scalable and easy-to-use - tool suite for profiling, event tracing, and online analysis of HPC - applications. -""" - -toolchain = {'name': 'gompi', 'version': '2018a'} - -source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] -sources = ['scorep-%(version)s.tar.gz'] -checksums = [ - 'c050525606965950ad9b35c14077b88571bcf9bfca08599279a3d8d1bb00e655', # scorep-4.0.tar.gz -] - -builddependencies = [ - ('CubeLib', '4.4'), - ('CubeWriter', '4.4'), - # Unwinding/sampling support (optional): - ('libunwind', '1.2.1'), -] - -dependencies = [ - # binutils is implicitly available via GCC toolchain - # ('binutils', '2.28'), - ('OPARI2', '2.0.3'), - ('OTF2', '2.1.1'), - # Hardware counter support (optional): - ('PAPI', '5.5.1'), - # PDT source-to-source instrumentation support (optional): - ('PDT', '3.25'), -] - -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/scorep', 'include/scorep/SCOREP_User.h', - ('lib/libscorep_adapter_mpi_event.a', 'lib64/libscorep_adapter_mpi_event.a'), - ('lib/libscorep_adapter_mpi_event.%s' % SHLIB_EXT, 'lib64/libscorep_adapter_mpi_event.%s' % SHLIB_EXT)], - 'dirs': [], -} - -# Ensure that local metric documentation is found by CubeGUI -modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} - -moduleclass = 'perf' From 27cca42c73160796c9e7ec57c117ef0214a29046 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 May 2019 14:04:00 +0200 Subject: [PATCH 1568/5331] Add missing sanity_check_paths to Pango. --- easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb | 6 ++++++ easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb | 6 ++++++ 10 files changed, 60 insertions(+) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb index a69bff0ec36..6766a2171f8 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-foss-2016a.eb @@ -25,6 +25,12 @@ dependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb index f9db731af7c..5baa8348076 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.39.0-intel-2016a.eb @@ -25,6 +25,12 @@ dependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb index 7a6e824e2c2..9a4d1667a7a 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb @@ -34,6 +34,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb index 35fe9dce66a..5940c160c5b 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb @@ -34,6 +34,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb index 0a7f75f9998..7adedf373fd 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.12-intel-2017a.eb @@ -28,6 +28,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb index 91f70c3f43f..8e245d82779 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-foss-2017b.eb @@ -28,6 +28,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb index 4b6cb5c3ad1..34631ccf210 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.14-intel-2017b.eb @@ -28,6 +28,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb index f806f291d7f..584bf1cf1fd 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-foss-2016b.eb @@ -28,6 +28,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb index ec003df5386..f74760234e8 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.3-intel-2016b.eb @@ -28,6 +28,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb index 81ecf8512a3..5ba6ce875ff 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.5-intel-2017a.eb @@ -28,6 +28,12 @@ builddependencies = [ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static --enable-shared " +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + modextrapaths = { 'GI_TYPELIB_PATH': 'share', 'XDG_DATA_DIRS': 'share', From b4de7a0aa5d2294ccc336faa6498ca2d44dae2cb Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 14:37:19 +0200 Subject: [PATCH 1569/5331] Add `pkg-config` to all remaining `DBus` easyconfigs as build dep --- .../d/DBus/DBus-1.10.12-intel-2016b.eb | 5 ++++ .../d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb | 1 + .../d/DBus/DBus-1.10.8-foss-2016a.eb | 5 ++++ .../d/DBus/DBus-1.10.8-intel-2016a.eb | 5 ++++ .../d/DBus/DBus-1.11.20-intel-2017a.eb | 4 +++ .../d/DBus/DBus-1.13.0-intel-2017b.eb | 4 +++ .../pkg-config-0.29.2-intel-2017b.eb | 27 +++++++++++++++++++ 7 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb index 7697871a459..eb7e719c675 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb @@ -14,6 +14,11 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['210a79430b276eafc6406c71705e9140d25b9956d18068df98a70156dc0e475d'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] sanity_check_paths = { 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb index 36b727c1789..9999484b706 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.20-GCCcore-6.4.0.eb @@ -22,6 +22,7 @@ checksums = ['e574b9780b5425fde4d973bb596e7ea0f09e00fe2edd662da9016e976c460b48'] builddependencies = [ ('binutils', '2.28'), + ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb index 7dab289eff3..46fffa56214 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb @@ -14,6 +14,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['baf3d22baa26d3bdd9edc587736cd5562196ce67996d65b82103bedbe1f0c014'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] sanity_check_paths = { 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb index e221d7bbc5c..ea6580d4e75 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -14,6 +14,11 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['baf3d22baa26d3bdd9edc587736cd5562196ce67996d65b82103bedbe1f0c014'] + +builddependencies = [ + ('pkg-config', '0.29.1'), +] sanity_check_paths = { 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.11.20-intel-2017a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.11.20-intel-2017a.eb index 6a30192f7f1..cd003480eff 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.11.20-intel-2017a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.11.20-intel-2017a.eb @@ -19,6 +19,10 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] checksums = ['7fd9d0536f7ec2f2afc94b84d5b5487f88c464e8d47c661d8e0b54aa83974bfa'] +builddependencies = [ + ('pkg-config', '0.29.2'), +] + configopts = '--without-systemdsystemunitdir' sanity_check_paths = { diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.0-intel-2017b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.0-intel-2017b.eb index be0d52b5a2d..a29b8fbd3f4 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.13.0-intel-2017b.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.0-intel-2017b.eb @@ -16,6 +16,10 @@ source_urls = ['http://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_GZ] checksums = ['837abf414c0cdac4c8586ea6f93a999446470b10abcfeefe19ed8a7921854d2e'] +builddependencies = [ + ('pkg-config', '0.29.2'), +] + dependencies = [('expat', '2.2.4')] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb new file mode 100644 index 00000000000..4ba4d2f4ddd --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' From f4564a6f3df07a5d197e2fbbc6d46b1d22ec2f23 Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Fri, 10 May 2019 14:46:19 +0200 Subject: [PATCH 1570/5331] IPython-5.8.0: changed exts order according to #7647, removed certifi. --- .../IPython-5.8.0-foss-2018b-Python-2.7.15.eb | 116 +++++++++--------- ...IPython-5.8.0-intel-2018b-Python-2.7.15.eb | 116 +++++++++--------- 2 files changed, 112 insertions(+), 120 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb index dab61d49acd..2fcc937bde5 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-foss-2018b-Python-2.7.15.eb @@ -31,40 +31,15 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], - }), - ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + ('ipython', version, { + 'modulename': 'IPython', + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('pexpect', '4.6.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], }), - ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], - }), - ('futures', '3.2.0', { - 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], - 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], - }), - ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], - 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], - }), - ('ptyprocess', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], - }), - ('simplegeneric', '0.8.1', { - 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], - 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], - }), ('scandir', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], @@ -77,6 +52,23 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], }), + ('wcwidth', '0.1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + }), + ('prompt_toolkit', '1.0.15', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], + 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], + }), + ('ptyprocess', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), ('traitlets', '4.3.2', { 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], @@ -89,14 +81,6 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], }), - ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], - 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], - }), - ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], - 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], - }), ('testpath', '0.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], @@ -105,13 +89,21 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), - ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], - 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + ('configparser', '3.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], + 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), - ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], - 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], + ('defusedxml', '0.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], + 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], + }), + ('nbconvert', '5.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], + }), + ('nbformat', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('MarkupSafe', '1.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], @@ -145,6 +137,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/pyrsistent/'], 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), ('attrs', '19.1.0', { 'modulename': 'attr', 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], @@ -158,11 +154,6 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], }), - ('ipython', version, { - 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], - 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], - }), ('pandocfilters', '1.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], @@ -180,26 +171,31 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), - ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], - }), ('mistune', '0.8.4', { 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], }), - ('defusedxml', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], - 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], - }), - ('nbconvert', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], - }), ('terminado', '0.8.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), + ('futures', '3.2.0', { + 'modulename': 'concurrent.futures', + 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], + 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], + }), ('tornado', '5.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb index 2d0c1c43dba..7dec9dbe500 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.8.0-intel-2018b-Python-2.7.15.eb @@ -31,40 +31,15 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], - }), - ('certifi', '2018.11.29', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - 'checksums': ['47f9c83ef4c0c621eaef743f133f09fa8a74a9b75f037e8624f83bd1b6626cb7'], + ('ipython', version, { + 'modulename': 'IPython', + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], }), ('pexpect', '4.6.0', { 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], 'checksums': ['2a8e88259839571d1251d278476f3eec5db26deb73a70be5ed5dc5435e418aba'], }), - ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], - }), - ('futures', '3.2.0', { - 'modulename': 'concurrent.futures', - 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], - 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], - }), - ('functools32', '3.2.3-2', { - 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], - 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], - }), - ('ptyprocess', '0.6.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], - 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], - }), - ('simplegeneric', '0.8.1', { - 'source_tmpl': 'simplegeneric-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], - 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], - }), ('scandir', '1.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'], 'checksums': ['44975e209c4827fc18a3486f257154d34ec6eaec0f90fef0cca1caa482db7064'], @@ -77,6 +52,23 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], }), + ('wcwidth', '0.1.7', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + }), + ('prompt_toolkit', '1.0.15', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], + 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], + }), + ('ptyprocess', '0.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), ('traitlets', '4.3.2', { 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], 'checksums': ['9c4bd2d267b7153df9152698efb1050a5d84982d3384a37b2c1f7723ba3e7835'], @@ -89,14 +81,6 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/j/jedi/'], 'checksums': ['b7493f73a2febe0dc33d51c99b474547f7f6c0b2c8fb2b21f453eef204c12148'], }), - ('configparser', '3.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], - 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], - }), - ('backports.shutil_get_terminal_size', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], - 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], - }), ('testpath', '0.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/t/testpath/'], 'checksums': ['b694b3d9288dbd81685c5d2e7140b81365d46c29f5db4bc659de5aa6b98780f8'], @@ -105,13 +89,21 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], }), - ('wcwidth', '0.1.7', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], - 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], + ('configparser', '3.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/configparser/'], + 'checksums': ['5308b47021bc2340965c371f0f058cc6971a04502638d4244225c49d80db273a'], }), - ('prompt_toolkit', '1.0.15', { - 'source_urls': ['https://pypi.python.org/packages/source/p/prompt_toolkit/'], - 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], + ('defusedxml', '0.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], + 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], + }), + ('nbconvert', '5.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], + }), + ('nbformat', '4.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], }), ('MarkupSafe', '1.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/m/MarkupSafe/'], @@ -145,6 +137,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/pyrsistent/'], 'checksums': ['3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2'], }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), ('attrs', '19.1.0', { 'modulename': 'attr', 'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'], @@ -158,11 +154,6 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], }), - ('ipython', version, { - 'modulename': 'IPython', - 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], - 'checksums': ['4bac649857611baaaf76bc82c173aa542f7486446c335fe1a6c05d0d491c8906'], - }), ('pandocfilters', '1.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/pandocfilters/'], 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], @@ -180,26 +171,31 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], 'checksums': ['ba70754aa680300306c699790128f6fbd8c306ee5927976cbe48adacf240c0b7'], }), - ('nbformat', '4.4.0', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], - 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], - }), ('mistune', '0.8.4', { 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], }), - ('defusedxml', '0.5.0', { - 'source_urls': ['https://pypi.python.org/packages/source/d/defusedxml/'], - 'checksums': ['24d7f2f94f7f3cb6061acb215685e5125fbcdc40a857eff9de22518820b0a4f4'], - }), - ('nbconvert', '5.4.1', { - 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], - 'checksums': ['302554a2e219bc0fc84f3edd3e79953f3767b46ab67626fdec16e38ba3f7efe4'], - }), ('terminado', '0.8.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], 'checksums': ['55abf9ade563b8f9be1f34e4233c7b7bde726059947a593322e8a553cc4c067a'], }), + ('futures', '3.2.0', { + 'modulename': 'concurrent.futures', + 'source_urls': ['https://pypi.python.org/packages/source/f/futures/'], + 'checksums': ['9ec02aa7d674acb8618afb127e27fde7fc68994c0437ad759fa094a574adb265'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], + }), ('tornado', '5.1.1', { 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], From 41dcb6678f419c6555c2ca77631c7618e1d2473a Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Fri, 10 May 2019 14:03:47 +0100 Subject: [PATCH 1571/5331] zlib changed to version 1.2.11 --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb index aeb80c3c5ae..d4bcf5b48f6 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb @@ -24,7 +24,7 @@ patches = [ ] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.11'), ('Szip', '2.1.1'), ] From 037ffee888deca1bfed16b5c2964a6c6110c25db Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 15:17:17 +0200 Subject: [PATCH 1572/5331] Add missing checksum --- .../easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb index 4ba4d2f4ddd..28a39d8e85b 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://pkg-config.freedesktop.org/releases/'] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] # don't use PAX, it might break. tar_config_opts = True From f79459635d044171df1e7cd9dbe6a38a46648c68 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Fri, 10 May 2019 14:24:20 +0100 Subject: [PATCH 1573/5331] Incorporating CUDA-9.2.88-1-ppc64le.eb from Dugan at Warwick --- .../c/CUDA/CUDA-9.2.88-1-ppc64le.eb | 46 ----------------- .../easyconfigs/c/CUDA/CUDA-9.2.88-ppc64le.eb | 51 +++++++++++++++++++ .../easyconfigs/f/fosscuda/fosscuda-2018b.eb | 2 +- .../easyconfigs/g/gcccuda/gcccuda-2018b.eb | 2 +- .../easyconfigs/g/gompic/gompic-2018b.eb | 2 +- 5 files changed, 54 insertions(+), 49 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-1-ppc64le.eb create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-ppc64le.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-1-ppc64le.eb b/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-1-ppc64le.eb deleted file mode 100644 index 005ab9d430d..00000000000 --- a/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-1-ppc64le.eb +++ /dev/null @@ -1,46 +0,0 @@ -# This easyconfig was created by the BEAR Software team at the University of Birmingham -easyblock = 'Tarball' -name = 'CUDA' -version = '9.2.88-1' -versionsuffix = '-ppc64le' - -homepage = 'https://developer.nvidia.com/cuda-toolkit' -description = """CUDA (formerly Compute Unified Device Architecture) is a parallel - computing platform and programming model created by NVIDIA and implemented by the - graphics processing units (GPUs) that they produce. CUDA gives developers access - to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -# Manually create the source tarball like this: -# Install CUDA 9.2.88 on a ppc64le machine (via the RPMS) -# for x in $(rpm -qa |grep cuda); do echo "$x "; done > cuda_rpms -# rpm -ql $(cuda_rpms) > cuda_files -# tar cvzf cuda-9.2.88-1.ppc64le.tar.gz $(cuda_files) -sources = ['cuda-%(version)s.ppc64le.tar.gz'] -checksums = ['4a220b07919162c891c0e1b6327057d9775d74b9ba89c995a05600ab9d326d78'] - -postinstallcmds = [ - # We don't want the nccl libraries that may have been bundled with CUDA. They cause conflicts in PyTorch. - 'cd %(installdir)s && find . -name *nccl* -delete', - 'cd %(installdir)s && mv usr/local/cuda-9.2/* . ', - 'cd %(installdir)s && mv usr/lib64/pkgconfig . ', - 'cd %(installdir)s && rmdir usr/local/cuda-9.2 && rmdir usr/local && rmdir usr/lib64 && rmdir usr', -] - -modextrapaths = { - 'LD_LIBRARY_PATH': ('targets/ppc64le-linux/lib', 'extras/CUPTI/lib64'), - 'LIBRARY_PATH': 'lib64' -} - -modextravars = { - 'CUDA_HOME': '', - 'CUDA_ROOT': '', -} - -sanity_check_paths = { - 'files': ['bin/nvcc', 'bin/ptxas'], - 'dirs': ['include', 'pkgconfig'], -} - -moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-ppc64le.eb b/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-ppc64le.eb new file mode 100644 index 00000000000..6951316f1fa --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88-ppc64le.eb @@ -0,0 +1,51 @@ +# Contributed by the Scientific Computing RTP, University of Warwick +easyblock = 'Binary' +name = 'CUDA' +version = '9.2.88' +versionsuffix = '-ppc64le' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +base_filename = 'cuda-repo-rhel7-9-2-local-%(version)s-1.ppc64le' +filename_rpm = '%s.rpm' % base_filename + +sources = [{ + 'source_urls': ['https://developer.nvidia.com/compute/cuda/9.2/Prod2/local_installers/'], + 'filename': '%s' % filename_rpm, + 'download_filename': '%s' % base_filename, +}] + +checksums = ['49bcbb6479e933f0851dd4e291e6fdff627076cf7b367d7f74786e13ce07ea0c'] + +extract_sources = False + +install_cmd = "mkdir -p %(builddir)s/repo/ && " +install_cmd += "mkdir -p %(builddir)s/extract/ && " +install_cmd += "rpm2cpio %s | (cd %%(builddir)s/repo/; cpio -idmv) && " % filename_rpm +install_cmd += "for f in $(find %(builddir)s/repo/ -name \"cuda*.rpm\" -print); do rpm2cpio $f | (cd %(builddir)s/extract/; cpio -idmv) ; done && " +install_cmd += "mv %(builddir)s/extract/usr/local/cuda-%(version_major_minor)s/* %(installdir)s && " +install_cmd += "mv %(builddir)s/extract/usr/lib64/pkgconfig %(installdir)s " + + +modextrapaths = { + 'LD_LIBRARY_PATH': ('targets/ppc64le-linux/lib', 'extras/CUPTI/lib64'), + 'LIBRARY_PATH': 'lib64', + 'CUDA_HOME': '', + 'CUDA_ROOT': '', +} + +modextravars = { +} + +sanity_check_paths = { + 'files': ['bin/nvcc', 'bin/ptxas'], + 'dirs': ['include', 'pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb index 844664be610..e1e516bb256 100644 --- a/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb @@ -25,7 +25,7 @@ comp_mpi_tc = (comp_mpi_tc_name, version) dependencies = [ ('GCC', gccver), # part of gompic {'name': 'CUDA', 'version': '9.2.88', 'toolchain': ('GCC', gccver), 'arch': True}, - {'name': 'CUDA', 'version': '9.2.88-1', 'toolchain': ('dummy', 'dummy'), + {'name': 'CUDA', 'version': '9.2.88', 'toolchain': ('dummy', 'dummy'), 'versionsuffix': '-ppc64le', 'arch': 'POWER'}, ('OpenMPI', '3.1.1', '', ('gcccuda', version)), # part of gompic (blaslib, blasver, '', ('GCC', gccver)), diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb index b32f0d87c3f..1b65e2c3cba 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb @@ -16,7 +16,7 @@ comp = (comp_name, comp_ver) dependencies = [ comp, {'name': 'CUDA', 'version': '9.2.88', 'toolchain': comp, 'arch': True}, - {'name': 'CUDA', 'version': '9.2.88-1', 'toolchain': ('dummy', 'dummy'), + {'name': 'CUDA', 'version': '9.2.88', 'toolchain': ('dummy', 'dummy'), 'versionsuffix': '-ppc64le', 'arch': 'POWER'}, ] diff --git a/easybuild/easyconfigs/g/gompic/gompic-2018b.eb b/easybuild/easyconfigs/g/gompic/gompic-2018b.eb index 65c213f9842..9217eda5a45 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2018b.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2018b.eb @@ -17,7 +17,7 @@ comp = (comp_name, comp_ver) dependencies = [ comp, # part of gcccuda {'name': 'CUDA', 'version': '9.2.88', 'toolchain': comp, 'arch': True}, # part of gcccuda - {'name': 'CUDA', 'version': '9.2.88-1', 'toolchain': ('dummy', 'dummy'), + {'name': 'CUDA', 'version': '9.2.88', 'toolchain': ('dummy', 'dummy'), 'versionsuffix': '-ppc64le', 'arch': 'POWER'}, # part of gcccuda ('OpenMPI', '3.1.1', '', ('gcccuda', version)), ] From 4c55de051c43521a7bbfdfd81b2155824bf8084e Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Fri, 10 May 2019 14:28:40 +0100 Subject: [PATCH 1574/5331] Drop not used zlib easyconfig --- .../z/zlib/zlib-1.2.8-GCCcore-7.3.0.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-7.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-7.3.0.eb deleted file mode 100644 index 7e9a1629cf5..00000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-7.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -# Contribution from the Crick HPC team -# uploaded by J. Sassmannshausen - -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.2.8' - -homepage = 'http://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -toolchainopts = {'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] -checksums = ['36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d'] - -builddependencies = [('binutils', '2.30')] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' From 0dd3c364fd76fbe112ef5164898cc9b5f8dfb6f9 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Fri, 10 May 2019 14:31:34 +0100 Subject: [PATCH 1575/5331] zlib changed to version 1.2.11 --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2018b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2018b.eb index eb564213be5..a0d82954cfe 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2018b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2018b.eb @@ -24,7 +24,7 @@ patches = [ ] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.11'), ('Szip', '2.1.1'), ] From ef24a9b53a93b325f3c914abb361244f15a40bba Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 15:40:00 +0200 Subject: [PATCH 1576/5331] Remove config that is already covered by `pkg-config-0.29.2-GCCcore-6.4.0.eb` --- .../pkg-config-0.29.2-intel-2017b.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb deleted file mode 100644 index 28a39d8e85b..00000000000 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-intel-2017b.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'pkg-config' -version = '0.29.2' - -homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' -description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the - correct compiler options on the command line so an application can use - gcc -o test test.c `pkg-config --libs --cflags glib-2.0` - for instance, rather than hard-coding values on where to find glib (or other libraries).""" - -toolchain = {'name': 'intel', 'version': '2017b'} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['https://pkg-config.freedesktop.org/releases/'] -checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] - -# don't use PAX, it might break. -tar_config_opts = True - -configopts = " --with-internal-glib" - -sanity_check_paths = { - 'files': ['bin/pkg-config'], - 'dirs': [], -} - -moduleclass = 'devel' From 4225b9bf86707753e85b535fa3c9cb86b95a480e Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 15:43:06 +0200 Subject: [PATCH 1577/5331] Add `expat` dependency --- easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb | 4 ++++ easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb | 4 ++++ easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb | 4 ++++ easybuild/easyconfigs/d/DBus/DBus-1.11.20-intel-2017a.eb | 4 ++++ 4 files changed, 16 insertions(+) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb index eb7e719c675..d8629f82937 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.12-intel-2016b.eb @@ -20,6 +20,10 @@ builddependencies = [ ('pkg-config', '0.29.1'), ] +dependencies = [ + ('expat', '2.2.0'), +] + sanity_check_paths = { 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb index 46fffa56214..4e0e24f6e70 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-foss-2016a.eb @@ -20,6 +20,10 @@ builddependencies = [ ('pkg-config', '0.29.1'), ] +dependencies = [ + ('expat', '2.1.1'), +] + sanity_check_paths = { 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb index ea6580d4e75..416171db09f 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -20,6 +20,10 @@ builddependencies = [ ('pkg-config', '0.29.1'), ] +dependencies = [ + ('expat', '2.1.1'), +] + sanity_check_paths = { 'files': ['bin/dbus-%s' % x for x in ['cleanup-sockets', 'daemon', 'launch', 'monitor', 'run-session', 'send', 'uuidgen']] + diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.11.20-intel-2017a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.11.20-intel-2017a.eb index cd003480eff..33a34026fb6 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.11.20-intel-2017a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.11.20-intel-2017a.eb @@ -23,6 +23,10 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] +dependencies = [ + ('expat', '2.2.0'), +] + configopts = '--without-systemdsystemunitdir' sanity_check_paths = { From 1fa3e17654e715582fd72f4c828fbc9c7925bd69 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 10 May 2019 16:18:29 +0200 Subject: [PATCH 1578/5331] Try to clean up the dependency hell --- easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb index 416171db09f..a09620e5464 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.10.8-intel-2016a.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('expat', '2.1.1'), + ('expat', '2.1.0'), ] sanity_check_paths = { From 8fb3f38e0926f779d9a648dc37d4269824bdeb48 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 10 May 2019 17:26:45 +0200 Subject: [PATCH 1579/5331] remove zlib dep (it's provided by foss toolchain) --- easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb index f1e422c404a..c1934f83bab 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb @@ -23,7 +23,6 @@ builddependencies = [ dependencies = [ ('GSL', '2.5'), - ('zlib', '1.2.11'), ] files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES.md", "scripts", "VERSION"] From a0cb81ee955d5a335766fbd9e6a0dd5764db8205 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 May 2019 19:42:29 +0200 Subject: [PATCH 1580/5331] Drop libpangoxft from sanity_check_path for Pango 1.40.1 --- easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb index 9a4d1667a7a..e13ad289c3c 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-foss-2016a.eb @@ -36,7 +36,7 @@ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static sanity_check_paths = { 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, - 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb index 5940c160c5b..615d8d213f0 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.40.1-intel-2016a.eb @@ -36,7 +36,7 @@ configopts = "--disable-silent-rules --enable-introspection=yes --enable-static sanity_check_paths = { 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, - 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT], 'dirs': [], } From 1aa0ba12149cd7d870a4000a1f1a8d081a7397e8 Mon Sep 17 00:00:00 2001 From: cclauss Date: Fri, 10 May 2019 20:47:19 +0200 Subject: [PATCH 1581/5331] Old style exceptions are syntax errors in Python 3 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 07428d587cf..cb78e61417e 100644 --- a/setup.py +++ b/setup.py @@ -75,7 +75,7 @@ log.info("Installing with setuptools.setup...") install_package = 'setuptools' -except ImportError, err: +except ImportError as err: log.info("Failed to import setuptools.setup (%s), so falling back to distutils.setup" % err) from distutils.core import setup install_package = 'distutils' From 402752da756b9494c2a2e9b6cc5bc49003317f37 Mon Sep 17 00:00:00 2001 From: fizwit Date: Sat, 11 May 2019 07:15:31 -0700 Subject: [PATCH 1582/5331] GEOS 2019a --- .../GEOS-3.7.2-foss-2019a-Python-3.7.2.eb | 33 +++++++++++++++++++ .../g/GEOS/GEOS-3.7.2_fix-Python3.patch | 27 +++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.7.2-foss-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.7.2_fix-Python3.patch diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.7.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.7.2-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..5f873facfb2 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.7.2-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.7.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['GEOS-%(version)s_fix-Python3.patch'] +checksums = [ + '2166e65be6d612317115bfec07827c11b403c3f303e0a7420a2106bc999d7707', # geos-3.7.2.tar.bz2 + 'e14b54796d9d41261caae64b5a106b4bd8a77f37a51aa9b8ada30d87d208e2e0', # GEOS-3.7.2_fix-Python3.patch +] + +dependencies = [('Python', '3.7.2')] + +builddependencies = [('SWIG', '3.0.12', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.7.2_fix-Python3.patch b/easybuild/easyconfigs/g/GEOS/GEOS-3.7.2_fix-Python3.patch new file mode 100644 index 00000000000..b680f3f7554 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.7.2_fix-Python3.patch @@ -0,0 +1,27 @@ +Fix search for Python library path when configuring with Python 3 +source: GEOS-3.7.2_fix-Python3.patch from easybuild-easyconfigs repository +diff -ruN geos-3.7.2.orig/configure geos-3.7.2/configure +--- geos-3.7.2.orig/configure 2019-05-02 15:29:59.000000000 -0700 ++++ geos-3.7.2/configure 2019-05-07 17:22:57.755195000 -0700 +@@ -19210,18 +19210,19 @@ + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Python library path" >&5 + $as_echo_n "checking for Python library path... " >&6; } + for i in "$base_python_path/lib/python$PYTHON_VERSION/config/" "$base_python_path/lib/python$PYTHON_VERSION/" "$base_python_path/lib/python/config/" "$base_python_path/lib/python/" "$base_python_path/" "$base_python_path/libs/" ; do +- python_path=`find $i -name libpython$PYTHON_VERSION.* -print 2> /dev/null | sed "1q"` ++ python_path=`find $i -name libpython$PYTHON_VERSION*.so* -print 2> /dev/null | sed "1q"` + if test -n "$python_path" ; then + break + fi + done ++ lpython_name=`python -c "import os; print(os.path.split(\"$python_path\")[1].split(\".so\")[0].split(\"lib\")[1])"` + python_path=`echo $python_path | sed "s,/libpython.*$,,"` + { $as_echo "$as_me:${as_lineno-$LINENO}: result: $python_path" >&5 + $as_echo "$python_path" >&6; } + if test -z "$python_path" ; then + as_fn_error $? "cannot find Python library path" "$LINENO" 5 + fi +- PYTHON_LDFLAGS="-L$python_path -lpython$PYTHON_VERSION" ++ PYTHON_LDFLAGS="-L$python_path -l$lpython_name" + + # + python_site=`echo $base_python_path | sed "s/config/site-packages/"` From 6c065e5ccb3c8cce47e60886ead91ec8d172c946 Mon Sep 17 00:00:00 2001 From: fizwit Date: Sat, 11 May 2019 07:59:00 -0700 Subject: [PATCH 1583/5331] NLopt new version 2.6.1 GCCcore 8.2.0 --- .../n/NLopt/NLopt-2.6.1-GCCcore-8.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..9261390007a --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.6.1-GCCcore-8.2.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.6.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = [{ + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ +}] +checksums = ['66d63a505187fb6f98642703bd0ef006fedcae2f9a6d1efa4f362ea919a02650'] + +builddependencies = [ + ('CMake', '3.13.3'), + ('binutils', '2.31.1'), +] + +configopts = '--enable-shared --without-matlab --without-octave' + +sanity_check_paths = { + 'files': ['lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' From 6d500c08b8f712c2339222fd163a25beffcc371a Mon Sep 17 00:00:00 2001 From: cclauss Date: Sat, 11 May 2019 18:44:28 +0200 Subject: [PATCH 1584/5331] setup.py: Update the PyPI trove classifiers --- setup.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index cb78e61417e..c2f0068f832 100644 --- a/setup.py +++ b/setup.py @@ -118,7 +118,11 @@ def get_data_files(): "Intended Audience :: System Administrators", "License :: OSI Approved :: GNU General Public License v2 (GPLv2)", "Operating System :: POSIX :: Linux", - "Programming Language :: Python :: 2.4", + "Programming Language :: Python :: 2.6", + "Programming Language :: Python :: 2.7", + "Programming Language :: Python :: 3.5", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", "Topic :: Software Development :: Build Tools", ], platforms = "Linux", From 31f67b08b54ad1fc39bbc2e8d35aee95c99f090f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 May 2019 15:41:29 +0200 Subject: [PATCH 1585/5331] fix Python classifiers in setup.py, should be (only) Python 2.6 & 2.7 --- setup.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/setup.py b/setup.py index ab6ac620876..b6a538e30ab 100644 --- a/setup.py +++ b/setup.py @@ -113,14 +113,15 @@ def get_data_files(): data_files = get_data_files(), long_description = read("README.rst"), classifiers = [ - "Development Status :: 5 - Production/Stable", - "Environment :: Console", - "Intended Audience :: System Administrators", - "License :: OSI Approved :: GNU General Public License v2 (GPLv2)", - "Operating System :: POSIX :: Linux", - "Programming Language :: Python :: 2.4", - "Topic :: Software Development :: Build Tools", - ], + "Development Status :: 5 - Production/Stable", + "Environment :: Console", + "Intended Audience :: System Administrators", + "License :: OSI Approved :: GNU General Public License v2 (GPLv2)", + "Operating System :: POSIX :: Linux", + "Programming Language :: Python :: 2.6", + "Programming Language :: Python :: 2.7", + "Topic :: Software Development :: Build Tools", + ], platforms = "Linux", # install_requires list is not enforced, because of 'old-and-unmanageable' setup? # do we even want the dependency, since it's artificial? From 2fab54d6ae02d494b3b1b956043bd2d7bf80b013 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 May 2019 07:41:21 +0200 Subject: [PATCH 1586/5331] Reorder things in exts_list to our preferred ordering. --- ...Flow-1.13.1-fosscuda-2019a-Python-3.7.2.eb | 35 ++++++++++--------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb index e9d9d63f875..c41916f1a93 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb @@ -28,21 +28,22 @@ use_pip = True exts_list = [ ('protobuf-python', '3.6.1', { - 'modulename': 'google.protobuf', - 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', 'patches': ['TensorFlow-1.13.1_protobuf-3.6.1.2_fix_26155.patch'], - 'start_dir': 'python', - 'use_pip': False, 'checksums': [ - '40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6', + '40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6', # protobuf-python-3.6.1.tar.gz + # TensorFlow-1.13.1_protobuf-3.6.1.2_fix_26155.patch 'db514d3698d37e329cecdd2245dcd6ff65f2b739a66730f303e8a9f6c107392b', ], + 'start_dir': 'python', + 'use_pip': False, + 'modulename': 'google.protobuf', }), ('absl-py', '0.7.1', { - 'modulename': 'absl', 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], 'checksums': ['b943d1c567743ed0455878fcd60bc28ac9fae38d129d1ccfad58079da00b8951'], + 'modulename': 'absl', }), ('astor', '0.7.1', { 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], @@ -53,19 +54,19 @@ exts_list = [ 'checksums': ['fe939df4583692f0512161ec1c880e0a10e71e6a232da045ab8edd3756fbadf0'], }), ('grpcio', '1.20.1', { - 'modulename': 'grpc', 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], 'checksums': ['84eb47b1a47e206e78f453fb92a155ed0d18d2ca8747f5c67e4b50b9c37180a7'], + 'modulename': 'grpc', }), ('Markdown', '3.1', { 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], 'checksums': ['fc4a6f69a656b8d858d7503bda633f4dd63c2d70cf80abdc6eafa64c4ae8c250'], }), ('tensorboard', version, { - 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], - 'unpack_sources': False, + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'checksums': ['b664fe7772be5670d8b04200342e681af7795a12cd752709aed565c06c0cc196'], + 'unpack_sources': False, }), ('termcolor', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], @@ -76,24 +77,26 @@ exts_list = [ 'checksums': ['0a73e8bb2ff2feecfc5d56e6f458f5b99290ef34f565ffb2665801ff7de6af7a'], }), ('Keras-Applications', '1.0.7', { - 'modulename': 'keras_applications', - 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['60607b2b98868983e5153bf1cc6aa468ba73adc93bc977a90edaa4bc595e69fa'], + 'modulename': 'keras_applications', }), ('Keras-Preprocessing', '1.0.9', { - 'modulename': 'keras_preprocessing', - 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['5e3700117981c2db762e512ed6586638124fac5842170701628088a11aeb51ac'], + 'modulename': 'keras_preprocessing', }), ('tensorflow-estimator', '1.13.0', { - 'source_tmpl': 'tensorflow_estimator-1.13.0-py2.py3-none-any.whl', 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow-estimator'], - 'unpack_sources': False, + 'source_tmpl': 'tensorflow_estimator-1.13.0-py2.py3-none-any.whl', 'checksums': ['7cfdaa3e83e3532f31713713feb98be7ea9f3065722be4267e49b6c301271419'], + 'unpack_sources': False, }), (name, version, { + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', 'patches': [ 'TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', @@ -103,8 +106,6 @@ exts_list = [ 'TensorFlow-1.13.1_fix_protobuf_problem.patch', 'TensorFlow-1.13.1_fix_cudalib_version_for_cuda10.1.patch', ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'checksums': [ '7cd19978e6bc7edc2c847bce19f95515a742b34ea5e28e4389dade35348f58ed', # v1.13.1.tar.gz 'aa53c7f6d42b4a9e91e0ba639d79f69a7db3c0a88c3b8e43d332479b6368391a', # TensorFlow-1.11.0_swig-env.patch From 4185deda3d6ffa8c136c26c43accee4150c24c5c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 May 2019 07:44:02 +0200 Subject: [PATCH 1587/5331] adding easyconfigs: TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb --- ...nsorFlow-1.13.1-foss-2019a-Python-3.7.2.eb | 119 ++++++++++++++++++ 1 file changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..2d69314d4a7 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,119 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '1.13.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True} + +builddependencies = [ + # must be Bazel <= 0.21, and Bazel 0.21.0 fails to install... + ('Bazel', '0.20.0'), + ('protobuf', '3.6.1.2'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('h5py', '2.9.0'), +] + +use_pip = True + +exts_list = [ + ('protobuf-python', '3.6.1', { + 'source_urls': ['https://github.com/google/protobuf/releases/download/v%(version)s/'], + 'source_tmpl': 'protobuf-python-%(version)s.tar.gz', + 'patches': ['TensorFlow-1.13.1_protobuf-3.6.1.2_fix_26155.patch'], + 'checksums': [ + '40f009cb0c190816a52fc21d45c26558ee7d63c3bd511b326bd85739b2fd99a6', # protobuf-python-3.6.1.tar.gz + # TensorFlow-1.13.1_protobuf-3.6.1.2_fix_26155.patch + 'db514d3698d37e329cecdd2245dcd6ff65f2b739a66730f303e8a9f6c107392b', + ], + 'start_dir': 'python', + 'use_pip': False, + 'modulename': 'google.protobuf', + }), + ('absl-py', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/absl-py'], + 'checksums': ['b943d1c567743ed0455878fcd60bc28ac9fae38d129d1ccfad58079da00b8951'], + 'modulename': 'absl', + }), + ('astor', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/astor'], + 'checksums': ['95c30d87a6c2cf89aa628b87398466840f0ad8652f88eb173125a6df8533fb8d'], + }), + ('gast', '0.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gast'], + 'checksums': ['fe939df4583692f0512161ec1c880e0a10e71e6a232da045ab8edd3756fbadf0'], + }), + ('grpcio', '1.20.1', { + 'source_urls': ['https://pypi.python.org/packages/source/g/grpcio'], + 'checksums': ['84eb47b1a47e206e78f453fb92a155ed0d18d2ca8747f5c67e4b50b9c37180a7'], + 'modulename': 'grpc', + }), + ('Markdown', '3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/Markdown'], + 'checksums': ['fc4a6f69a656b8d858d7503bda633f4dd63c2d70cf80abdc6eafa64c4ae8c250'], + }), + ('tensorboard', version, { + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorboard'], + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'checksums': ['b664fe7772be5670d8b04200342e681af7795a12cd752709aed565c06c0cc196'], + 'unpack_sources': False, + }), + ('termcolor', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/termcolor'], + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('Werkzeug', '0.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], + 'checksums': ['0a73e8bb2ff2feecfc5d56e6f458f5b99290ef34f565ffb2665801ff7de6af7a'], + }), + ('Keras-Applications', '1.0.7', { + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Applications'], + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', + 'checksums': ['60607b2b98868983e5153bf1cc6aa468ba73adc93bc977a90edaa4bc595e69fa'], + 'modulename': 'keras_applications', + }), + ('Keras-Preprocessing', '1.0.9', { + 'source_urls': ['https://pypi.python.org/packages/source/K/Keras-Preprocessing'], + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['5e3700117981c2db762e512ed6586638124fac5842170701628088a11aeb51ac'], + 'modulename': 'keras_preprocessing', + }), + ('tensorflow-estimator', '1.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tensorflow-estimator'], + 'source_tmpl': 'tensorflow_estimator-1.13.0-py2.py3-none-any.whl', + 'checksums': ['7cfdaa3e83e3532f31713713feb98be7ea9f3065722be4267e49b6c301271419'], + 'unpack_sources': False, + }), + (name, version, { + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'patches': [ + 'TensorFlow-1.11.0_swig-env.patch', + 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', + 'TensorFlow-1.13.1_lrt-flag.patch', + 'TensorFlow-1.13.1_remove_usrbin_from_linker_bin_path_flag.patch', + 'TensorFlow-1.13.1_fix_protobuf_problem.patch', + ], + 'checksums': [ + '7cd19978e6bc7edc2c847bce19f95515a742b34ea5e28e4389dade35348f58ed', # v1.13.1.tar.gz + 'aa53c7f6d42b4a9e91e0ba639d79f69a7db3c0a88c3b8e43d332479b6368391a', # TensorFlow-1.11.0_swig-env.patch + # TensorFlow-1.11.0_remove-msse-hardcoding.patch + 'a0f00ee4d03bb4fd3a645ee06045cedaf97d0b85675ec35187e9dd7e479d7bb6', + 'b388be35f2581786bcd533b1bfa375165d7f35e38a3aab74570019312816bf1b', # TensorFlow-1.13.1_lrt-flag.patch + # TensorFlow-1.13.1_remove_usrbin_from_linker_bin_path_flag.patch + 'e6122f34557fbe9e705ce1999403053b0ac4bdd058e4a31a182a16446c87bdb3', + # TensorFlow-1.13.1_fix_protobuf_problem.patch + 'd2fab1497078a2980a68adeea4d0f8719be5bef03741ea4775163745a1e52d40', + ], + }), +] + +moduleclass = 'lib' From 8282a0d5b29551d06ec0872fb68a674e848aadf3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 May 2019 12:14:51 +0200 Subject: [PATCH 1588/5331] adding easyconfigs: Theano-1.0.4-fosscuda-2019a.eb --- .../t/Theano/Theano-1.0.4-fosscuda-2019a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019a.eb diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019a.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019a.eb new file mode 100644 index 00000000000..d8db7f69f1a --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-fosscuda-2019a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.0.4' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [ + ('libgpuarray', '0.7.6'), + ('cuDNN', '7.4.2.24'), +] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/theano-cache', 'bin/theano-nose'] + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From 58331e58fb5251394b882d8cdec49ffda3a5da32 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 May 2019 12:49:42 +0200 Subject: [PATCH 1589/5331] adding easyconfigs: Keras-2.2.4-fosscuda-2019a-Python-3.7.2.eb --- ...Keras-2.2.4-fosscuda-2019a-Python-3.7.2.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..1854e8a770a --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.2.4-fosscuda-2019a-Python-3.7.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Keras' +version = '2.2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://keras.io/' +description = """Keras is a minimalist, highly modular neural networks library, written in Python and +capable of running on top of either TensorFlow or Theano.""" + +toolchain = {'name': 'fosscuda', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['90b610a3dbbf6d257b20a079eba3fdf2eed2158f64066a7c6f7227023fd60bc9'] + +dependencies = [ + ('Python', '3.7.2'), + ('TensorFlow', '1.13.1', versionsuffix), + ('Theano', '1.0.4'), + ('PyYAML', '5.1'), + ('h5py', '2.9.0'), +] + +use_pip = True +download_dep_fail = True + +fix_python_shebang_for = ['bin/conv-template', 'bin/from-template'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From a9443a3725e5d0d63481a25d9f98ec92ac8deb39 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Mon, 13 May 2019 12:33:09 +0100 Subject: [PATCH 1590/5331] More sanity checks added --- easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb index 987bb25c7c0..5ff49255844 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb @@ -29,4 +29,9 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = [ + "nextflow -v", + "nextflow help", +] + moduleclass = 'tools' From 2c1bd824f9e77ae9a35ea77aae828f0b36164aed Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 13 May 2019 14:37:44 +0200 Subject: [PATCH 1591/5331] INTEGRATE: use CMakeMakeCp easyblock --- .../i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb index c7cb191adc1..0f7602d0def 100644 --- a/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/i/INTEGRATE/INTEGRATE-0.2.6-GCCcore-8.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakeMakeCp' name = 'INTEGRATE' version = '0.2.6' @@ -23,14 +23,7 @@ separate_build_dir = True parallel = 1 -skipsteps = ['install'] - -postinstallcmds = [ - 'mkdir -p %(installdir)s/bin', - 'cp -a bin/Integrate %(installdir)s/bin/', - 'cp -a vendor/divsufsort/lib %(installdir)s/', - 'cp -a vendor/divsufsort/include %(installdir)s/', -] +files_to_copy = [(['bin/Integrate'], 'bin'), 'vendor/divsufsort/lib', 'vendor/divsufsort/include'] sanity_check_paths = { 'files': ['bin/Integrate'], From 5a1600cad34b8c714e13cb455c2dd4d3b5d8b5c8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 13 May 2019 15:54:12 +0100 Subject: [PATCH 1592/5331] Update PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb --- .../p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb index c93da010136..0d52fb5598e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -217,8 +217,8 @@ download_dep_fail = True # This environment is needed to prevent setup.py from invoking git to determine version. prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' -prebuildopts += ' LDFLAGS="$LDFLAGS -ldl"' -preinstallopts = 'VERBOSE=1 LDFLAGS="$LDFLAGS -ldl"' +prebuildopts += ' LDFLAGS="$LDFLAGS -ldl" CUDNN_ROOT_DIR=$EBROOTCUDNN ' +preinstallopts = 'VERBOSE=1 LDFLAGS="$LDFLAGS -ldl" ' # you can choice here: either give a list of CUDA cc version or tell it All # by default it does autodetect of the GPU on the local machine From 09c0e1de2dc8a85afe7012daa548193626820d27 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 13 May 2019 16:02:15 +0100 Subject: [PATCH 1593/5331] fix date on FXdiv --- .../p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb index 6de7fae4fc3..b6e8a0be442 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb @@ -72,7 +72,7 @@ sources = [ { 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], 'download_filename': 'b742d1143724d646cd0f914646f1240eacf5bd73.tar.gz', - 'filename': 'FXdiv-20181016.tar.gz', + 'filename': 'FXdiv-20181116.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/FXdiv'), }, { From 4def83e44cfc5f687fad176c166b00331939f652 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 13 May 2019 16:03:14 +0100 Subject: [PATCH 1594/5331] fix date on FXdiv --- .../p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb index 0d52fb5598e..18979d4c521 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -71,7 +71,7 @@ sources = [ { 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], 'download_filename': 'b742d1143724d646cd0f914646f1240eacf5bd73.tar.gz', - 'filename': 'FXdiv-20181016.tar.gz', + 'filename': 'FXdiv-20181116.tar.gz', 'extract_cmd': extract_cmd_pattern % (pytorchdir, 'third_party/FXdiv'), }, { From 572c6e3dd0288e2a4baff9787eb2bd4555b8196e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 May 2019 17:37:16 +0200 Subject: [PATCH 1595/5331] adding easyconfigs: socat-1.7.3.3-GCCcore-8.2.0.eb --- .../s/socat/socat-1.7.3.3-GCCcore-8.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/socat/socat-1.7.3.3-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/s/socat/socat-1.7.3.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/socat/socat-1.7.3.3-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..d582ba0d892 --- /dev/null +++ b/easybuild/easyconfigs/s/socat/socat-1.7.3.3-GCCcore-8.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'socat' +version = '1.7.3.3' + +homepage = 'http://www.dest-unreach.org/socat' +description = "socat is a relay for bidirectional data transfer between two independent data channels." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://www.dest-unreach.org/%(name)s/download'] +sources = [SOURCE_TAR_GZ] +checksums = ['8cc0eaee73e646001c64adaab3e496ed20d4d729aaaf939df2a761e99c674372'] + +builddependencies = [('binutils', '2.31.1')] + +sanity_check_paths = { + 'files': ['bin/filan', 'bin/procan', 'bin/socat'], + 'dirs': ['share'], +} + +sanity_check_commands = ["socat -V"] + +moduleclass = 'tools' From 5b2c5842eb21deb3fbea9d01bab574cb60e01d7e Mon Sep 17 00:00:00 2001 From: Josef Dvoracek Date: Mon, 13 May 2019 18:16:31 +0200 Subject: [PATCH 1596/5331] adding easyconfigs: Mathematica-12.0.0.eb --- .../m/Mathematica/Mathematica-12.0.0.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb new file mode 100644 index 00000000000..d78f7e39dfc --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb @@ -0,0 +1,17 @@ +name = 'Mathematica' +version = '12.0.0' + +homepage = 'http://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['Mathematica_%(version)s_LINUX.sh'] +checksums = ['b9fb71e1afcc1d72c200196ffa434512d208fa2920e207878433f504e58ae9d7'] + +license_server = 'license.example.com' + +sanity_check_commands = [('mathematica', '--version')] + +moduleclass = 'math' From 80470c69b04eb80c25a147a2edb64ca45e30708d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 May 2019 18:21:35 +0200 Subject: [PATCH 1597/5331] adding easyconfigs: hypothesis-4.23.4-GCCcore-8.2.0.eb --- .../hypothesis-4.23.4-GCCcore-8.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-4.23.4-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.23.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.23.4-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..ad60febd74a --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.23.4-GCCcore-8.2.0.eb @@ -0,0 +1,32 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'hypothesis' +version = '4.23.4' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +builddependencies = [('binutils', '2.31.1')] + +use_pip = True + +exts_list = [ + ('attrs', '19.1.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/h/hypothesis/'], + 'checksums': ['a9708beea61b45ee11de99aa61e06fe6d559aeccabe5017f9080522449727f18'], + }), +] + +moduleclass = 'tools' From 0fd199c408b92498783f0e102e2ff996a6408c61 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 13 May 2019 12:07:36 -0700 Subject: [PATCH 1598/5331] libgeotiff 1.5.1 GCCcore 8.2.0 --- .../libgeotiff-1.5.1-GCCcore-8.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..e7178beaf09 --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.5.1' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/OSGeo/libgeotiff/archive'] +sources = [{ + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ +}] + +builddependencies = [ + ('libtool', '2.4.6'), + ('Automake', '1.16.1'), + ('Autoconf', '2.69'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.10'), + ('PROJ', '6.0.0'), + ('libjpeg-turbo', '2.0.2'), +] + +start_dir = 'libgeotiff' +preconfigopts = 'autoreconf --install && ' +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 7cff7b1ac39dc64cdb265870195f05df31c2bb05 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 13 May 2019 12:10:28 -0700 Subject: [PATCH 1599/5331] add pkg-config build dep to support Ubuntu --- easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb index d3ff2dd7a8d..d97b16341e0 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb @@ -22,7 +22,10 @@ source_urls = ['http://download.osgeo.org/proj/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['4510a2c1c8f9056374708a867c51b1192e8d6f9a5198dd320bf6a168e44a3657'] -builddependencies = [('binutils', '2.31.1')] +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.31.1'), +] dependencies = [('SQLite', '3.27.2')] From 685aef2f62ee6e123b661c9b0c8e6c9015924be7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 May 2019 21:10:33 +0200 Subject: [PATCH 1600/5331] update CVXOPT 1.2.3 to foss/2019a + Python 3.7.2 & 2.7.15 --- ...thon-3.6.6.eb => CVXOPT-1.2.3-foss-2019a.eb} | 17 ++++++----------- 1 file changed, 6 insertions(+), 11 deletions(-) rename easybuild/easyconfigs/c/CVXOPT/{CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb => CVXOPT-1.2.3-foss-2019a.eb} (78%) diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2019a.eb similarity index 78% rename from easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb rename to easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2019a.eb index f68aa1a298e..65228962048 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-foss-2019a.eb @@ -1,8 +1,7 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'CVXOPT' version = '1.2.3' -versionsuffix = '-Python-%(pyver)s' homepage = 'http://cvxopt.org' description = """CVXOPT is a free software package for convex optimization based on the Python programming language. @@ -10,7 +9,7 @@ description = """CVXOPT is a free software package for convex optimization based building on Python's extensive standard library and on the strengths of Python as a high-level programming language. """ -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'pic': True} source_urls = [PYPI_LOWER_SOURCE] @@ -21,9 +20,10 @@ checksums = [ '85d8475098895e9af45f330489a712b5b944489c5fb4a6c67f59bef8fed4303d', # CVXOPT-1.2.1-fix-setup-py.patch ] +multi_deps = {'Python': ['3.7.2', '2.7.15']} + dependencies = [ - ('Python', '3.6.6'), - ('SuiteSparse', '5.1.2', '-METIS-5.1.0'), + ('SuiteSparse', '5.4.0', '-METIS-5.1.0'), ('GSL', '2.5'), ] @@ -35,11 +35,6 @@ preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_ installopts = ' --no-binary cvxopt' -postinstallcmds = ['nosetests'] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} +sanity_check_commands = ['nosetests'] moduleclass = 'math' From 91a2c37430d5709a41493a937c9355b8e20e7cf2 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 13 May 2019 14:16:59 -0700 Subject: [PATCH 1601/5331] adding binutils --- .../easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb index e7178beaf09..7dad1e95cdf 100644 --- a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb @@ -15,6 +15,7 @@ sources = [{ }] builddependencies = [ + ('binutils', '2.31.1'), ('libtool', '2.4.6'), ('Automake', '1.16.1'), ('Autoconf', '2.69'), From 39bc8dbaaf06bdc3a96932227ee0f9e2517ef768 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 13 May 2019 14:32:18 -0700 Subject: [PATCH 1602/5331] adding binutils --- .../easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb index 7dad1e95cdf..7fc68cd85c6 100644 --- a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb @@ -13,6 +13,7 @@ sources = [{ 'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ }] +checksums = ['fb04491572afb25ffe60239fdfdcfa2c64e6cf644cad9b0b922b10115ccbd488'] builddependencies = [ ('binutils', '2.31.1'), From 91e0322e208f9016b86e5cea5c6abc663f1d87b6 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 13 May 2019 14:59:28 -0700 Subject: [PATCH 1603/5331] LittleCMS 2.9 GCCcore 8.2.0 --- .../LittleCMS/LittleCMS-2.9-GCCcore-8.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..9b18741a71d --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.9-GCCcore-8.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.9' + +homepage = 'http://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['48c6fdf98396fa245ed86e622028caf49b96fa22f3e5734f853f806fbc8e7d20'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.31.1'), +] + +dependencies = [('libjpeg-turbo', '2.0.2')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' From b06cfa76bf5587c02a4e2ccf113afe97fede5c62 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 13 May 2019 15:12:53 -0700 Subject: [PATCH 1604/5331] Ghostscript for GCCcore 8.2.0 --- .../Ghostscript-9.27-GCCcore-8.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.27-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.27-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.27-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..59ee5837427 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.27-GCCcore-8.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.27' + +homepage = 'http://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%(version_major)s%(version_minor)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9760e8bdd07a08dbd445188a6557cb70e60ccb6a5601f7dbfba0d225e28ce285'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.36'), + ('freetype', '2.9.1'), + ('libjpeg-turbo', '2.0.2'), + ('expat', '2.2.6'), + ('GLib', '2.60.1'), + ('cairo', '1.16.0'), + ('LibTIFF', '4.0.10'), +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.31.1'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +sanity_check_paths = { + 'files': ['bin/gs'], + 'dirs': ['lib/ghostscript', 'share/man'], +} + +moduleclass = 'tools' From f21042a1a1f6fc767be98ff1d8d433791a7c43b5 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 May 2019 07:43:26 +0200 Subject: [PATCH 1605/5331] ctffind should be at GCC level not foss. --- ....eb => ctffind-4.1.13-GCC-8.2.0-2.31.1.eb} | 2 +- .../ctffind/ctffind-4.1.13-fosscuda-2019a.eb | 47 ------------------- 2 files changed, 1 insertion(+), 48 deletions(-) rename easybuild/easyconfigs/c/ctffind/{ctffind-4.1.13-foss-2019a.eb => ctffind-4.1.13-GCC-8.2.0-2.31.1.eb} (95%) delete mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-GCC-8.2.0-2.31.1.eb similarity index 95% rename from easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb rename to easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-GCC-8.2.0-2.31.1.eb index dc89a712855..a20febe7849 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-GCC-8.2.0-2.31.1.eb @@ -13,7 +13,7 @@ version = '4.1.13' homepage = 'http://grigoriefflab.janelia.org/ctffind4' description = """Program for finding CTFs of electron micrographs.""" -toolchain = {'name': 'foss', 'version': '2019a'} +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} toolchainopts = {'openmp': True} source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb deleted file mode 100644 index c1cc350084f..00000000000 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb +++ /dev/null @@ -1,47 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# -# Author: Ake Sandgren, HPC2N, Umea University - -easyblock = 'ConfigureMake' - -name = 'ctffind' -version = '4.1.13' - -homepage = 'http://grigoriefflab.janelia.org/ctffind4' -description = """Program for finding CTFs of electron micrographs.""" - -toolchain = {'name': 'fosscuda', 'version': '2019a'} -toolchainopts = {'openmp': True} - -source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['ctffind-4.1.13_remove_bogus_include_lines.patch'] -checksums = [ - '48231f8511b222176ea39b80c58ae8fb8a6bac5e0da247c54f5a84b52c8750cf', # ctffind-4.1.13.tar.gz - # ctffind-4.1.13_remove_bogus_include_lines.patch - 'ae218a61a24cec2e35fa4a7ddd497c0d1bb997957bfeb8866d941442afe26365', -] - -dependencies = [ - ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.2'), - ('LibTIFF', '4.0.10'), - ('GSL', '2.5'), - ('wxWidgets', '3.0.4'), -] - -separate_build_dir = True - -configopts = '--enable-openmp ' - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/ctffind'], - 'dirs': [], -} - -moduleclass = 'bio' From 0058cd9f6e6ba6c2c8b47b11b11ba84991648257 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 May 2019 08:01:14 +0200 Subject: [PATCH 1606/5331] ctffind needs FFT and must thus be at gompi(c) level not GCC. --- ....31.1.eb => ctffind-4.1.13-gompi-2019a.eb} | 2 +- .../c/ctffind/ctffind-4.1.13-gompic-2019a.eb | 47 +++++++++++++++++++ 2 files changed, 48 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/c/ctffind/{ctffind-4.1.13-GCC-8.2.0-2.31.1.eb => ctffind-4.1.13-gompi-2019a.eb} (95%) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompic-2019a.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompi-2019a.eb similarity index 95% rename from easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-GCC-8.2.0-2.31.1.eb rename to easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompi-2019a.eb index a20febe7849..d36880692a1 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompi-2019a.eb @@ -13,7 +13,7 @@ version = '4.1.13' homepage = 'http://grigoriefflab.janelia.org/ctffind4' description = """Program for finding CTFs of electron micrographs.""" -toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchain = {'name': 'gompi', 'version': '2019a'} toolchainopts = {'openmp': True} source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompic-2019a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompic-2019a.eb new file mode 100644 index 00000000000..08fe677fd00 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompic-2019a.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.13' + +homepage = 'http://grigoriefflab.janelia.org/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'gompic', 'version': '2019a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ctffind-4.1.13_remove_bogus_include_lines.patch'] +checksums = [ + '48231f8511b222176ea39b80c58ae8fb8a6bac5e0da247c54f5a84b52c8750cf', # ctffind-4.1.13.tar.gz + # ctffind-4.1.13_remove_bogus_include_lines.patch + 'ae218a61a24cec2e35fa4a7ddd497c0d1bb997957bfeb8866d941442afe26365', +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.2'), + ('LibTIFF', '4.0.10'), + ('GSL', '2.5'), + ('wxWidgets', '3.0.4'), +] + +separate_build_dir = True + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From b02f1c03274493caff14b3751f460954371efd85 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 May 2019 08:07:52 +0200 Subject: [PATCH 1607/5331] ctffind needs FFTW, so it is, after all, much better to keep it at foss(cuda) level. --- ...ffind-4.1.13-gompi-2019a.eb => ctffind-4.1.13-foss-2019a.eb} | 2 +- ...-4.1.13-gompic-2019a.eb => ctffind-4.1.13-fosscuda-2019a.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/ctffind/{ctffind-4.1.13-gompi-2019a.eb => ctffind-4.1.13-foss-2019a.eb} (95%) rename easybuild/easyconfigs/c/ctffind/{ctffind-4.1.13-gompic-2019a.eb => ctffind-4.1.13-fosscuda-2019a.eb} (95%) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompi-2019a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb similarity index 95% rename from easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompi-2019a.eb rename to easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb index d36880692a1..dc89a712855 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompi-2019a.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb @@ -13,7 +13,7 @@ version = '4.1.13' homepage = 'http://grigoriefflab.janelia.org/ctffind4' description = """Program for finding CTFs of electron micrographs.""" -toolchain = {'name': 'gompi', 'version': '2019a'} +toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'openmp': True} source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompic-2019a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb similarity index 95% rename from easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompic-2019a.eb rename to easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb index 08fe677fd00..c1cc350084f 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-gompic-2019a.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb @@ -13,7 +13,7 @@ version = '4.1.13' homepage = 'http://grigoriefflab.janelia.org/ctffind4' description = """Program for finding CTFs of electron micrographs.""" -toolchain = {'name': 'gompic', 'version': '2019a'} +toolchain = {'name': 'fosscuda', 'version': '2019a'} toolchainopts = {'openmp': True} source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] From 8fb0d8b17793ce6dad6778b037380698ddbb6a89 Mon Sep 17 00:00:00 2001 From: HPC-uniOldenburg Date: Tue, 14 May 2019 09:12:51 +0200 Subject: [PATCH 1608/5331] adding easyconfigs: Bowtie2-2.3.4.3-foss-2017b.eb --- .../b/Bowtie2/Bowtie2-2.3.4.3-foss-2017b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.4.3-foss-2017b.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.4.3-foss-2017b.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.4.3-foss-2017b.eb new file mode 100644 index 00000000000..80f53d322df --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.4.3-foss-2017b.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp + +name = 'Bowtie2' +version = '2.3.4.3' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['07ad2e1ce338ee461fb9559d6d21eacb10b16cfe2c973c2df08fbf0e33a9647a'] + +dependencies = [('tbb', '2018_U3')] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From e540a939e9f8a78e551756e8926452448f036993 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 May 2019 09:30:35 +0200 Subject: [PATCH 1609/5331] adding easyconfigs: glog-0.4.0-GCCcore-8.2.0.eb --- .../g/gflags/gflags-2.2.2-GCCcore-8.2.0.eb | 35 +++++++++++++++++++ .../g/glog/glog-0.4.0-GCCcore-8.2.0.eb | 32 +++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/g/glog/glog-0.4.0-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..0a0d09b9bde --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glog/glog-0.4.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/glog/glog-0.4.0-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..1b37b2e0c73 --- /dev/null +++ b/easybuild/easyconfigs/g/glog/glog-0.4.0-GCCcore-8.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'glog' +version = '0.4.0' + +homepage = 'https://github.com/google/glog' +description = "A C++ implementation of the Google logging module." + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/google/glog/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f28359aeba12f30d73d9e4711ef356dc842886968112162bc73002645139c39c'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), +] + +dependencies = [ + ('gflags', '2.2.2'), + ('libunwind', '1.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['include/glog/logging.h', 'include/glog/raw_logging.h', 'lib/libglog.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From 205d73a437a0dc4e973b64047ea2d0c97fd8beb4 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 14 May 2019 09:29:42 +0100 Subject: [PATCH 1610/5331] Update PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb --- .../p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb index 18979d4c521..7b35c90d404 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -217,7 +217,7 @@ download_dep_fail = True # This environment is needed to prevent setup.py from invoking git to determine version. prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' -prebuildopts += ' LDFLAGS="$LDFLAGS -ldl" CUDNN_ROOT_DIR=$EBROOTCUDNN ' +prebuildopts += ' LDFLAGS="$LDFLAGS -ldl" CUDNN_LIB_DIR=$EBROOTCUDNN/lib CUDNN_INCLUDE_DIR=$EBROOTCUDNN/include ' preinstallopts = 'VERBOSE=1 LDFLAGS="$LDFLAGS -ldl" ' # you can choice here: either give a list of CUDA cc version or tell it All From 4a23ac682f68ccca9ce08290914fb56650c27013 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 10:41:35 +0200 Subject: [PATCH 1611/5331] loosen up check on dump easyconfig w.r.t. string-valued easyconfig parameters like configopts --- test/easyconfigs/easyconfigs.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 7a308f89188..e25a2051762 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -681,6 +681,10 @@ def template_easyconfig_test(self, spec): # it should *not* be the same as the parent toolchain self.assertNotEqual(dumped_dep[3], (orig_toolchain['name'], orig_toolchain['version'])) + # take into account that for some string-valued easyconfig parameters (configopts & co), + # the easyblock may have injected additional values, which affects the dumped easyconfig file + elif isinstance(orig_val, basestring): + self.assertTrue(dumped_val.startswith(orig_val)) else: self.assertEqual(orig_val, dumped_val) From a0502dfb2546ed017d10a65371c278aa9ae4ea26 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 11:13:03 +0200 Subject: [PATCH 1612/5331] adding easyconfigs: NCO-4.7.9-intel-2018b.eb, ANTLR-2.7.7-intel-2018b.eb --- .../a/ANTLR/ANTLR-2.7.7-intel-2018b.eb | 31 ++++++++++++++++ .../n/NCO/NCO-4.7.9-intel-2018b.eb | 37 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018b.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-4.7.9-intel-2018b.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018b.eb new file mode 100644 index 00000000000..472b977829e --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' + +homepage = 'http://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['http://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +dependencies = [('Java', '1.8', '', True)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.7.9-intel-2018b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.7.9-intel-2018b.eb new file mode 100644 index 00000000000..a8738174dd4 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-4.7.9-intel-2018b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '4.7.9' + +homepage = "http://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'lowopt': True} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['048f6298bceb40913c3ae433f875dea1e9129b1c86019128e7271d08f274a879'] + +builddependencies = [ + ('Bison', '3.0.5'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.26'), + ('expat', '2.2.5'), + ('ANTLR', '2.7.7'), + ('libdap', '3.20.3'), + ('GSL', '2.5'), + ('netCDF', '4.6.1'), +] + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 965cf8f1addf37ffd338534b48aa68ea5cd475a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 12:01:38 +0200 Subject: [PATCH 1613/5331] {data}[intel/2018b] wrf-python v1.3.1, xarray v0.12.1, netcdf4-python v1.4.1 w/ Python 3.6.6 --- .../cftime-1.0.1-intel-2018b-Python-3.6.6.eb | 29 +++++++++++ ...4-python-1.4.1-intel-2018b-Python-3.6.6.eb | 30 +++++++++++ ...f-python-1.3.1-intel-2018b-Python-3.6.6.eb | 50 +++++++++++++++++++ .../xarray-0.12.1-intel-2018b-Python-3.6.6.eb | 23 +++++++++ 4 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/c/cftime/cftime-1.0.1-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.1-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.1-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.12.1-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/c/cftime/cftime-1.0.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/cftime/cftime-1.0.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..1632a9a2fb7 --- /dev/null +++ b/easybuild/easyconfigs/c/cftime/cftime-1.0.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'cftime' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Unidata/cftime' +description = """Time-handling functionality from netcdf4-python""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/Unidata/cftime/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['930089f389f68485077019faa30e1d66f57d3a46148e67f51e401504e8a15f7d'] + +dependencies = [ + ('Python', '3.6.6'), + ('cURL', '7.60.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..edd968a1b8b --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.4.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,30 @@ +name = 'netcdf4-python' +version = '1.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] +sources = ['v%(version)srel.tar.gz'] +patches = ['netcdf4-python-1.1.8-avoid-diskless-test.patch'] +checksums = [ + 'b42d50220387f16e20b42e2e6f6f5d2cb62ba8edc2787618db677c40ba7b1bf4', # v1.4.1rel.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', +] + +download_dep_fail = True +use_pip = True + +dependencies = [ + ('Python', '3.6.6'), + ('cftime', '1.0.1', '-Python-%(pyver)s'), + ('netCDF', '4.6.1'), + ('cURL', '7.60.0'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..b78844dd5a1 --- /dev/null +++ b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'wrf-python' +version = '1.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wrf-python.readthedocs.io' +description = """A collection of diagnostic and interpolation routines for use with output from + the Weather Research and Forecasting (WRF-ARW) Model.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.6.6'), + ('netcdf4-python', '1.4.1', versionsuffix), + ('xarray', '0.12.1', versionsuffix), + ('matplotlib', '3.0.0', versionsuffix), + ('basemap', '1.2.0', versionsuffix), + ('PROJ', '5.0.0'), # required for Cartopy +] + +use_pip = True + +exts_list = [ + ('wrapt', '1.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wrapt'], + 'checksums': ['4aea003270831cceb8a90ff27c4031da6ead7ec1886023b80ce0dfe0adf61533'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/w/wrf-python'], + 'checksums': ['24af2618b5bf436830d780af3366c423fc540244ba644307ca71633020d052a2'], + 'modulename': 'wrf', + }), + ('Shapely', '1.6.4.post2', { + 'source_urls': ['https://pypi.python.org/packages/source/S/Shapely'], + 'checksums': ['c4b87bb61fc3de59fc1f85e71a79b0c709dc68364d9584473697aad4aa13240f'], + }), + ('pyshp', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyshp'], + 'checksums': ['e65c7f24d372b97d0920b864bbeb78322bb37b83f2606e2a2212631d5d51e5c0'], + 'modulename': 'shapefile', + }), + ('Cartopy', '0.17.0', { + 'source_urls': ['https://pypi.python.org/packages/source/C/Cartopy'], + 'checksums': ['424bd9e9ddef6e48cbdee694ce589ec431be8591f15b6cb93cb2b333a29b2c61'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.12.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/x/xarray/xarray-0.12.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..5411f6e6d09 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.12.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.12.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ac09a819e791be208ae33fa7ecee19d0fe7b5479906f927d358a61957ce27e10'] + +dependencies = [('Python', '3.6.6')] + +download_dep_fail = True +use_pip = True + +moduleclass = 'data' From 938d98699e8b67d5b3f826dc292694527d302932 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 12:08:35 +0200 Subject: [PATCH 1614/5331] trivial style fix in parasail 2.4 easyconfig --- easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb b/easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb index 9f9a6930671..fa193f0695e 100644 --- a/easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb +++ b/easybuild/easyconfigs/p/parasail/parasail-2.4-foss-2018b.eb @@ -18,8 +18,7 @@ builddependencies = [('CMake', '3.11.4')] sanity_check_paths = { 'files': ['bin/parasail_aligner', 'bin/parasail_stats', - 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h' - ], + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], 'dirs': [], } From da2072618c831488ac7a130038f35664c4eb2993 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 12:30:04 +0200 Subject: [PATCH 1615/5331] adding easyconfigs: Pysolar-0.8-intel-2018b-Python-3.6.6.eb --- .../Pysolar-0.8-intel-2018b-Python-3.6.6.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..35b28a9d42b --- /dev/null +++ b/easybuild/easyconfigs/p/Pysolar/Pysolar-0.8-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pysolar' +version = '0.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pysolar.org/' +description = """Pysolar is a collection of Python libraries for simulating the irradiation + of any point on earth by the sun.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['548c05177acd2845143d9624e670635cd3e5c3a63782449ca35e090ca755c617'] + +dependencies = [('Python', '3.6.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' From 815bf16558c8ead973a5deab0a47c401c5f105f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 12:30:43 +0200 Subject: [PATCH 1616/5331] adding easyconfigs: Calendrical-2.0.2a-intel-2018b-Python-3.6.6.eb --- ...ndrical-2.0.2a-intel-2018b-Python-3.6.6.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/Calendrical/Calendrical-2.0.2a-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/c/Calendrical/Calendrical-2.0.2a-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/Calendrical/Calendrical-2.0.2a-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..9d211c43989 --- /dev/null +++ b/easybuild/easyconfigs/c/Calendrical/Calendrical-2.0.2a-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'Calendrical' +version = '2.0.2a' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.funaba.org/code#calendrical' +description = "Calendrical module is for calendrical calculations." + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['http://www.funaba.org/archives/'] +sources = ['python-calendrical-%(version)s.tar.gz'] +checksums = ['297ea00c305642c46d321feb4893e12d32e55a4258f662de2e98e60d81dd1c25'] + +dependencies = [('Python', '3.6.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' From 508b0b7ac5b03d05cb6053aeaeeee30f6082d675 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 12:31:22 +0200 Subject: [PATCH 1617/5331] adding easyconfigs: BeautifulSoup-4.7.1-intel-2018b-Python-3.6.6.eb --- ...ifulSoup-4.7.1-intel-2018b-Python-3.6.6.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.7.1-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.7.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.7.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..c39f815fe57 --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.7.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [('Python', '3.6.6')] + +use_pip = True + +exts_list = [ + ('soupsieve', '1.8', { + 'source_urls': ['https://pypi.python.org/packages/source/s/soupsieve'], + 'checksums': ['eaed742b48b1f3e2d45ba6f79401b2ed5dc33b2123dfe216adb90d4bfa0ade26'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'checksums': ['945065979fb8529dd2f37dbb58f00b661bdbcbebf954f93b32fdf5263ef35348'], + 'modulename': 'bs4', + }), +] + +moduleclass = 'data' From b9685a6e9de8f2bf6be99db8defdfb809207f1da Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 14 May 2019 11:32:49 +0100 Subject: [PATCH 1618/5331] Add CUDNN_* items to preinstallopts --- .../p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb index 7b35c90d404..953c1a4be59 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -219,6 +219,7 @@ download_dep_fail = True prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' prebuildopts += ' LDFLAGS="$LDFLAGS -ldl" CUDNN_LIB_DIR=$EBROOTCUDNN/lib CUDNN_INCLUDE_DIR=$EBROOTCUDNN/include ' preinstallopts = 'VERBOSE=1 LDFLAGS="$LDFLAGS -ldl" ' +preinstallopts += 'CUDNN_LIB_DIR=$EBROOTCUDNN/lib CUDNN_INCLUDE_DIR=$EBROOTCUDNN/include ' # you can choice here: either give a list of CUDA cc version or tell it All # by default it does autodetect of the GPU on the local machine From e4140f45ddce3b7457985513b7d20d2ff28fdd25 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 May 2019 13:11:59 +0200 Subject: [PATCH 1619/5331] Drop unused separate_build_dir setting --- easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb | 2 -- .../easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb index dc89a712855..5f490fda760 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-foss-2019a.eb @@ -33,8 +33,6 @@ dependencies = [ ('wxWidgets', '3.0.4'), ] -separate_build_dir = True - configopts = '--enable-openmp ' parallel = 1 diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb index c1cc350084f..6d868024d2a 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.13-fosscuda-2019a.eb @@ -33,8 +33,6 @@ dependencies = [ ('wxWidgets', '3.0.4'), ] -separate_build_dir = True - configopts = '--enable-openmp ' parallel = 1 From 3f6a6d53862899693664603998a612f70761ddcb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 14:47:33 +0200 Subject: [PATCH 1620/5331] adding easyconfigs: Beast-2.5.2-GCC-8.2.0-2.31.1.eb, beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb --- .../b/Beast/Beast-2.5.2-GCC-8.2.0-2.31.1.eb | 32 +++++++++++++++++++ .../beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb | 29 +++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-2.5.2-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.5.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/Beast/Beast-2.5.2-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..5646af98f98 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.5.2-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,32 @@ +easyblock = "Tarball" + +name = 'Beast' +version = '2.5.2' + +homepage = 'http://beast2.org/' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%(version)s.Linux.tgz'] +checksums = ['2feb2281b4f7cf8f7de1a62de50f52a8678ed0767fc72f2322e77dde9b8cd45f'] + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '3.1.2'), +] + +sanity_check_paths = { + 'files': ["bin/beast"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..5d0bc3d60e9 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '3.1.2' +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] + +dependencies = [('Java', '11', '', True)] + +builddependencies = [('Autotools', '20180311')] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % libfile + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' From 7f15eb38056aa2741bc6f593662472f9d0450725 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 15:12:35 +0200 Subject: [PATCH 1621/5331] adding easyconfigs: scikit-learn-0.20.3-foss-2019a.eb --- .../scikit-learn-0.20.3-foss-2019a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb new file mode 100755 index 00000000000..dfa2daf7146 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.20.3' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c503802a81de18b8b4d40d069f5e363795ee44b1605f38bc104160ca3bfe2c41'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [('SciPy-bundle', '2019.03')] + +download_dep_fail = True +use_pip = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +options = {'modulename': 'sklearn'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn'], +} + +moduleclass = 'data' From 43be5909b8bb7708632df79d8d5fea24d61e3c4c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 15:13:15 +0200 Subject: [PATCH 1622/5331] adding easyconfigs: networkx-2.3-foss-2019a-Python-3.7.2.eb --- .../networkx-2.3-foss-2019a-Python-3.7.2.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.3-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.3-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/n/networkx/networkx-2.3-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..c39af502105 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.3-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] +checksums = ['8311ddef63cf5c5c5e7c1d0212dd141d9a1fe3f474915281b73597ed5f1d4e3d'] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True + +moduleclass = 'tools' From f250ff54cb850c868d618a8c88110ebd0f5be5ad Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 14 May 2019 14:35:34 +0100 Subject: [PATCH 1623/5331] Remove `sanity_check_paths` as this is a `PythonPackage` --- .../p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb index b6e8a0be442..a2228269cf9 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-foss-2018b-Python-3.6.6.eb @@ -225,9 +225,4 @@ runtest += '&& python test/run_test.py --exclude autograd cpp_extensions c10d to options = {'modulename': 'torch'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'devel' From 89a71ab0f38353a32bbc8344baf0f8f47a9cec8d Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 14 May 2019 14:36:23 +0100 Subject: [PATCH 1624/5331] Remove sanity_check_paths as this is a PythonPackage --- .../p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb index 953c1a4be59..506ee15e035 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.0.1-fosscuda-2018b-Python-3.6.6.eb @@ -233,9 +233,4 @@ runtest += '&& python test/run_test.py --exclude autograd cpp_extensions c10d to options = {'modulename': 'torch'} -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'devel' From 062f94ddb84e58cd767646a462c3cebf5e9adfba Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 May 2019 15:58:04 +0200 Subject: [PATCH 1625/5331] adding easyconfigs: LMDB-0.9.23-GCCcore-8.2.0.eb --- .../l/LMDB/LMDB-0.9.23-GCCcore-8.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMDB/LMDB-0.9.23-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.23-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.23-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..8c511013c9e --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.23-GCCcore-8.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.23' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['abf42e91f046787ed642d9eb21812a5c473f3ba5854124484d16eadbe0aa9c81'] + +builddependencies = [('binutils', '2.31.1')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'], 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From d70cc1df0e6d1e236ec909c11f5448f06b332698 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 May 2019 16:18:01 +0200 Subject: [PATCH 1626/5331] adding easyconfigs: LevelDB-1.22-GCCcore-8.2.0.eb --- .../l/LevelDB/LevelDB-1.22-GCCcore-8.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..f92ecf1761b --- /dev/null +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-8.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'LevelDB' +version = '1.22' + +homepage = 'https://github.com/google/leveldb' +description = """LevelDB is a fast key-value storage library written at Google that provides an + ordered mapping from string keys to string values.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/google/leveldb/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['55423cac9e3306f4a9502c738a001e4a339d1a38ffbee7572d4a07d5d63949b2'] + +builddependencies = [ + ('binutils', '2.31.1'), + ('CMake', '3.13.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DLEVELDB_BUILD_BENCHMARKS=OFF ' + +sanity_check_paths = { + 'files': ['include/leveldb/cache.h', 'include/leveldb/table.h', + 'lib/libleveldb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From e41cb9d8a66a108d849bcd126e5ec59129555ee1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 17:41:10 +0200 Subject: [PATCH 1627/5331] update to Qiskit 0.10.1 --- ...n-3.6.6.eb => Qiskit-0.10.1-foss-2019a.eb} | 75 ++++++++----------- 1 file changed, 32 insertions(+), 43 deletions(-) rename easybuild/easyconfigs/q/Qiskit/{Qiskit-0.7.2-foss-2018b-Python-3.6.6.eb => Qiskit-0.10.1-foss-2019a.eb} (50%) diff --git a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.7.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.10.1-foss-2019a.eb similarity index 50% rename from easybuild/easyconfigs/q/Qiskit/Qiskit-0.7.2-foss-2018b-Python-3.6.6.eb rename to easybuild/easyconfigs/q/Qiskit/Qiskit-0.10.1-foss-2019a.eb index d0c238e4f9e..45e6dcffc68 100644 --- a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.7.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.10.1-foss-2019a.eb @@ -1,100 +1,89 @@ easyblock = 'PythonBundle' name = 'Qiskit' -version = '0.7.2' +version = '0.10.1' versionsuffix = '-Python-%(pyver)s' homepage = 'https://qiskit.org' description = """Qiskit is an open-source framework for working with noisy quantum computers at the level of pulses, circuits, and algorithms.""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'foss', 'version': '2019a'} # required for building/installing qiskit-aer builddependencies = [ - ('CMake', '3.12.1'), + ('CMake', '3.13.3'), ('Ninja', '1.9.0'), ] dependencies = [ - ('Python', '3.6.6'), - ('sympy', '1.3', versionsuffix), - ('Pillow', '5.3.0', versionsuffix), - ('networkx', '2.2', versionsuffix), - ('h5py', '2.8.0', versionsuffix), - ('scikit-learn', '0.20.0', versionsuffix), - ('CVXOPT', '1.2.3', versionsuffix), + ('Python', '3.7.2'), + ('sympy', '1.4'), + ('Pillow', '6.0.0'), + ('networkx', '2.3', versionsuffix), + ('h5py', '2.9.0'), + ('scikit-learn', '0.20.3'), + ('CVXOPT', '1.2.3'), ] use_pip = True exts_list = [ - ('setuptools', '40.8.0', { - 'source_tmpl': 'setuptools-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], - 'checksums': ['6e4eec90337e849ade7103723b9a99631c1f0d19990d6e8412dc42f5ae8b304d'], - }), - ('ntlm-auth', '1.2.0', { + ('ntlm-auth', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/n/ntlm-auth/'], - 'checksums': ['7bc02a3fbdfee7275d3dc20fce8028ed8eb6d32364637f28be9e9ae9160c6d5c'], + 'checksums': ['bb2fd03c665f0f62c5f65695b62dcdb07fb7a45df6ebc86c770be2054d6902dd'], }), ('requests_ntlm', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/r/requests_ntlm/'], 'checksums': ['9189c92e8c61ae91402a64b972c4802b2457ce6a799d658256ebf084d5c7eb71'], }), - ('psutil', '5.5.0', { + ('psutil', '5.6.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/psutil/'], - 'checksums': ['1aba93430050270750d046a179c5f3d6e1f5f8b96c20399ba38c596b28fc4d37'], + 'checksums': ['828e1c3ca6756c54ac00f1427fdac8b12e21b8a068c3bb9b631a1734cada25ed'], }), ('ply', '3.11', { 'source_urls': ['https://pypi.python.org/packages/source/p/ply/'], 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], }), - ('marshmallow', '2.18.0', { + ('marshmallow', '2.19.2', { 'source_urls': ['https://pypi.python.org/packages/source/m/marshmallow/'], - 'checksums': ['958e6640bec9a04ca15701e3d99b12c4269d0f43be596f00eeca1f2baf530abc'], + 'checksums': ['e21a4dea20deb167c723e0ffb13f4cf33bcbbeb8a334e92406a3308cedea2826'], }), - ('marshmallow-polyfield', '3.2', { + ('marshmallow-polyfield', '5.6', { 'source_urls': ['https://pypi.python.org/packages/source/m/marshmallow-polyfield/'], - 'checksums': ['72980cb9a43a7c750580b4b08e9d01a8cbd583e1f59360f1924a1ed60f065a4c'], + 'checksums': ['b18cae5563d854fbd15c05b4ff223e4c0074a02436ad12f74838e614dfd1ebc2'], }), - ('jsonschema', '2.6.0', { + ('jsonschema', '3.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], + 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], }), - ('qiskit-terra', '0.7.0', { + ('qiskit-terra', '0.8.0', { 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-terra/'], - 'checksums': ['9cc57da08896627d0f34cf6ae76bd3358a5e6e155f612137ff343dd787134720'], + 'checksums': ['6d14ba28025bdf25be1240271bb500dd23adf71d4e057162b397fe266bf53f8e'], 'modulename': 'qiskit.qobj', }), - ('packaging', '19.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/packaging/'], - }), - ('wheel', '0.33.0', { - 'source_urls': ['https://pypi.python.org/packages/source/w/wheel/'], - }), - ('scikit-build', '0.8.1', { + ('scikit-build', '0.9.0', { 'source_urls': ['https://pypi.python.org/packages/source/s/scikit-build/'], - 'checksums': ['2aa4411a7de928d395eca240a6a794aa05c8d1c42ee53a4ae48fa324693902c2'], + 'checksums': ['81119231cd9c4eba7acc1aaf7351a33b69494c2ccf94a31c2902a80622f089a9'], 'modulename': 'skbuild', }), - ('qiskit-aer', '0.1.1', { - 'source_tmpl': '%(version)s.tar.gz', + ('qiskit-aer', '0.2.0', { 'source_urls': ['https://github.com/Qiskit/qiskit-aer/archive/'], - 'checksums': ['98d74e2a362e5620b59d9f91edf25d20a909766bd1cea6e910913521913136ac'], + 'source_tmpl': '%(version)s.tar.gz', + 'checksums': ['b61857dc3e56903d9fc1bbbf594f5db4174718828515e233e7efcaa52a0da27b'], 'modulename': 'qiskit.providers.aer', }), ('qiskit', version, { 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit/'], - 'checksums': ['08c7f7ccd32a5cb0c0a0c4f63d6ff068d659c9c0b51e2df6f2054e586e8bfa19'], + 'checksums': ['b86893287ec154e0a9422fd773915afee138cb3ac716a5303973dc99429f2fed'], }), - ('qiskit-aqua', '0.4.1', { + ('qiskit-aqua', '0.5.0', { 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-aqua/'], - 'checksums': ['53098c1c57d8ec956826badcbade41ac7b5a047ef562c2d4384a02a5b33c71a2'], + 'checksums': ['6302a6d1107a1c2b5ed06d5fc40b190743a0956cbe68b3d07d604b4ccd4aacc4'], }), - ('qiskit-chemistry', '0.4.2', { + ('qiskit-chemistry', '0.5.0', { 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-chemistry/'], - 'checksums': ['d6164517a41f88c388795e7f3c1162a32c167bd84378ec4a0e28602b7dff038d'], + 'checksums': ['cb1dafa0753acfc98cb258ed773d7506d96f16cd203ed2f2d18bb8f10346ede0'], }), ] From b91c668f231c4f16387ad95620cd7cee20cc9237 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 14 May 2019 18:16:23 +0200 Subject: [PATCH 1628/5331] remove extensions that are already in R --- ...dle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb | 518 +----------------- 1 file changed, 4 insertions(+), 514 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb index e31cf8c354b..fd4fcc3a727 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb @@ -38,6 +38,10 @@ exts_filter = ("R -q --no-save", "library(%(ext_name)s)") # !! order of packages is important !! # packages updated on Sept 25th 2018 exts_list = [ + # readr-1.1.1 is included in R-3.5.1, but GEOquery-2.50.5 needs version 1.3.1 + ('readr', '1.3.1', { + 'checksums': ['33f94de39bb7f2a342fbb2bd4e5afcfec08798eac39672ee18042ac0b349e4f3'], + }), ('BiocGenerics', '0.28.0', { 'checksums': ['68e5a2737f847dd49c6cbd60a77291fd48b39fd219effef0a5c7eaf360d67733'], }), @@ -53,57 +57,9 @@ exts_list = [ ('GenomeInfoDbData', '1.2.0', { 'checksums': ['ac8c370b85021786ef67d9fdd1872930368abd2a46593147320e7b7d31b52636'], }), - ('bitops', '1.0-6', { - 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], - }), - ('RCurl', '1.95-4.11', { - 'checksums': ['792a091cf5b80c460d98ed80fe1cad5d9406d0afc32e466e970ee4d2f68c97bf'], - }), ('GenomeInfoDb', '1.18.1', { 'checksums': ['1a843ca7ede511fe9cb11408060a697f9db7cfbfc3e1c6cf1bfbeb88f2f73711'], }), - ('DBI', '1.0.0', { - 'checksums': ['ff16f118eb3f759183441835e932b87358dd80ab9800ce576a8f3df1b6f01cf5'], - }), - ('Rcpp', '1.0.0', { - 'checksums': ['b7378bf0dda17ef72aa3f2a318a9cb5667bef50b601dc1096431e17426e18bc2'], - }), - ('BH', '1.69.0-1', { - 'checksums': ['a0fd4364b7e368f09c56dec030823f52c16da0787580af7e4615eddeb99baca2'], - }), - ('plogr', '0.2.0', { - 'checksums': ['0e63ba2e1f624005fe25c67cdd403636a912e063d682eca07f2f1d65e9870d29'], - }), - ('bit', '1.1-14', { - 'checksums': ['5cbaace1fb643a665a6ca69b90f7a6d624270de82420ca7a44f306753fcef254'], - }), - ('bit64', '0.9-7', { - 'checksums': ['7b9aaa7f971198728c3629f9ba1a1b24d53db5c7e459498b0fdf86bbd3dff61f'], - }), - ('digest', '0.6.18', { - 'checksums': ['726de348dc41140cdc3c0111590e4824b03536ce36bf0ad93f1c798e32d8714c'], - }), - ('memoise', '1.1.0', { - 'checksums': ['b276f9452a26aeb79e12dd7227fcc8712832781a42f92d70e86040da0573980c'], - }), - ('pkgconfig', '2.0.2', { - 'checksums': ['25997754d1adbe7a251e3bf9879bb52dced27dd8b84767d558f0f644ca8d69ca'], - }), - ('magrittr', '1.5', { - 'checksums': ['05c45943ada9443134caa0ab24db4a962b629f00b755ccf039a2a2a7b2c92ae8'], - }), - ('assertthat', '0.2.0', { - 'checksums': ['d73ef79b1e75293ed889a99571b237a95829c099f7da094d4763f83ea6fde5f2'], - }), - ('prettyunits', '1.0.2', { - 'checksums': ['35a4980586c20650538ae1e4fed4d80fdde3f212b98546fc3c7d9469a1207f5c'], - }), - ('blob', '1.1.1', { - 'checksums': ['accbf9c9746c983e4108c8709995e54e61611ea7e2c51d4b6a0d813261484f53'], - }), - ('RSQLite', '2.1.1', { - 'checksums': ['dfdc7de4f453efeed8361b7bec271a9ed7f0c00110e93c24f486e93206993cbe'], - }), ('AnnotationDbi', '1.44.0', { 'checksums': ['adf4a36fe832569c414e0b0d6ec69bd20f07b0d61be17b734ccb973e6bdca4a4'], }), @@ -119,54 +75,21 @@ exts_list = [ ('GenomicRanges', '1.34.0', { 'checksums': ['49acbcb651dbc9415bfe0a3ee026ce8558930be13662337c14eeb6121a09f02d'], }), - ('futile.options', '1.0.1', { - 'checksums': ['7a9cc974e09598077b242a1069f7fbf4fa7f85ffe25067f6c4c32314ef532570'], - }), - ('formatR', '1.5', { - 'checksums': ['874c197ae3720ec11b44984a055655b99a698e1912104eb9034c11fdf6104da7'], - }), - ('lambda.r', '1.2.3', { - 'checksums': ['0cd8e37ba1a0960888016a85d492da51a57df54bd65ff920b08c79a3bfbe8631'], - }), - ('futile.logger', '1.4.3', { - 'checksums': ['5e8b32d65f77a86d17d90fd8690fc085aa0612df8018e4d6d6c1a60fa65776e4'], - }), - ('snow', '0.4-3', { - 'checksums': ['8512537daf334ea2b8074dbb80cf5e959a403a78d68bc1e97664e8a4f64576d8'], - }), ('BiocParallel', '1.16.5', { 'checksums': ['3490ee29b9c229d5b002d8aebd8966c1e15240085ab2eb66de6249e5c06cc484'], }), ('Rsamtools', '1.34.0', { 'checksums': ['71c1dbe522e20bd5c71c2061dd4b22308aebeaa66983e9f935224421a15c6407'], }), - ('matrixStats', '0.54.0', { - 'checksums': ['8f0db4e181300a208b9aedbebfdf522a2626e6675d2662656efb8ba71b05a06f'], - }), ('DelayedArray', '0.8.0', { 'checksums': ['4eac6d8579a0c020104482ba18275b115d86e4071f4aab53e8787339b1558532'], }), - ('lattice', '0.20-38', { - 'checksums': ['fdeb5e3e50dbbd9d3c5e2fa3eef865132b3eef30fbe53a10c24c7b7dfe5c0a2d'], - }), - ('Matrix', '1.2-15', { - 'checksums': ['7b2624036cefd22948ec8c55cd0e553488cd41ec4b5174d348b046a3a28750d7'], - }), ('SummarizedExperiment', '1.12.0', { 'checksums': ['fa6e20f2707605ea9ddacd130837a6eaf120140c7c1acc5d2df2c22e4e29001d'], }), ('GenomicAlignments', '1.18.1', { 'checksums': ['4d8a103c7e053a6a05b7a7cc5ee2c931d8280c529c5a01bf979c8c2cb6a25ad5'], }), - ('hwriter', '1.3.2', { - 'checksums': ['6b3531d2e7a239be9d6e3a1aa3256b2745eb68aa0bdffd2076d36552d0d7322b'], - }), - ('RColorBrewer', '1.1-2', { - 'checksums': ['f3e9781e84e114b7a88eb099825936cc5ae7276bbba5af94d35adb1b3ea2ccdd'], - }), - ('latticeExtra', '0.6-28', { - 'checksums': ['780695323dfadac108fb27000011c734e2927b1e0f069f247d65d27994c67ec2'], - }), ('ShortRead', '1.40.0', { 'checksums': ['c15fb6ba910ff9534e92cf6e790cf22dc95a1b769b132c625ab3a91087087a46'], }), @@ -200,9 +123,6 @@ exts_list = [ ('org.Hs.eg.db', '3.7.0', { 'checksums': ['3536c87fbe9b0c7c6482fd82f65688ee667a2ed3ba19fd356e783c0f104dbfe3'], }), - ('XML', '3.98-1.16', { - 'checksums': ['57da12ded81e1d6f881a9eb43a95617873752a39aca66b24b41a6552c69c815a'], - }), ('AnnotationForge', '1.24.0', { 'checksums': ['940e8d18ccd79a7b438229c0a1702f302038129fd9e8af9186bb4eed8783db8f'], }), @@ -215,24 +135,9 @@ exts_list = [ ('gcrma', '2.54.0', { 'checksums': ['353ea7be2a6152b4495f03927f0b1f757442c5d32f03ecb30040d6f6508aaeec'], }), - ('ff', '2.2-14', { - 'checksums': ['1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0'], - }), - ('iterators', '1.0.10', { - 'checksums': ['a9e1b2302828d4527766ce12fa9ae06faf8d51e819a43f8efef632b6ddf471e8'], - }), - ('codetools', '0.2-16', { - 'checksums': ['f67a66175cb5d8882457d1e9b91ea2f16813d554fa74f80c1fd6e17cf1877501'], - }), - ('foreach', '1.4.4', { - 'checksums': ['c0a71090d5b70b9a95a6936091dabae9c26e1fc6b9609bfe5fb6346033905e48'], - }), ('oligoClasses', '1.44.0', { 'checksums': ['237c7808a9e0d0f99aca4945f11d8710e62717512ca87a8f274074fbf3eb6d0e'], }), - ('locfit', '1.5-9.1', { - 'checksums': ['f524148fdb29aac3a178618f88718d3d4ac91283014091aa11a01f1c70cd4e51'], - }), ('edgeR', '3.24.3', { 'checksums': ['af0be10708ac096b58c83177dcc9ff08588c9a3bb2f0579da6b0d7ae97aed197'], }), @@ -242,135 +147,21 @@ exts_list = [ ('perm', '1.0-0.0', { 'checksums': ['53c6ee598d5b7b04388915dddc5adf1f8f313b73c3bceb3708db7a632857e500'], }), - ('abind', '1.4-5', { - 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], - }), ('baySeq', '2.16.0', { 'checksums': ['a5ced0c22cdea41c17c7d913e53183add9e320294f6ce6db809c950ae364de38'], }), - ('gtable', '0.2.0', { - 'checksums': ['801e4869830ff3da1d38e41f5a2296a54fc10a7419c6ffb108582850c701e76f'], - }), - ('withr', '2.1.2', { - 'checksums': ['41366f777d8adb83d0bdbac1392a1ab118b36217ca648d3bb9db763aa7ff4686'], - }), - ('R6', '2.3.0', { - 'checksums': ['05b5e117659796c67a16de0854661b25d0739da53a8cb93dcfc528d4c185fac9'], - }), - ('viridisLite', '0.3.0', { - 'checksums': ['780ea12e7c4024d5ba9029f3a107321c74b8d6d9165262f6e64b79e00aa0c2af'], - }), - ('labeling', '0.3', { - 'checksums': ['0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f'], - }), - ('colorspace', '1.4-0', { - 'checksums': ['ce003c5958dd704697959e9dc8a108c8cb568f8d78ece113235732afc5dff556'], - }), - ('munsell', '0.5.0', { - 'checksums': ['d0f3a9fb30e2b5d411fa61db56d4be5733a2621c0edf017d090bdfa5e377e199'], - }), - ('scales', '1.0.0', { - 'checksums': ['0c1f4a14edd336a404da34a3cc71a6a9d0ca2040ba19360c41a79f36e06ca30c'], - }), - ('rlang', '0.3.1', { - 'checksums': ['30427b2be2288e88acd30c4ea348ee06043a649fd73623a63148b1ad96317151'], - }), - ('lazyeval', '0.2.1', { - 'checksums': ['83b3a43e94c40fe7977e43eb607be0a3cd64c02800eae4f2774e7866d1e93f61'], - }), - ('plyr', '1.8.4', { - 'checksums': ['60b522d75961007658c9806f8394db27989f1154727cb0bb970062c96ec9eac5'], - }), - ('glue', '1.3.0', { - 'checksums': ['789e5a44c3635c3d3db26666e635e88adcf61cd02b75465125d95d7a12291cee'], - }), - ('stringi', '1.2.4', { - 'checksums': ['01570a200a25bde62c47b241636e67d73425efa10b924b63959a867796ea86f8'], - }), - ('stringr', '1.3.1', { - 'checksums': ['7a8b8ea038e45978bd797419b16793f44f10c5355ad4c64b74d15276fef20343'], - }), - ('reshape2', '1.4.3', { - 'checksums': ['8aff94c935e75032344b52407593392ddd4e16a88bb206984340c816d42c710e'], - }), - ('MASS', '7.3-51.1', { - 'checksums': ['d82f3f1cee4326a14619b3a1947e99d3acd2831331e81ceeb8150582543c2091'], - }), - ('crayon', '1.3.4', { - 'checksums': ['fc6e9bf990e9532c4fcf1a3d2ce22d8cf12d25a95e4779adfa17713ed836fa68'], - }), - ('cli', '1.0.1', { - 'checksums': ['ef80fbcde15760fd55abbf9413b306e3971b2a7034ab8c415fb52dc0088c5ee4'], - }), - ('utf8', '1.1.4', { - 'checksums': ['f6da9cadfc683057d45f54b43312a359cf96ec2731c0dda18a8eae31d1e31e54'], - }), - ('fansi', '0.4.0', { - 'checksums': ['e104e9d01c7ff8a847f6b332ef544c0ef912859f9c6a514fe2e6f3b34fcfc209'], - }), - ('pillar', '1.3.1', { - 'checksums': ['b338b55f956dd7134f379d39bb94dfb25e13cf27999d6a6e6dc9f292755acbf6'], - }), - ('tibble', '2.0.1', { - 'checksums': ['7ab2cc295eecf00a5310993c99853cd6622ad468e7a60d004b8a73957a713d13'], - }), - ('nlme', '3.1-137', { - 'checksums': ['01049bb9c53826ff4ec5ba7117d766b17a0108c85f80871a5adb0c0b58ef7e87'], - }), - ('mgcv', '1.8-26', { - 'checksums': ['986c81775b5fb9975ebfb13d3ffee2423b858d112db3572ff4b064570af97a09'], - }), - ('ggplot2', '3.1.0', { - 'checksums': ['49e77ccbe1ee9e4278312b001ad34aa1d93a3d98a90aaefcb595da20b2195ed7'], - }), ('qvalue', '2.14.1', { 'checksums': ['4c7b86e6f00ac6cf8f9e1fbed8db808593de2d48555616b111b30a19eadfaa4f'], }), ('impute', '1.56.0', { 'checksums': ['6328aaddbf6a7c9af53afb3d6155a927c7a3a6c7c7486e8f493896df82bce023'], }), - ('zip', '1.0.0', { - 'checksums': ['6fa9ec7b093b8c717c50f205d4335c31c43c2ecb51c0242c9a0337d8d84df965'], - }), - ('openxlsx', '4.1.0', { - 'checksums': ['ab7b127353061a0e1cd621783366ffdd7c858c6df31cbbdd39aaa353af10ffd8'], - }), ('fs', '1.2.6', { 'checksums': ['12a929d8e1c7a561d90eb0692c8a13927aa02d8f8034da6ac8a3235a3156184f'], }), - ('htmltools', '0.3.6', { - 'checksums': ['44affb82f9c2fd76c9e2b58f9229adb003217932b68c3fdbf1327c8d74c868a2'], - }), - ('jsonlite', '1.6', { - 'checksums': ['88c5b425229966b7409145a6cabc72db9ed04f8c37ee95901af0146bb285db53'], - }), - ('later', '0.7.5', { - 'checksums': ['317cdee7555b08de27d03327f32deb2bfead0f63aa70b37e41f54f55cfb01c76'], - }), - ('promises', '1.0.1', { - 'checksums': ['c2dbc7734adf009377a41e570dfe0d82afb91335c9d0ca1ef464b9bdcca65558'], - }), - ('httpuv', '1.4.5.1', { - 'checksums': ['76739878c8583527a3aa6124389ba103acc91b030635290397f3b6c924200d57'], - }), - ('xtable', '1.8-3', { - 'checksums': ['53b2b0fff8d7a8bba434063c2a01b867f510a4389ded2691fbedbc845f08c325'], - }), - ('mime', '0.6', { - 'checksums': ['4775b605ab0117406bee7953c8af59eea8b35e67d1bd63f4007686a7097fc401'], - }), - ('sourcetools', '0.1.7', { - 'checksums': ['47984406efb3b3face133979ccbae9fefb7360b9a6ca1a1c11473681418ed2ca'], - }), - ('shiny', '1.2.0', { - 'checksums': ['fece84fdeb6e9009d4f6b95b4e7c1bea1754ecc9dd79685dc17451f6e54666f1'], - }), ('shinyFiles', '0.7.2', { 'checksums': ['a5bd53a9b3332212dc33c8de24cca12875d4c1012524695e7ee2749378968c36'], }), - ('GSA', '1.03', { - 'checksums': ['dfb84f92508765c74b170bb5bb2b206a11d10fdb4a74473821b0e51cec5d3ac0'], - }), ('samr', '3.0', { 'checksums': ['25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506'], }), @@ -386,57 +177,21 @@ exts_list = [ ('askpass', '1.1', { 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], }), - ('openssl', '1.2', { - 'checksums': ['19a590a7f03faaf92834fbda5e4bb77c1d8557e60d6d0f66388e1706aec58dce'], - }), - ('base64', '2.0', { - 'checksums': ['8e259c2b12446197d1152b83a81bab84ccb5a5b77021a9b5645dd4c63c804bd1'], - }), ('illuminaio', '0.24.0', { 'checksums': ['da66436f85cb2309a82cdfd756bb9374daa14199a7dda3d6f7216ddac94ab7e5'], }), ('rtracklayer', '1.42.1', { 'checksums': ['a60b240d4dba80b4bc72f56d200eca27227c4d04af5258ce96fbebfd766795f9'], }), - ('hms', '0.4.2', { - 'checksums': ['a57820b3e3221e973cba9500b4ad7953730110ee398693d150af833f26d5d0bc'], - }), - ('progress', '1.2.0', { - 'checksums': ['5bb9044d1376cf45e8231c94707ccb7f50996f37c52e40771e1f0cde16a81ce6'], - }), - ('curl', '3.3', { - 'checksums': ['0cb0b9a9280edc42ebed94708541ec86b4f48779e722171e45227eab8a88a5bd'], - }), - ('httr', '1.4.0', { - 'checksums': ['d633f1425da514f65f3b8c034ae0a8b6911995009840c6bb9657ceedb99ddb48'], - }), ('biomaRt', '2.38.0', { 'checksums': ['825ebdd6d3a87ac9e4405126f8de28301cc60cdaeb8bd6cc1db9b673ed9c50d3'], }), ('GenomicFeatures', '1.34.1', { 'checksums': ['063b8117c6ef9a635be5309e65a4da6eac6672fd920844f35b83d5553634986a'], }), - ('registry', '0.5', { - 'checksums': ['5d8be59ba791987b2400e9e8eaaac614cd544c1aece785ec4782ea6d5ea00efb'], - }), - ('bibtex', '0.4.2', { - 'checksums': ['1f06ab3660c940405230ad16ff6e4ba38d4418a59cd9b16d78a4349f8b488372'], - }), - ('pkgmaker', '0.27', { - 'checksums': ['17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a'], - }), - ('rngtools', '1.3.1', { - 'checksums': ['763fc493cb821a4d3e514c0dc876d602a692c528e1d67f295dde70c77009e224'], - }), - ('doRNG', '1.7.1', { - 'checksums': ['27533d54464889d1c21301594137fc0f536574e3a413d61d7df9463ab12a67e9'], - }), ('bumphunter', '1.24.5', { 'checksums': ['2b8588339fad59465b29bd0282d1071778a250681610f5af447d3997f5983bb9'], }), - ('survival', '2.43-3', { - 'checksums': ['996ccd1430b1d997ed1015c58260a15a94b9e5a9ef2d0a580c96c8169494b951'], - }), ('multtest', '2.38.0', { 'checksums': ['f37c0fc21b6b29b3e0c670a8872568fc9e22fd2a369904089ae9c380b8140653'], }), @@ -482,9 +237,6 @@ exts_list = [ ('interactiveDisplayBase', '1.20.0', { 'checksums': ['33abf30d9f376bb68009fd29875f0d8482fa9e756df21a582c5a58c5671bbf13'], }), - ('yaml', '2.2.0', { - 'checksums': ['55bcac87eca360ab5904914fcff473a6981a1f5e6d2215d2634344d0ac30c546'], - }), ('AnnotationHub', '2.14.2', { 'checksums': ['2fb0180c84276f8c0201c149e30ee9ce61d85702b2e05c76d429c665d9cecf9d'], }), @@ -497,123 +249,24 @@ exts_list = [ ('ensembldb', '2.6.3', { 'checksums': ['8b06ac667cf5cff4541cb90359f631cc964e8f634212ae4fb994b76aa6d3ed4f'], }), - ('Formula', '1.2-3', { - 'checksums': ['1411349b20bd09611a9fd0ee6d15f780c758ad2b0e490e908facb49433823872'], - }), - ('acepack', '1.4.1', { - 'checksums': ['82750507926f02a696f6cc03693e8d4a5ee7e92500c8c15a16a9c12addcd28b9'], - }), - ('nnet', '7.3-12', { - 'checksums': ['2723523e8581cc0e2215435ac773033577a16087a3f41d111757dd96b8c5559d'], - }), - ('gridExtra', '2.3', { - 'checksums': ['81b60ce6f237ec308555471ae0119158b115463df696d2eca9b177ded8988e3b'], - }), - ('viridis', '0.5.1', { - 'checksums': ['ddf267515838c6eb092938133035cee62ab6a78760413bfc28b8256165701918'], - }), - ('foreign', '0.8-71', { - 'checksums': ['3bd2392fbcd9dd4f385ac1418a5e454b9769e6414a21fbb5ae1e7ce6072760d7'], - }), - ('rpart', '4.1-13', { - 'checksums': ['8e11a6552224e0fbe23a85aba95acd21a0889a3fe48277f3d345de3147c7494c'], - }), - ('cluster', '2.0.7-1', { - 'checksums': ['b10141090cf3c2b62260611a0ea822eb2f7bab9f4fd656c48bdc12b65c5c3dbf'], - }), - ('base64enc', '0.1-3', { - 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], - }), - ('data.table', '1.12.0', { - 'checksums': ['611b112123dbd4ebd5200770fcdfaaeaab622adeb2b290d36018d3092742e3f7'], - }), - ('rstudioapi', '0.9.0', { - 'checksums': ['5149a2830ae7134c396ce64764b263cf9f348d4399f53da3804f40d7d5bec13e'], - }), - ('backports', '1.1.3', { - 'checksums': ['e41bd146824ec921994f1b176d0e4cca0b36dd3db32ca7a954d872a5ba214cc1'], - }), - ('checkmate', '1.9.1', { - 'checksums': ['b71c368b8ac14c0568a366e4a8a0996cb411485a3da7cefe75fece52eca79ef8'], - }), - ('htmlwidgets', '1.3', { - 'checksums': ['f1e4ffabc29e6cfe857f627da095be3cfcbe0e1f02ae75e572f10b4a026c5a12'], - }), - ('markdown', '0.9', { - 'checksums': ['3068c6a41ca7a76cbedeb93b7371798f4d8437eea69a23c0ed5204c716d1bf23'], - }), - ('evaluate', '0.12', { - 'checksums': ['0f01b00123db52dbf39880eaefcdcb0e19ed70a3e2419731de6c8e1200b13787'], - }), - ('highr', '0.7', { - 'checksums': ['cabba5b6f2ea82024a49c5ced5f1aa476f864bc52bc129038e319e4e26b6f3b7'], - }), - ('xfun', '0.4', { - 'checksums': ['9bdff1d44c3a36081162e75b2680fdf03b38d51972ce90d4525937c11ef72125'], - }), - ('knitr', '1.21', { - 'checksums': ['124c95914f6039bc8801ab1ed7f9fc5beda6c2fcc92bb18a5298c6f948acfe77'], - }), - ('htmlTable', '1.13.1', { - 'checksums': ['689f32b65da6a57ad500e8d9ef3309d346401dca277c6b264a46c8d7c75884d0'], - }), - ('Hmisc', '4.1-1', { - 'checksums': ['991db21cdf73ffbf5b0239a4876b2e76fd243ea33528afd88dc968792f281498'], - }), - ('dichromat', '2.0-0', { - 'checksums': ['31151eaf36f70bdc1172da5ff5088ee51cc0a3db4ead59c7c38c25316d580dd1'], - }), ('biovizBase', '1.30.1', { 'checksums': ['756983116beb732d03f1df97cbf17b8337b55482b7857810291603143adbaf6c'], }), ('OrganismDbi', '1.24.0', { 'checksums': ['d18f7e3d693629674fd1a351b2f4339036792b986602024b023e12cf4cd9fe86'], }), - ('reshape', '0.8.8', { - 'checksums': ['4d5597fde8511e8fe4e4d1fd7adfc7ab37ff41ac68c76a746f7487d7b106d168'], - }), - ('GGally', '1.4.0', { - 'checksums': ['9a47cdf004c41f5e4024327b94227707f4dad3a0ac5556d8f1fba9bf0a6355fe'], - }), ('ggbio', '1.30.0', { 'checksums': ['6424f2b56cae436774cc1bc2754f1ba6a8208316aeabd753d0c8b2f9314e0473'], }), ('geneplotter', '1.60.0', { 'checksums': ['1f530aa91950fa50dad4b7baaaf6d88c6749ab4f93fd571ca8c375fb2fc87082'], }), - ('RcppArmadillo', '0.9.200.7.0', { - 'checksums': ['57ecc51f966b10371c536278e13a2cd421e31664fdff764c310818d8b627a086'], - }), ('DESeq2', '1.22.2', { 'checksums': ['39a4c5d59134bcb7d306fb99587090bfdae905e4c0ffdc0ab907d95e0982aa58'], }), - ('R.methodsS3', '1.7.1', { - 'checksums': ['44b840399266cd27f8f9157777b4d9d85ab7bd31bfdc143b3fc45079a2d8e687'], - }), - ('R.oo', '1.22.0', { - 'checksums': ['c0862e4608fb2b8f91ec4494d46c2f3ba7bc44999f9aa3d7b9625d3792e7dd4c'], - }), - ('R.utils', '2.7.0', { - 'checksums': ['f640ba0019d9d6883a1c634d7c9904b013de4c0bdf5d9e3d7ba49fa248b0b033'], - }), ('ReportingTools', '2.22.1', { 'checksums': ['2a96d5f07a132c760e8ec3cef1983c9e0b9c220b2cb48fca094819269fe137bd'], }), - ('KernSmooth', '2.23-15', { - 'checksums': ['8b72d23ed121a54af188b2cda4441e3ce2646359309885f6455b82c0275210f6'], - }), - ('gtools', '3.8.1', { - 'checksums': ['051484459bd8ad1b03425b8843d24f6828fea18f7357cfa1c192198cc3f4ba38'], - }), - ('gdata', '2.18.0', { - 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], - }), - ('caTools', '1.17.1.1', { - 'checksums': ['d53e2c5c77f1bd4744703d7196dbc9b4671a120bbb5b9b3edc45fc57c0650c06'], - }), - ('gplots', '3.0.1', { - 'checksums': ['343df84327ac3d03494992e79ee3afc78ba3bdc08af9a305ee3fb0a38745cb0a'], - }), ('affycoretools', '1.54.0', { 'checksums': ['fffb5511271e3a5c1e03d687cbef785c42b651ac4f2ce68604ecf69766ac5708'], }), @@ -635,75 +288,27 @@ exts_list = [ ('geneLenDataBase', '1.18.0', { 'checksums': ['8a2ccf555d1ba4a15fe495736494ace21447dc655e8227e7e94c2ba7f725f50d'], }), - ('BiasedUrn', '1.07', { - 'checksums': ['2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e'], - }), ('goseq', '1.34.1', { 'checksums': ['b68e8aa086994c1b63e0c0f0b116ec1deb8e59fd6665b397c29249c5509207c9'], }), - ('png', '0.1-7', { - 'checksums': ['e269ff968f04384fc9421d17cfc7c10cf7756b11c2d6d126e9776f5aca65553c'], - }), ('KEGGREST', '1.22.0', { 'checksums': ['090c49ad8583289972bbea01e454f5063c880a3ca161e8b8d6a2417e5469972e'], }), ('KEGGgraph', '1.42.0', { 'checksums': ['c3bf6a08b8de2bed6b0f46020e2832c5404c20f4f41b89d2672007c3b0bbc067'], }), - ('TeachingDemos', '2.10', { - 'checksums': ['2ef4c2e36ba13e32f66000e84281a3616584c86b255bca8643ff3fe4f78ed704'], - }), ('KEGGprofile', '1.24.0', { 'checksums': ['6f151bb767c5f34d62ae53122a0ef53a0cc850fde20f3a0d2c3e73dac8400e90'], }), - ('clipr', '0.5.0', { - 'checksums': ['fd303f8b7f29badcdf490bb2d579acdfc4f4e1aa9c90ac77ab9d05ce3d053dbf'], - }), - ('readr', '1.3.1', { - 'checksums': ['33f94de39bb7f2a342fbb2bd4e5afcfec08798eac39672ee18042ac0b349e4f3'], - }), - ('xml2', '1.2.0', { - 'checksums': ['0a7a916fe9c5da9ac45aeb4c6b6b25d33c07652d422b9f2bb570f2e8f4ac9494'], - }), - ('bindr', '0.1.1', { - 'checksums': ['7c785ca77ceb3ab9282148bcecf64d1857d35f5b800531d49483622fe67505d0'], - }), - ('bindrcpp', '0.2.2', { - 'checksums': ['48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467'], - }), - ('purrr', '0.2.5', { - 'checksums': ['a4a68a453f5341ae84c3e8d77b0587ed586f36eb51f64f1315750eabfe1f8535'], - }), - ('tidyselect', '0.2.5', { - 'checksums': ['5ce2e86230fa35cfc09aa71dcdd6e05e1554a5739c863ca354d241bfccb86c74'], - }), - ('dplyr', '0.7.8', { - 'checksums': ['37799ac5734d14b14ab9594ddec7f79e9a798907b87ff8b2d281a148a14de51a'], - }), - ('tidyr', '0.8.2', { - 'checksums': ['99a508d0539390364789c5f4835b36c4a383927f0ec1648e2a4636c1cc6e490f'], - }), ('GEOquery', '2.50.5', { 'checksums': ['e6c104433f3c731029045682156fdcef41e177a2fbf0292f8c217ac400a08d1c'], }), - ('RcppEigen', '0.3.3.5.0', { - 'checksums': ['e5c6af17770c5f57b7cf2fba04ad1a519901b446e8138bfff221952458207f05'], - }), ('RSpectra', '0.13-1', { 'checksums': ['4731e667dbb60d4ef96808f62269e6d093746b37141dd16f715f7acf210388eb'], }), ('rARPACK', '0.11-0', { 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], }), - ('igraph', '1.2.2', { - 'checksums': ['9da2dadf9c1ed495413b32464c6a32fae9d33636822754043e708d8dd6a9efad'], - }), - ('ellipse', '0.4.1', { - 'checksums': ['1a9a9c52195b26c2b4d51ad159ab98aff7aa8ca25fdc6b2198818d1a0adb023d'], - }), - ('corpcor', '1.6.9', { - 'checksums': ['2e4fabd1d3936fecea67fa365233590147ca50bb45cf80efb53a10345a8a23c2'], - }), ('mixOmics', '6.6.1', { 'checksums': ['0d2e326d5db55fce5182f066b8d9551d1a313cc08c6b58d11d764b305e6f41c4'], }), @@ -719,18 +324,6 @@ exts_list = [ ('DelayedMatrixStats', '1.4.0', { 'checksums': ['9c789a06aad6d6750f693546a472b8f5838c0562f333aab9d8d2ef40b712d30d'], }), - ('beanplot', '1.2', { - 'checksums': ['49da299139a47171c5b4ccdea79ffbbc152894e05d552e676f135147c0c9b372'], - }), - ('nor1mix', '1.2-3', { - 'checksums': ['435e6519e832ef5229c51ccb2619640e6b50dfc7470f70f0c938d18a114273af'], - }), - ('mclust', '5.4.2', { - 'checksums': ['a4a31e9a832dafc860369bd4b05fdc3defd767599c159c2bfc6ea8ebb8162524'], - }), - ('quadprog', '1.5-5', { - 'checksums': ['d999620688354c283de5bb305203f5db70271b4dfdc23577cae8c2ba94c9e349'], - }), ('minfi', '1.28.3', { 'checksums': ['06763a808d39fe522da6b0c275ee01f7064ad0b6d66a8a6eac269f288e054451'], }), @@ -740,9 +333,6 @@ exts_list = [ ('methylumi', '2.28.0', { 'checksums': ['823fdd55a13dc91b9fc40923048780fc1f8648dde1d9fec4da2e5f8642c4e292'], }), - ('nleqslv', '3.3.2', { - 'checksums': ['f54956cf67f9970bb3c6803684c84a27ac78165055745e444efc45cfecb63fed'], - }), ('lumi', '2.34.0', { 'checksums': ['1875282d270ae0d59a2a7edb5428c038b22aa11c3559c85387c016cfde95f5ba'], }), @@ -752,12 +342,6 @@ exts_list = [ ('tkWidgets', '1.60.0', { 'checksums': ['07fe5b4450ab81a62538fd2d77a56264702f249fcec16b18d0d012edf125e09f'], }), - ('class', '7.3-15', { - 'checksums': ['f6bf33d610c726d58622b6cea78a808c7d6a317d02409d27c17741dfd1c730f4'], - }), - ('e1071', '1.7-0', { - 'checksums': ['93699a2e16826459221cf7c9896d99e87fdc1c0e2e270bda302670760cbf643a'], - }), ('Mfuzz', '2.42.0', { 'checksums': ['4f6e827fdfd2b5c064eabf81e5b7b6cade0c3f588c7807bc2f4db00e4599bd80'], }), @@ -773,9 +357,6 @@ exts_list = [ ('Gviz', '1.26.4', { 'checksums': ['3e71c331b19e588b06ac9fd1a88f83abaa6e0ee7b9f6a664161b2ac0df8e6c4b'], }), - ('fastcluster', '1.1.25', { - 'checksums': ['f3661def975802f3dd3cec5b2a1379f3707eacff945cf448e33aec0da1ed4205'], - }), ('cummeRbund', '2.24.0', { 'checksums': ['21adb07dd4830b376fc7e715e0cb24246acd4c79185a55928b5d86fc87b988ba'], }), @@ -788,9 +369,6 @@ exts_list = [ ('derfinder', '1.16.1', { 'checksums': ['557cfeec77cb4a2927d7d78efddca3baf35faacaf5da81561926e0eb3e7ab1f1'], }), - ('logspline', '2.1.11', { - 'checksums': ['781e6eaf31a7000c303f7c8494160d00eaceebc31dfb6946622f4e7301ed871c'], - }), ('polyester', '1.18.0', { 'checksums': ['378fb7719088a438795f8bd37018b356d10a860002aa7ec1de6a61c87f559c29'], }), @@ -806,21 +384,9 @@ exts_list = [ ('CGHbase', '1.42.0', { 'checksums': ['4c0728c47a21b8f5984720e7f089744a627205ce2d732cdcb809c4d613b91d3e'], }), - ('mvtnorm', '1.0-8', { - 'checksums': ['2010cab50fb7a5117e3c61f06e4a797ea6bf92b1ab20c132cb929d453d154451'], - }), - ('penalized', '0.9-51', { - 'checksums': ['eaa80dca99981fb9eb576261f30046cfe492d014cc2bf286c447b03a92e299fd'], - }), - ('snowfall', '1.84-6.1', { - 'checksums': ['5c446df3a931e522a8b138cf1fb7ca5815cc82fcf486dbac964dcbc0690e248d'], - }), ('sigaR', '1.30.0', { 'checksums': ['8f952ba5677edad47aabf36a2c100b77ad9de6c1b9b728f7dfe9c386b36995ee'], }), - ('glmnet', '2.0-16', { - 'checksums': ['a54ccd802fce6625f3b69d747b28efe62ed8cc23397a5f8df4777d177e2839af'], - }), ('metagenomeSeq', '1.24.1', { 'checksums': ['e8785142935fd01357c1a27f182768bdc43e1f2607100ef7e975cf4ae34e4b7f'], }), @@ -833,18 +399,6 @@ exts_list = [ ('biomformat', '1.10.1', { 'checksums': ['f8ddc44ed0a1897fdc172eb4cd98ca1899666f2b914ab87ca3b72db52b868ea8'], }), - ('ade4', '1.7-13', { - 'checksums': ['f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b'], - }), - ('ape', '5.2', { - 'checksums': ['27eb02856c130d59de6e06276be4981709923756319e465a7f2d4756d4f46415'], - }), - ('permute', '0.9-4', { - 'checksums': ['a541a5f5636ddd67fd856d3e11224f15bc068e96e23aabe3e607a7e7c2fc1cf1'], - }), - ('vegan', '2.5-3', { - 'checksums': ['6c5c8f0ad7ba8dbb29df0e119da41d330f756e6d0ab2cba24904f808a0fd7d08'], - }), ('phyloseq', '1.26.1', { 'checksums': ['fcea94a1d59b022764fd0d44839ecb038f6b58128b896e7a7102c16ca40c578d'], }), @@ -869,75 +423,21 @@ exts_list = [ ('beachmat', '1.4.0', { 'checksums': ['b93696765f628c9c7eebb1c0a09490eec2b58a49866809fae10f3d0c74adef1f'], }), - ('beeswarm', '0.2.3', { - 'checksums': ['0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843'], - }), - ('vipor', '0.4.5', { - 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], - }), - ('ggbeeswarm', '0.6.0', { - 'checksums': ['bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333'], - }), ('scater', '1.10.1', { 'checksums': ['aa14e6516a7288863563306c97b2f2d0054587699e077f44b2ace2f28e873266'], }), - ('dynamicTreeCut', '1.63-1', { - 'checksums': ['831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9'], - }), ('RcppAnnoy', '0.0.11', { 'checksums': ['a149cf6681bbb6d80825189cf6563605388aa6e4584b6207809b3dc7ac0265c6'], }), ('BiocNeighbors', '1.0.0', { 'checksums': ['9406fb3842902b9aa7e7f50180eb64a8c4c6ad3bbb170381e39db6c894494bbb'], }), - ('statmod', '1.4.30', { - 'checksums': ['9d2c1722a85f53623a9ee9f73d835119ae22ae2b8ec7b50d675401e314ea641f'], - }), ('scran', '1.10.2', { 'checksums': ['ef585de49f2f799c5bb0747a0de502271d4e3efca94a176ab674e037328daf1e'], }), - ('doParallel', '1.0.14', { - 'checksums': ['cbbb7f37606d608a9603915ee65587f8ed4bb4a8405ecfaa7f33b8c423d11207'], - }), - ('pheatmap', '1.0.12', { - 'checksums': ['579d96ee0417203b85417780eca921969cda3acc210c859bf9dfeff11539b0c1'], - }), - ('ROCR', '1.0-7', { - 'checksums': ['e7ef710f847e441a48b20fdc781dbc1377f5a060a5ee635234053f7a2a435ec9'], - }), - ('DEoptimR', '1.0-8', { - 'checksums': ['846911c1b2561a9fae73a8c60a21a5680963ebb0050af3c1f1147ae9a121e5ef'], - }), - ('robustbase', '0.93-3', { - 'checksums': ['8c1d402b3d8ddf8e617224076fe5c7a5507c3a6e05151e68cf38341c1e0e10db'], - }), - ('pcaPP', '1.9-73', { - 'checksums': ['ca4566b0babfbe83ef9418283b08a12b3420dc362f93c6562f265df7926b53fc'], - }), - ('rrcov', '1.4-7', { - 'checksums': ['cbd08ccce8b583a2f88946a3267c8fc494ee2b44ba749b9296a6e3d818f6f293'], - }), - ('WriteXLS', '4.0.0', { - 'checksums': ['a0541da45e16bc4bf994cdf3f07a0e202c38d52386460c64e27fe6c1cd889d5b'], - }), ('SC3', '1.10.1', { 'checksums': ['dc5034387915f7d1e2c994bf7b03f74c1c50319533afc44a9c56b831115f1812'], }), - ('shape', '1.4.4', { - 'checksums': ['f4cb1b7d7c84cf08d2fa97f712ea7eb53ed5fa16e5c7293b820bceabea984d41'], - }), - ('GlobalOptions', '0.1.0', { - 'checksums': ['567a0a51f6b7b14127302f00e6e4944befd4964c069f96a9e61256e8c3c79ef2'], - }), - ('circlize', '0.4.5', { - 'checksums': ['092a445b090286ef9802775e649496d0505c7c5d34e39ad395a0bdc3bf4c1662'], - }), - ('rjson', '0.2.20', { - 'checksums': ['3a287c1e5ee7c333ed8385913c0a307daf99335fbdf803e9dcca6e3d5adb3f6c'], - }), - ('GetoptLong', '0.1.7', { - 'checksums': ['b9a98881db407eae9b711c4fa9170168fd5f3be1f8485cd8f28d0a60ace083ba'], - }), ('ComplexHeatmap', '1.20.0', { 'checksums': ['5209bffdaa033bd239239fa644fc7779a282483e1c2f7d1dbe9506e9d86f0168'], }), @@ -954,24 +454,14 @@ exts_list = [ 'checksums': ['1872da8a1b041a13b9d8d3135f93587f572c95b720c5abdd784075591851f233'], }), ('ballgown', '2.14.1', { - 'checksum': ['3e9d90b9f345d122824260c588d1d36a602a525a9daa1826190193d8c24ba483'], 'checksums': ['51234729544bc1815d638d369b115f3a4c002103820d6451efac008dd2f6721c'], }), ('DropletUtils', '1.2.2', { 'checksums': ['5c330a2dd3a0e74229f718eac0e830d311448b490de8fbeb023764914f83ae4f'], }), - ('lpSolve', '5.6.13', { - 'checksums': ['d5d41c53212dead4fd8e6425a9d3c5767cdc5feb19d768a4704116d791cf498d'], - }), - ('limSolve', '1.5.5.3', { - 'checksums': ['2f27c03411e0d771ad50d5412125bf4fa0ba461051610edc77e20d28488e86d2'], - }), ('DeconRNASeq', '1.24.0', { 'checksums': ['5612f66173d7523b35f857c5778e80d40ce7fd6a9c8b6b9f12b60f0bbaa5b5c8'], }), - ('shinythemes', '1.1.2', { - 'checksums': ['2e13d4d5317fc61082e8f3128b15e0b10ed9736ce81e152dd7ae7f6109f9b18a'], - }), ('GSVA', '1.30.0', { 'checksums': ['91502b2f1ccae239bbc3a0e6623741e408f345fdedbd13c93fb570b17be51261'], }), From 9d883483b2e0142a59ed81180d6c50515c59f7dc Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 14 May 2019 18:18:20 +0200 Subject: [PATCH 1629/5331] remove unused options --- .../R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb index fd4fcc3a727..1d5c48ad112 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.8-foss-2018b-R-3.5.1.eb @@ -28,8 +28,6 @@ exts_default_options = { ], 'source_tmpl': '%(name)s_%(version)s.tar.gz' } -ext_options = exts_default_options -bioconductor_options = exts_default_options exts_defaultclass = 'RPackage' exts_filter = ("R -q --no-save", "library(%(ext_name)s)") From f7675e93b0841b9c6d415406304c619ce7481070 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 18:27:45 +0200 Subject: [PATCH 1630/5331] adding easyconfigs: SymEngine-0.4.0-GCC-8.2.0-2.31.1.eb, JiTCODE-1.4.0-foss-2019a-Python-3.7.2.eb --- .../JiTCODE-1.4.0-foss-2019a-Python-3.7.2.eb | 56 +++++++++++++++++++ .../SymEngine-0.4.0-GCC-8.2.0-2.31.1.eb | 25 +++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.4.0-foss-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/s/SymEngine/SymEngine-0.4.0-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.4.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.4.0-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..34bf107599e --- /dev/null +++ b/easybuild/easyconfigs/j/JiTCODE/JiTCODE-1.4.0-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'JiTCODE' +version = '1.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://jitcde-common.readthedocs.io' +description = "Just-in-time compilation for ordinary/delay/stochastic differential equations (DDEs)" + +toolchain = {'name': 'foss', 'version': '2019a'} + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('SymEngine', '0.4.0'), +] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.10.1', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + 'checksums': ['065c4f02ebe7f7cf559e49ee5a95fb800a9e4528727aec6f24402a5374c65013'], + }), + ('symengine', '0.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/symengine'], + 'checksums': ['54c553692ca94262377923d5064ac89da84e12de4ef63f2b1db5b7850ac9d1c2'], + 'preinstallopts': "export SymEngine_DIR=$EBROOTSYMENGINE/lib/cmake/symengine && ", + }), + ('jitcxde-common', '1.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jitcxde-common'], + 'source_tmpl': 'jitcxde_common-%(version)s.tar.gz', + 'checksums': ['dbdfc7121d5f8ea44f680d6d24a8406477381e9db94ce72dc77924f7ccdac219'], + 'modulename': 'jitcxde_common', + }), + ('jitcdde', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jitcdde'], + 'checksums': ['68e9fcc2bb0da764fc17c77666e2de6cecbaf480003086a775a241a308f9669a'], + }), + ('jitcsde', version, { + 'source_urls': ['https://pypi.python.org/packages/source/j/jitcsde'], + 'checksums': ['2697740a8921adab68fd54563c6693eb57bdf498f1ff44e382562dad43dc0794'], + }), + ('jitcode', version, { + 'source_urls': ['https://pypi.python.org/packages/source/j/jitcode'], + 'checksums': ['01dca542b24252d038e3fe601192362a32e7c0ab3184591b46b00b549cb36868'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SymEngine/SymEngine-0.4.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/s/SymEngine/SymEngine-0.4.0-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..db7176c4cae --- /dev/null +++ b/easybuild/easyconfigs/s/SymEngine/SymEngine-0.4.0-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'SymEngine' +version = '0.4.0' + +homepage = 'https://github.com/symengine/symengine' +description = "SymEngine is a standalone fast C++ symbolic manipulation library." + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/symengine/symengine/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd755901a9e2a49e53ba3bbe3f565f94265af05299e57a7b592186dd35916a1b'] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [('GMP', '6.1.2')] + +sanity_check_paths = { + 'files': ['lib/libsymengine.a'], + 'dirs': ['include/symengine', 'lib/cmake/symengine'], +} + +moduleclass = 'lib' From 0fab3429f19a3dec91efc99f89dfe3d61d221fb5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 18:44:43 +0200 Subject: [PATCH 1631/5331] check_ldshared is not needed when building with foss toolchain --- .../s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb index dfa2daf7146..c685c2a82e1 100755 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3-foss-2019a.eb @@ -22,9 +22,6 @@ dependencies = [('SciPy-bundle', '2019.03')] download_dep_fail = True use_pip = True -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True - options = {'modulename': 'sklearn'} sanity_check_paths = { From c31497a43768b252a27d056f130e92886c14fd72 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 14 May 2019 20:39:47 +0200 Subject: [PATCH 1632/5331] Add libc++ and lld --- .../easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb index 4fa097341fb..ad4efd5e5da 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb @@ -28,6 +28,10 @@ sources = [ 'compiler-rt-%(version)s.src.tar.xz', 'polly-%(version)s.src.tar.xz', 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', ] checksums = [ '8872be1b12c61450cacc82b3d153eab02be2546ef34fa3580ed14137bb26224c', # llvm-8.0.0.src.tar.xz @@ -35,6 +39,9 @@ checksums = [ 'b435c7474f459e71b2831f1a4e3f1d21203cb9c0172e94e9d9b69f50354f21b1', # compiler-rt-8.0.0.src.tar.xz 'e3f5a3d6794ef8233af302c45ceb464b74cdc369c1ac735b6b381b21e4d89df4', # polly-8.0.0.src.tar.xz 'f7b1705d2f16c4fc23d6531f67d2dd6fb78a077dd346b02fed64f4b8df65c9d5', # openmp-8.0.0.src.tar.xz + '9caec8ec922e32ffa130f0fb08e4c5a242d7e68ce757631e425e9eba2e1a6e37', # lld-8.0.0.src.tar.xz + 'c2902675e7c84324fb2c1e45489220f250ede016cc3117186785d9dc291f9de2', # libcxx-8.0.0.src.tar.xz + 'c2d6de9629f7c072ac20ada776374e9e3168142f20a46cdb9d6df973922b07cd', # libcxxabi-8.0.0.src.tar.xz ] dependencies = [ @@ -51,6 +58,9 @@ builddependencies = [ assertions = True usepolly = True +build_lld = True +libcxx = True + skip_all_tests = True moduleclass = 'compiler' From 0760402c4725f9f80b3dd14ca97bb1d477d479c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 May 2019 22:19:58 +0200 Subject: [PATCH 1633/5331] fix a bunch of missing extensions in Qiskit easyconfig (WIP) --- .../q/Qiskit/Qiskit-0.10.1-foss-2019a.eb | 86 ++++++++++++++++--- 1 file changed, 72 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.10.1-foss-2019a.eb b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.10.1-foss-2019a.eb index 45e6dcffc68..5597defb1ae 100644 --- a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.10.1-foss-2019a.eb +++ b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.10.1-foss-2019a.eb @@ -24,10 +24,12 @@ dependencies = [ ('h5py', '2.9.0'), ('scikit-learn', '0.20.3'), ('CVXOPT', '1.2.3'), +# ('PyTorch', '1.1.0', versionsuffix), ] -use_pip = True +#use_pip = True +# see https://github.com/Qiskit/qiskit/blob/master/setup.py for qiskit-* package versions exts_list = [ ('ntlm-auth', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/n/ntlm-auth/'], @@ -45,21 +47,33 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/ply/'], 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], }), + # qiskit-terra requires marshmallow 2.x + marshmallow-polyfield 3.2 ('marshmallow', '2.19.2', { 'source_urls': ['https://pypi.python.org/packages/source/m/marshmallow/'], 'checksums': ['e21a4dea20deb167c723e0ffb13f4cf33bcbbeb8a334e92406a3308cedea2826'], }), - ('marshmallow-polyfield', '5.6', { + ('marshmallow-polyfield', '3.2', { 'source_urls': ['https://pypi.python.org/packages/source/m/marshmallow-polyfield/'], - 'checksums': ['b18cae5563d854fbd15c05b4ff223e4c0074a02436ad12f74838e614dfd1ebc2'], + 'checksums': ['72980cb9a43a7c750580b4b08e9d01a8cbd583e1f59360f1924a1ed60f065a4c'], }), - ('jsonschema', '3.0.1', { + ('pyrsistent', '0.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyrsistent/'], + 'checksums': ['16692ee739d42cf5e39cef8d27649a8c1fdb7aa99887098f1460057c5eb75c3a'], + }), + # jsonschema 2.6.x is required by qiskit-terra + ('jsonschema', '2.6.0', { 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], - 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], + 'checksums': ['6ff5f3180870836cae40f06fa10419f557208175f13ad7bc26caa77beb1f6e02'], + }), + ('pylatexenc', '1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pylatexenc/'], + 'checksums': ['7e7a86285bc1a2197b2734fe075b0dded9dabfc553c2dcb56b14d28ee33918f9'], }), ('qiskit-terra', '0.8.0', { - 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-terra/'], - 'checksums': ['6d14ba28025bdf25be1240271bb500dd23adf71d4e057162b397fe266bf53f8e'], + 'source_urls': ['https://github.com/Qiskit/qiskit-terra/archive/'], + 'source_tmpl': '%(version)s.tar.gz', + 'checksums': ['cbb52b27b8389fcb6a5c1f69f23f7366533d147d61babdb28c104ee106d8d91d'], + 'preinstallopts': "python setup.py build_ext --inplace && ", 'modulename': 'qiskit.qobj', }), ('scikit-build', '0.9.0', { @@ -68,27 +82,71 @@ exts_list = [ 'modulename': 'skbuild', }), ('qiskit-aer', '0.2.0', { - 'source_urls': ['https://github.com/Qiskit/qiskit-aer/archive/'], - 'source_tmpl': '%(version)s.tar.gz', - 'checksums': ['b61857dc3e56903d9fc1bbbf594f5db4174718828515e233e7efcaa52a0da27b'], + 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-aer/'], + 'checksums': ['00a663ca066eea50cd42b852241351bb178f9e4910a47ab2a4706cc3a49534d5'], 'modulename': 'qiskit.providers.aer', }), - ('qiskit', version, { - 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit/'], - 'checksums': ['b86893287ec154e0a9422fd773915afee138cb3ac716a5303973dc99429f2fed'], + ('pyeda', '0.28.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyeda/'], + 'checksums': ['07185f458d5d0b2ba5058da8b95dad6ab7684ceaf41237a25bcd3f005490f59d'], + }), + ('more-itertools', '5.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'], + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + ('inflection', '0.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/inflection/'], + 'checksums': ['18ea7fb7a7d152853386523def08736aa8c32636b047ade55f7578c4edeb16ca'], + }), + ('Quandl', '3.4.8', { + 'source_urls': ['https://pypi.python.org/packages/source/Q/Quandl/'], + 'checksums': ['63cdd98e192e85abc2e9a5f5bead243dc82b663bcb98894d379f4617c4b7339d'], + }), + ('fastdtw', '0.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/fastdtw/'], + 'checksums': ['09a24d62a8eb72f87c03692dffae4b8d8499b53f503e9abce5e717c5b705dff9'], + }), + ('docplex', '2.9.141', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docplex/'], + 'checksums': ['8bc4b4f073af18ffec139cf244bf58146b8be46fd45dfba88361c4c6ab68e313'], + }), + ('dlx', '1.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/dlx/'], + 'checksums': ['ef75bc9d590216ebde7d4811f9ae6b2d6c6dc2a54772d94ae13384dc517a5aae'], + }), + ('docloud', '1.0.369', { + 'source_urls': ['https://pypi.python.org/packages/source/d/docloud/'], + 'checksums': ['01cb439f5bbc6366f4fbb9a9185655301f645d3356476b6191199f334dd7a771'], + }), + ('qiskit-ignis', '0.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-ignis/'], + 'checksums': ['29af3f3dd8d485ad3d438713c3416f307bb743047f759039c28c789130028262'], }), ('qiskit-aqua', '0.5.0', { 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-aqua/'], 'checksums': ['6302a6d1107a1c2b5ed06d5fc40b190743a0956cbe68b3d07d604b4ccd4aacc4'], }), + ('pyscf', '1.6.1.post1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyscf/'], + }), ('qiskit-chemistry', '0.5.0', { 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-chemistry/'], 'checksums': ['cb1dafa0753acfc98cb258ed773d7506d96f16cd203ed2f2d18bb8f10346ede0'], }), + ('qiskit-ibmq-provider', '0.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit-ibmq-provider/'], + 'checksums': ['5fc05803ead012ed38601ae7fab5846ee23806929b1056a243c53ef615f92986'], + }), + ('qiskit', version, { + 'source_urls': ['https://pypi.python.org/packages/source/q/qiskit/'], + 'checksums': ['b86893287ec154e0a9422fd773915afee138cb3ac716a5303973dc99429f2fed'], + }), ] + + sanity_check_paths = { - 'files': ['bin/qiskit_aqua_cmd', 'bin/qiskit_chemistry_cmd'], + 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From 8ba361059c44d247e6c7b237ac874cab9aa25f76 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 15 May 2019 07:32:24 +0200 Subject: [PATCH 1634/5331] adding easyconfigs: ASE-3.17.0-foss-2019a-Python-3.7.2.eb, ASE-3.17.0-intel-2019a-Python-3.7.2.eb --- .../ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb | 60 +++++++++++++++++++ .../ASE-3.17.0-intel-2019a-Python-3.7.2.eb | 60 +++++++++++++++++++ 2 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..9943399eb73 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.17.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +dependencies = [ + ('Python', '3.7.2'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.0.3', '-Python-%(pyver)s'), +] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('Werkzeug', '0.14.1', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], + 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], + }), + ('Click', '7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('itsdangerous', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Flask', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], + 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], + }), + ('ase', version, { + 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], + 'checksums': ['8fe49ddc5a554b69b6468dd1f45a29f67c61997319d0cb7e217e41a5aeef8fb4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..f4d19d238ab --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.17.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +dependencies = [ + ('Python', '3.7.2'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.0.3', '-Python-%(pyver)s'), +] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('Werkzeug', '0.14.1', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Werkzeug'], + 'checksums': ['c3fd7a7d41976d9f44db327260e263132466836cef6f91512889ed60ad26557c'], + }), + ('Click', '7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/C/Click'], + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('itsdangerous', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/itsdangerous'], + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Flask', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/F/Flask'], + 'checksums': ['2271c0070dbcb5275fad4a82e29f23ab92682dc45f9dfbc22c02ba9b9322ce48'], + }), + ('ase', version, { + 'source_urls': ['https://pypi.python.org/packages/source/a/ase'], + 'checksums': ['8fe49ddc5a554b69b6468dd1f45a29f67c61997319d0cb7e217e41a5aeef8fb4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' From 526dfa83288d4ae7cbe5ee99648d141becc130a7 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 15 May 2019 08:23:57 +0200 Subject: [PATCH 1635/5331] Add check_ldshared as suggested by @akesandgren. --- .../easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb index f4d19d238ab..0f9a4f840c1 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb @@ -18,6 +18,9 @@ dependencies = [ use_pip = True +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + exts_list = [ ('MarkupSafe', '1.1.0', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], From c75a83c18d7977413e4a7e6f2831958641ec86ec Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 15 May 2019 09:14:32 +0200 Subject: [PATCH 1636/5331] DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb --- .../protobuf-python-3.6.0-fosscuda-2018b-Python-3.6.6.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.6.0-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.6.0-fosscuda-2018b-Python-3.6.6.eb index 61cd573dfd0..71d01fa9c2d 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.6.0-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.6.0-fosscuda-2018b-Python-3.6.6.eb @@ -18,6 +18,9 @@ dependencies = [ ('protobuf', version), ] +download_dep_fail = True +use_pip = False # installation fails with pip + start_dir = 'python' sanity_check_paths = { From 0db994a5ab1f60861dc62d7a22d22e6ed682c2fc Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 15 May 2019 10:20:15 +0200 Subject: [PATCH 1637/5331] revert Theano version --- .../d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb index 6fa95023492..6aba7c3a750 100644 --- a/easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/d/DeepSurv/DeepSurv-20180922-fosscuda-2018b-Python-3.6.6.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'fosscuda', 'version': '2018b'} dependencies = [ ('Python', '3.6.6'), - ('Theano', '1.0.4', versionsuffix), + ('Theano', '1.0.3', versionsuffix), ('h5py', '2.8.0', versionsuffix), ('protobuf-python', '3.6.0', versionsuffix), ('Pillow', '5.3.0', versionsuffix), From 6fe898f929c3ae4428435db9f9714b4140e54e49 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 15 May 2019 10:42:26 +0200 Subject: [PATCH 1638/5331] Add SciPy-bundle as an explicit dependency. Thanks, @akesandgren. --- .../easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb | 1 + .../easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb index 9943399eb73..40ff474e221 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'foss', 'version': '2019a'} dependencies = [ ('Python', '3.7.2'), ('Tkinter', '%(pyver)s'), + ('SciPy-bundle', '2019.03'), ('matplotlib', '3.0.3', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb index 0f9a4f840c1..71e468dd4a3 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'intel', 'version': '2019a'} dependencies = [ ('Python', '3.7.2'), ('Tkinter', '%(pyver)s'), + ('SciPy-bundle', '2019.03'), ('matplotlib', '3.0.3', '-Python-%(pyver)s'), ] From 9f9ec2c249c6526f8b5b609694e11d749f70fa8a Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 15 May 2019 10:44:55 +0200 Subject: [PATCH 1639/5331] Add SciPy-bundle as an explicit dependency. Thanks, @akesandgren. --- .../easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb index 71e468dd4a3..7d9d0f47dc1 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb @@ -19,7 +19,7 @@ dependencies = [ use_pip = True -# required because we're building Python packages using Intel compilers on top of Python built with GCC +# required because we're building Python packages (MarkupSafe) using Intel compilers on top of Python built with GCC check_ldshared = True exts_list = [ From 4afa36a9fca2a73d0e35192dc5d7937a1b47ee25 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 15 May 2019 11:01:28 +0200 Subject: [PATCH 1640/5331] add Theano easyconfig --- ...heano-1.0.3-fosscuda-2018b-Python-3.6.6.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.0.3-fosscuda-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.3-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.3-fosscuda-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..46c7130178c --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.3-fosscuda-2018b-Python-3.6.6.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/%(namelower)s' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'fosscuda', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['637f3b34d40ef5e0d54dd4c40618475aaa085c26d2491e925c98e2ad4bc2115a'] + +dependencies = [ + ('Python', '3.6.6'), + ('cuDNN', '7.1.4.18'), + ('libgpuarray', '0.7.6', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-cache', 'bin/%(namelower)s-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From f709f052cca7dfe23cddecf39912fe88c5cf9d56 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 15 May 2019 13:13:29 +0200 Subject: [PATCH 1641/5331] Add download_dep_fail=True --- .../easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb | 1 + .../easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb index 40ff474e221..c16398fd78c 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb @@ -18,6 +18,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True exts_list = [ ('MarkupSafe', '1.1.0', { diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb index 7d9d0f47dc1..92266a0dc89 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb @@ -18,6 +18,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True # required because we're building Python packages (MarkupSafe) using Intel compilers on top of Python built with GCC check_ldshared = True From a920e7cf38972ec17e8b3b731a820dbdb27e19a8 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 15 May 2019 13:17:38 +0200 Subject: [PATCH 1642/5331] Revert previous commit. --- .../easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb | 1 - .../easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb index c16398fd78c..40ff474e221 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-foss-2019a-Python-3.7.2.eb @@ -18,7 +18,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True exts_list = [ ('MarkupSafe', '1.1.0', { diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb index 92266a0dc89..7d9d0f47dc1 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.17.0-intel-2019a-Python-3.7.2.eb @@ -18,7 +18,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True # required because we're building Python packages (MarkupSafe) using Intel compilers on top of Python built with GCC check_ldshared = True From da6755bf061b7b89d693dea8132577da70bedc40 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Wed, 15 May 2019 12:34:00 +0100 Subject: [PATCH 1643/5331] adding easyconfigs: STAR-2.7.0f-foss-2018b.eb --- .../s/STAR/STAR-2.7.0f-foss-2018b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.0f-foss-2018b.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.0f-foss-2018b.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.0f-foss-2018b.eb new file mode 100644 index 00000000000..1ff83a32a9d --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.0f-foss-2018b.eb @@ -0,0 +1,39 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.0f' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['daead0a87b259e6311f48f31ccaab5bd53ef1da9d6e5cd7210e0d714b7e23204'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/STAR', 'bin/STARlong'], + 'dirs': [], +} + +moduleclass = 'bio' From 99b693af5e93aa2e8c8ff9b87ac204ddf774c9ad Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 15 May 2019 15:04:51 +0200 Subject: [PATCH 1644/5331] Consistently only use `lib` in `sanity_check_paths` --- .../easyconfigs/c/CubeGUI/CubeGUI-4.4.3-GCCcore-8.2.0.eb | 3 +-- .../easyconfigs/c/CubeLib/CubeLib-4.4.3-GCCcore-8.2.0.eb | 3 +-- .../c/CubeWriter/CubeWriter-4.4.2-GCCcore-8.2.0.eb | 3 +-- easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-8.2.0.eb | 3 +-- easybuild/easyconfigs/s/Scalasca/Scalasca-2.5-gompi-2019a.eb | 2 +- easybuild/easyconfigs/s/Score-P/Score-P-5.0-gompi-2019a.eb | 4 ++-- 6 files changed, 7 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4.3-GCCcore-8.2.0.eb index bcae9c3a646..a8ee1f1559d 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4.3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.4.3-GCCcore-8.2.0.eb @@ -46,8 +46,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/cube', 'bin/cubegui-config', - ('lib/libcube4gui.a', 'lib64/libcube4gui.a'), - ('lib/libcube4gui.%s' % SHLIB_EXT, 'lib64/libcube4gui.%s' % SHLIB_EXT)], + 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], 'dirs': ['include/cubegui', 'lib/cube-plugins'], } diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4.3-GCCcore-8.2.0.eb index 61861e220be..2e80db1efae 100644 --- a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4.3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.4.3-GCCcore-8.2.0.eb @@ -49,8 +49,7 @@ configopts = '--enable-shared' sanity_check_paths = { 'files': ['bin/cubelib-config', - ('lib/libcube4.a', 'lib64/libcube4.a'), - ('lib/libcube4.%s' % SHLIB_EXT, 'lib64/libcube4.%s' % SHLIB_EXT)], + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], 'dirs': ['include/cubelib'], } diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.2-GCCcore-8.2.0.eb index 17f0df4e6db..8eb4704806a 100644 --- a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.4.2-GCCcore-8.2.0.eb @@ -48,8 +48,7 @@ configopts = '--enable-shared' sanity_check_paths = { 'files': ['bin/cubew-config', - ('lib/libcube4w.a', 'lib64/libcube4w.a'), - ('lib/libcube4w.%s' % SHLIB_EXT, 'lib64/libcube4w.%s' % SHLIB_EXT)], + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], 'dirs': ['include/cubew'], } diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-8.2.0.eb index 89e1cd3074e..0e7681f4890 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.1.1-GCCcore-8.2.0.eb @@ -41,8 +41,7 @@ configopts = '--enable-shared' sanity_check_paths = { 'files': ['bin/otf2-config', 'include/otf2/otf2.h', - ('lib/libotf2.a', 'lib64/libotf2.a'), - ('lib/libotf2.%s' % SHLIB_EXT, 'lib64/libotf2.%s' % SHLIB_EXT)], + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.5-gompi-2019a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.5-gompi-2019a.eb index 668ba474f36..c249e12f18b 100644 --- a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.5-gompi-2019a.eb +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.5-gompi-2019a.eb @@ -43,7 +43,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/scalasca', ('lib/libpearl.replay.a', 'lib64/libpearl.replay.a')], + 'files': ['bin/scalasca', 'lib/libpearl.replay.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-5.0-gompi-2019a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-5.0-gompi-2019a.eb index f87087b32cc..409dc91a433 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-5.0-gompi-2019a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-5.0-gompi-2019a.eb @@ -51,8 +51,8 @@ configopts = '--enable-shared' sanity_check_paths = { 'files': ['bin/scorep', 'include/scorep/SCOREP_User.h', - ('lib/libscorep_adapter_mpi_event.a', 'lib64/libscorep_adapter_mpi_event.a'), - ('lib/libscorep_adapter_mpi_event.%s' % SHLIB_EXT, 'lib64/libscorep_adapter_mpi_event.%s' % SHLIB_EXT)], + 'lib/libscorep_adapter_mpi_event.a', + 'lib/libscorep_adapter_mpi_event.%s' % SHLIB_EXT], 'dirs': [], } From 090cadc6c76bbb749aa043d297fc6df42ea82407 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 15 May 2019 15:06:30 +0200 Subject: [PATCH 1645/5331] Explain version number --- easybuild/easyconfigs/c/Cube/Cube-20190321-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cube/Cube-20190321-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/Cube/Cube-20190321-GCCcore-8.2.0.eb index c86e8e8a3cf..e062a907b9e 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-20190321-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-20190321-GCCcore-8.2.0.eb @@ -12,7 +12,7 @@ easyblock = 'Bundle' name = 'Cube' -version = '20190321' +version = '20190321' # release date of newest package in bundle homepage = 'http://www.scalasca.org/software/cube-4.x/download.html' description = """ From 3d0fcf85d9cdbd99d3d3bb32fb39557abd9bdb66 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 15 May 2019 15:30:48 +0200 Subject: [PATCH 1646/5331] update source_urls --- .../easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb | 9 +++------ .../easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb | 9 +++------ 2 files changed, 6 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb index abbe58bfa0a..c05edd4f527 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb @@ -14,12 +14,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://apps.jcns.fz-juelich.de/src/libcerf/', - 'http://apps.jcns.fz-juelich.de/src/libcerf/old', -] -sources = [SOURCE_TGZ] -checksums = ['70101cac4a0d7863322d4d06cf95c507a9cfd64fc99ad1b31a8425204cfd9672'] +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v1.11/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['992271fef2f1ed5a477cb0a928eb650d5f1d3b9ec9cdb51816496ef8ef770f5f'] builddependencies = [ ('binutils', '2.30'), diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb index 33f40878949..001eb8ae8aa 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb @@ -14,12 +14,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://apps.jcns.fz-juelich.de/src/libcerf/', - 'http://apps.jcns.fz-juelich.de/src/libcerf/old', -] -sources = [SOURCE_TGZ] -checksums = ['70101cac4a0d7863322d4d06cf95c507a9cfd64fc99ad1b31a8425204cfd9672'] +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v1.11/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['992271fef2f1ed5a477cb0a928eb650d5f1d3b9ec9cdb51816496ef8ef770f5f'] builddependencies = [ ('binutils', '2.31.1'), From 4fa2a307fd96a931f9d010859014b976a2775c17 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 15 May 2019 15:46:09 +0200 Subject: [PATCH 1647/5331] Update to match changes in easyblock --- .../c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb index 469dfe1d84d..43ff66c2863 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb @@ -64,6 +64,8 @@ assertions = True usepolly = True build_lld = True libcxx = True +enable_rtti = True +default_openmp_runtime = "libomp" skip_all_tests = True From a6e8f5685439114015625151dda73604159602b0 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 15 May 2019 06:57:44 -0700 Subject: [PATCH 1648/5331] fix download source --- .../l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb index 7fc68cd85c6..0ff322b64b1 100644 --- a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb @@ -8,18 +8,12 @@ description = """Library for reading and writing coordinate system information f toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['https://github.com/OSGeo/libgeotiff/archive'] -sources = [{ - 'download_filename': '%(version)s.tar.gz', - 'filename': SOURCE_TAR_GZ -}] -checksums = ['fb04491572afb25ffe60239fdfdcfa2c64e6cf644cad9b0b922b10115ccbd488'] +source_urls = ['http://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['f9e99733c170d11052f562bcd2c7cb4de53ed405f7acdde4f16195cd3ead612c'] builddependencies = [ ('binutils', '2.31.1'), - ('libtool', '2.4.6'), - ('Automake', '1.16.1'), - ('Autoconf', '2.69'), ] dependencies = [ @@ -29,8 +23,6 @@ dependencies = [ ('libjpeg-turbo', '2.0.2'), ] -start_dir = 'libgeotiff' -preconfigopts = 'autoreconf --install && ' configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' sanity_check_paths = { From b69c3b99f83246c2c184f167dfb0366e1f848f34 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 15 May 2019 16:29:07 +0200 Subject: [PATCH 1649/5331] Add values for new options that ocaisa introduced --- easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb index ad4efd5e5da..3ffbb977e43 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb @@ -60,6 +60,8 @@ assertions = True usepolly = True build_lld = True libcxx = True +enable_rtti = True +default_openmp_runtime = 'libomp' skip_all_tests = True From 1d41f6282b9f8016b5f05e95cdc56c66d8e83c97 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 15 May 2019 16:37:24 +0200 Subject: [PATCH 1650/5331] adding easyconfigs: MCR-R2019a.eb --- easybuild/easyconfigs/m/MCR/MCR-R2019a.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2019a.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2019a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2019a.eb new file mode 100644 index 00000000000..c62b4dff524 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2019a.eb @@ -0,0 +1,16 @@ +name = 'MCR' +version = 'R2019a' # runtime version 9.6 + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://ssd.mathworks.com/supportfiles/downloads/%(version)s/Release/1/deployment_files/installer/' + 'complete/glnxa64/'] +sources = ['MATLAB_Runtime_%(version)s_Update_1_glnxa64.zip'] +checksums = ['2408fc2ad3dc1376be9655596c46f13d400e680a2da916f47a142027bb4e4acd'] + +moduleclass = 'math' From 287d2874d031d276757534f4a0644990aa71f642 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 15 May 2019 20:17:10 +0200 Subject: [PATCH 1651/5331] Add missing patches to OpenMPI/3.1.3 for gcccuda/2019a. --- .../o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb index 9090fca6b02..52720ffa78b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-gcccuda-2019a.eb @@ -10,7 +10,16 @@ toolchain = {'name': 'gcccuda', 'version': '2019a'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d'] +patches = [ + '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', + 'OpenMPI-3.1_fix-ib-query.patch', +] +checksums = [ + '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz + # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch + '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', + '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch +] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] From ae3565db237ee8deea114fc462fb8ef4bdc5ac5e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 16 May 2019 08:12:59 +0200 Subject: [PATCH 1652/5331] Add fix-ib-query patch to OpenMPI 2.1.x and 3.0.x easyconfigs. --- .../o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb | 6 +++- .../o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb | 6 +++- .../OpenMPI/OpenMPI-2.1.1-gcccuda-2017.02.eb | 6 +++- .../o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017b.eb | 6 +++- ....1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb | 6 +++- .../o/OpenMPI/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb | 6 +++- .../o/OpenMPI/OpenMPI-2.1.2-gcccuda-2018a.eb | 6 +++- ....1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 6 +++- ....1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb | 6 +++- .../o/OpenMPI/OpenMPI-2.1_fix-ib-query.patch | 28 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb | 6 +++- .../o/OpenMPI/OpenMPI-3.0_fix-ib-query.patch | 28 +++++++++++++++++++ 12 files changed, 106 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1_fix-ib-query.patch create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0_fix-ib-query.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb index 3364e4a6a5c..231c668d3af 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.0-GCC-6.3.0-2.28.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCC', 'version': '6.3.0-2.28'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['265a9c64a468cce464edd069ed8612e1865c5f112f84f4a7a855fb2a0d15e74b'] +patches = ['OpenMPI-2.1_fix-ib-query.patch'] +checksums = [ + '265a9c64a468cce464edd069ed8612e1865c5f112f84f4a7a855fb2a0d15e74b', # openmpi-2.1.0.tar.gz + '662d7ef1d0cd0890d2dc4ecb5243012be29bf6b4003da0f006e7cd2125d40e4c', # OpenMPI-2.1_fix-ib-query.patch +] dependencies = [('hwloc', '1.11.6')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb index a458923dae0..cd176a98cfc 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-GCC-6.4.0-2.28.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc'] +patches = ['OpenMPI-2.1_fix-ib-query.patch'] +checksums = [ + 'afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc', # openmpi-2.1.1.tar.gz + '662d7ef1d0cd0890d2dc4ecb5243012be29bf6b4003da0f006e7cd2125d40e4c', # OpenMPI-2.1_fix-ib-query.patch +] dependencies = [('hwloc', '1.11.7')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017.02.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017.02.eb index f892b0298f0..ea28897ead6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017.02.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017.02.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'gcccuda', 'version': '2017.02'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc'] +patches = ['OpenMPI-2.1_fix-ib-query.patch'] +checksums = [ + 'afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc', # openmpi-2.1.1.tar.gz + '662d7ef1d0cd0890d2dc4ecb5243012be29bf6b4003da0f006e7cd2125d40e4c', # OpenMPI-2.1_fix-ib-query.patch +] dependencies = [('hwloc', '1.11.7')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017b.eb index 03f221313d0..44d65f198a8 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-gcccuda-2017b.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'gcccuda', 'version': '2017b'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc'] +patches = ['OpenMPI-2.1_fix-ib-query.patch'] +checksums = [ + 'afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc', # openmpi-2.1.1.tar.gz + '662d7ef1d0cd0890d2dc4ecb5243012be29bf6b4003da0f006e7cd2125d40e4c', # OpenMPI-2.1_fix-ib-query.patch +] dependencies = [('hwloc', '1.11.7')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb index c5a9eca5c49..fd5e5e8c603 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'iccifort', 'version': '2017.4.196-GCC-6.4.0-2.28'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc'] +patches = ['OpenMPI-2.1_fix-ib-query.patch'] +checksums = [ + 'afe4bef3c4378bc76eea96c623d5aa4c1c98b9e057d281c646e68869292a77dc', # openmpi-2.1.1.tar.gz + '662d7ef1d0cd0890d2dc4ecb5243012be29bf6b4003da0f006e7cd2125d40e4c', # OpenMPI-2.1_fix-ib-query.patch +] dependencies = [('hwloc', '1.11.7')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb index e2a34f73f91..7dc4e510838 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-GCC-6.4.0-2.28.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['e5bf7b2d7517f5cb7c9e1fed15d2df2da501669072477b21a513e892a22663bc'] +patches = ['OpenMPI-2.1_fix-ib-query.patch'] +checksums = [ + 'e5bf7b2d7517f5cb7c9e1fed15d2df2da501669072477b21a513e892a22663bc', # openmpi-2.1.2.tar.gz + '662d7ef1d0cd0890d2dc4ecb5243012be29bf6b4003da0f006e7cd2125d40e4c', # OpenMPI-2.1_fix-ib-query.patch +] dependencies = [('hwloc', '1.11.8')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-gcccuda-2018a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-gcccuda-2018a.eb index 08dc0dfea8b..a7b134a56ce 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-gcccuda-2018a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-gcccuda-2018a.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'gcccuda', 'version': '2018a'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['e5bf7b2d7517f5cb7c9e1fed15d2df2da501669072477b21a513e892a22663bc'] +patches = ['OpenMPI-2.1_fix-ib-query.patch'] +checksums = [ + 'e5bf7b2d7517f5cb7c9e1fed15d2df2da501669072477b21a513e892a22663bc', # openmpi-2.1.2.tar.gz + '662d7ef1d0cd0890d2dc4ecb5243012be29bf6b4003da0f006e7cd2125d40e4c', # OpenMPI-2.1_fix-ib-query.patch +] dependencies = [('hwloc', '1.11.8')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 8a367e7662d..7a4c2aaf833 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['e5bf7b2d7517f5cb7c9e1fed15d2df2da501669072477b21a513e892a22663bc'] +patches = ['OpenMPI-2.1_fix-ib-query.patch'] +checksums = [ + 'e5bf7b2d7517f5cb7c9e1fed15d2df2da501669072477b21a513e892a22663bc', # openmpi-2.1.2.tar.gz + '662d7ef1d0cd0890d2dc4ecb5243012be29bf6b4003da0f006e7cd2125d40e4c', # OpenMPI-2.1_fix-ib-query.patch +] dependencies = [('hwloc', '1.11.8')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb index 98d18f520cb..7ca4b077d69 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'iccifort', 'version': '2018.2.199-GCC-6.4.0-2.28'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['3e2f7b349b7d28a85c88d65f71327fcc2300a56c1fb6cd9ff0647d806523435e'] +patches = ['OpenMPI-2.1_fix-ib-query.patch'] +checksums = [ + '3e2f7b349b7d28a85c88d65f71327fcc2300a56c1fb6cd9ff0647d806523435e', # openmpi-2.1.3.tar.gz + '662d7ef1d0cd0890d2dc4ecb5243012be29bf6b4003da0f006e7cd2125d40e4c', # OpenMPI-2.1_fix-ib-query.patch +] dependencies = [('hwloc', '1.11.8')] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1_fix-ib-query.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1_fix-ib-query.patch new file mode 100644 index 00000000000..2603fc72946 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1_fix-ib-query.patch @@ -0,0 +1,28 @@ +commit d70f27f9b209a00b89814fd11f7895eb82bec773 +Author: Howard Pritchard +Date: Wed Oct 31 14:50:15 2018 -0600 + + btl/openib: fix a problem with ib query + + Under certain circumstances, ibv_exp_query_device was + returning an error due to uninitialized fields in the + extended attributes struct. + + Fixes: #5810 + Fixes: #5914 + + Signed-off-by: Howard Pritchard + (cherry picked from commit 8126779a354b3e0c720d3e1790f7b936dd5b93b2) + +diff --git a/opal/mca/btl/openib/btl_openib_component.c b/opal/mca/btl/openib/btl_openib_component.c +index 44792a1..8b86cbb 100644 +--- a/opal/mca/btl/openib/btl_openib_component.c ++++ b/opal/mca/btl/openib/btl_openib_component.c +@@ -1642,6 +1642,7 @@ static int init_one_device(opal_list_t *btl_list, struct ibv_device* ib_dev) + goto error; + } + #if HAVE_DECL_IBV_EXP_QUERY_DEVICE ++ memset(&device->ib_exp_dev_attr, 0, sizeof(device->ib_exp_dev_attr)); + device->ib_exp_dev_attr.comp_mask = IBV_EXP_DEVICE_ATTR_RESERVED - 1; + if(ibv_exp_query_device(device->ib_dev_context, &device->ib_exp_dev_attr)){ + BTL_ERROR(("error obtaining device attributes for %s errno says %s", diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb index c1e81c2933e..4554afa65bd 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0.0-GCC-7.2.0-2.29.eb @@ -10,11 +10,15 @@ toolchain = {'name': 'GCC', 'version': '7.2.0-2.29'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] +patches = [ + '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', + 'OpenMPI-3.0_fix-ib-query.patch', +] checksums = [ '0bbb279b88edc25bbded39520dab6d4b32020277a6088fb1456c9437a8231cf8', # openmpi-3.0.0.tar.gz # OpenMPI-3.0.0-add_ompi_datatype_attribute_to_release_ucp_datatype.patch 'ea6fb132c67046d9c6d9af4ccae20963b4cc9816264d0ba755b246a68f2da808', + 'f7e1f0831d47499cf42f03daad60946b2096e89745c2cba677725ae9beafd0b5', # OpenMPI-3.0_fix-ib-query.patch ] # needed for --with-verbs diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0_fix-ib-query.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0_fix-ib-query.patch new file mode 100644 index 00000000000..ecb89828285 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.0_fix-ib-query.patch @@ -0,0 +1,28 @@ +commit c388378d3072f7a40cf63c86f01ed36fde13153b +Author: Howard Pritchard +Date: Wed Oct 31 14:50:15 2018 -0600 + + btl/openib: fix a problem with ib query + + Under certain circumstances, ibv_exp_query_device was + returning an error due to uninitialized fields in the + extended attributes struct. + + Fixes: #5810 + Fixes: #5914 + + Signed-off-by: Howard Pritchard + (cherry picked from commit 8126779a354b3e0c720d3e1790f7b936dd5b93b2) + +diff --git a/opal/mca/btl/openib/btl_openib_component.c b/opal/mca/btl/openib/btl_openib_component.c +index c7cfb83..02694c9 100644 +--- a/opal/mca/btl/openib/btl_openib_component.c ++++ b/opal/mca/btl/openib/btl_openib_component.c +@@ -1664,6 +1664,7 @@ static int init_one_device(opal_list_t *btl_list, struct ibv_device* ib_dev) + goto error; + } + #if HAVE_DECL_IBV_EXP_QUERY_DEVICE ++ memset(&device->ib_exp_dev_attr, 0, sizeof(device->ib_exp_dev_attr)); + device->ib_exp_dev_attr.comp_mask = IBV_EXP_DEVICE_ATTR_RESERVED - 1; + if(ibv_exp_query_device(device->ib_dev_context, &device->ib_exp_dev_attr)){ + BTL_ERROR(("error obtaining device attributes for %s errno says %s", From 65684b3dfafa279bb5a48a8b3010f7dc64d7034a Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 May 2019 10:08:06 +0200 Subject: [PATCH 1653/5331] Make `zlib` a real dependency rather than a build dep Also add checksums where missing and rearrange parameters to make easyconfigs more consistent --- .../binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 11 ++++++++--- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 9 +++++++-- .../binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 11 ++++++++--- .../b/binutils/binutils-2.25-GCC-4.9.3.eb | 9 +++++++-- .../binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 11 ++++++++--- .../b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 11 ++++++++--- .../b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 11 ++++++++--- .../b/binutils/binutils-2.25-GCCcore-4.9.4.eb | 11 ++++++++--- easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb | 9 +++++++-- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 9 +++++++-- .../b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 11 ++++++++--- .../b/binutils/binutils-2.26-GCCcore-5.4.0.eb | 10 +++++++--- .../b/binutils/binutils-2.26-GCCcore-5.5.0.eb | 10 +++++++--- .../b/binutils/binutils-2.26-GCCcore-6.3.0.eb | 13 +++++++++---- easybuild/easyconfigs/b/binutils/binutils-2.26.eb | 4 +++- .../b/binutils/binutils-2.27-GCCcore-6.1.0.eb | 11 ++++++++--- .../b/binutils/binutils-2.27-GCCcore-6.2.0.eb | 11 ++++++++--- .../b/binutils/binutils-2.27-GCCcore-6.3.0.eb | 11 ++++++++--- easybuild/easyconfigs/b/binutils/binutils-2.27.eb | 9 +++++++-- .../b/binutils/binutils-2.28-GCCcore-6.3.0.eb | 11 ++++++++--- .../b/binutils/binutils-2.28-GCCcore-6.4.0.eb | 11 +++++++---- .../b/binutils/binutils-2.28-GCCcore-7.1.0.eb | 11 ++++++++--- easybuild/easyconfigs/b/binutils/binutils-2.28.eb | 9 ++++++--- .../b/binutils/binutils-2.29-GCCcore-7.2.0.eb | 12 ++++++++---- .../b/binutils/binutils-2.29-GCCcore-system.eb | 10 +++++++--- easybuild/easyconfigs/b/binutils/binutils-2.29.eb | 9 ++++++--- .../b/binutils/binutils-2.30-GCCcore-7.3.0.eb | 6 ++++-- .../b/binutils/binutils-2.30-GCCcore-8.1.0.eb | 6 ++++-- easybuild/easyconfigs/b/binutils/binutils-2.30.eb | 5 +++-- .../b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb | 10 +++++++--- .../b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb | 10 +++++++--- easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb | 9 ++++++--- .../b/binutils/binutils-2.32-GCCcore-8.3.0.eb | 10 +++++++--- .../b/binutils/binutils-2.32-GCCcore-9.1.0.eb | 10 +++++++--- easybuild/easyconfigs/b/binutils/binutils-2.32.eb | 9 ++++++--- 35 files changed, 242 insertions(+), 98 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 08e10d150ca..8d99a6addde 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -6,16 +6,21 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-%s' % version} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz +] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index ea9a13974b4..ca83eb6fa7c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -6,13 +6,18 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCC', 'version': '4.9.2'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz +] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 9709696cf5d..4370f97620b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -6,16 +6,21 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-%s' % version} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz +] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index 7ccace85015..6e45ced018a 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -6,13 +6,18 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCC', 'version': '4.9.3'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz +] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index d6e68008e5b..9fb2cfbe865 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -6,16 +6,21 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-%s' % version} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz +] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb index 9ec7a3f3f32..6cd1a30c201 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -6,17 +6,22 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '4.9.2'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz +] builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index f411442d121..3fc5d09536a 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -6,17 +6,22 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '4.9.3'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz +] builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb index 4eee9df8fa2..f457102034d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb @@ -6,17 +6,22 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '4.9.4'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz +] builddependencies = [ ('M4', '1.4.17'), ('flex', '2.6.0'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb index e3f5b15724b..333e277670e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -6,13 +6,18 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + '82a40a37b13a12facb36ac7e87846475a1d80f2e63467b1b8d63ec8b6a2b63fc', # binutils-2.25.1.tar.gz +] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index e08cd975ad8..60fcc2a7de2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -6,14 +6,19 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz +] builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb index d7c829040f2..da0fa5b924c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -6,16 +6,21 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '5.3.0'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + '9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1', # binutils-2.26.tar.gz +] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep - ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb index 2ae6ba18a54..ee88b84916b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb @@ -8,15 +8,19 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1'] +checksums = [ + '9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1', # binutils-2.26.tar.gz +] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep - ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb index 2d41305b4cf..4b70b533cc7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb @@ -8,15 +8,19 @@ toolchain = {'name': 'GCCcore', 'version': '5.5.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1'] +checksums = [ + '9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1', # binutils-2.26.tar.gz +] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb index d95c058f0c8..62f6f0bddfa 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb @@ -6,18 +6,23 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -checksums = ['9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1'] +sources = [SOURCE_TAR_GZ] patches = ['binutils-%(version)s_build-with-GCCcore-6.3.0.patch'] +checksums = [ + '9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1', # binutils-2.26.tar.gz + 'eb766886ae76be046ec217c70afd1627db845891c4c7418311c10af21e7850e5', # binutils-2.26_build-with-GCCcore-6.3.0.patch +] builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb index 8cc66cacab0..ec85dfe32e5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb @@ -20,7 +20,9 @@ configopts = ' --disable-werror' builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - # zlib required, but being linked instatically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb index 215aaf0cb28..4ea09a9ed9f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb @@ -6,16 +6,21 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '6.1.0'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + '26253bf0f360ceeba1d9ab6965c57c6a48a01a8343382130d1ed47c468a3094f', # binutils-2.27.tar.gz +] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb index 88e16771dff..c5851cc3a42 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb @@ -6,16 +6,21 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '6.2.0'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + '26253bf0f360ceeba1d9ab6965c57c6a48a01a8343382130d1ed47c468a3094f', # binutils-2.27.tar.gz +] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.8'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb index 9346ceba7e7..b7437fbc909 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb @@ -6,16 +6,21 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + '26253bf0f360ceeba1d9ab6965c57c6a48a01a8343382130d1ed47c468a3094f', # binutils-2.27.tar.gz +] builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb index 6011a780095..f36edacc493 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb @@ -6,13 +6,18 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + '26253bf0f360ceeba1d9ab6965c57c6a48a01a8343382130d1ed47c468a3094f', # binutils-2.27.tar.gz +] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb index de910489db7..57eb8122dc0 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb @@ -6,16 +6,21 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + 'cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf', # binutils-2.28.tar.gz +] builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb index 4281a9f3238..9bf3a9cc18d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb @@ -2,23 +2,26 @@ name = 'binutils' version = '2.28' homepage = 'http://directory.fsf.org/project/binutils/' - description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf'] +checksums = [ + 'cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf', # binutils-2.28.tar.gz +] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, # to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb index 10ecc14d7a4..4df97f98f0c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb @@ -6,16 +6,21 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '7.1.0'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = [ + 'cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf', # binutils-2.28.tar.gz +] builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb index a50c4f25ca1..c06f4780fec 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb @@ -2,19 +2,22 @@ name = 'binutils' version = '2.28' homepage = 'http://directory.fsf.org/project/binutils/' - description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf'] +checksums = [ + 'cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf', # binutils-2.28.tar.gz +] builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb index 2e11b1cadfd..d33d5d9a717 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb @@ -6,17 +6,21 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '7.2.0'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -checksums = ['172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4'] +sources = [SOURCE_TAR_GZ] +checksums = [ + '172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4', # binutils-2.29.tar.gz +] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb index 2ef25643c91..07b9f5e1750 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb @@ -6,14 +6,18 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': 'system'} -sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -checksums = ['172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4'] +sources = [SOURCE_TAR_GZ] +checksums = [ + '172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4', # binutils-2.29.tar.gz +] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29.eb index 6efb559b8a6..7a35e6c14b9 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29.eb @@ -2,19 +2,22 @@ name = 'binutils' version = '2.29' homepage = 'http://directory.fsf.org/project/binutils/' - description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4'] +checksums = [ + '172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4', # binutils-2.29.tar.gz +] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb index a526a5584f6..f27b731fc30 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb @@ -17,10 +17,12 @@ checksums = [ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb index 017e4221132..577322b830c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb @@ -17,10 +17,12 @@ checksums = [ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb index 12fa985a5f4..a5ac0d7694c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb @@ -2,7 +2,6 @@ name = 'binutils' version = '2.30' homepage = 'http://directory.fsf.org/project/binutils/' - description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} @@ -18,7 +17,9 @@ checksums = [ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), - # zlib required, but being linked in statically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb index 40a7a398381..fc5d1ff6b6b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb @@ -8,15 +8,19 @@ toolchain = {'name': 'GCCcore', 'version': '7.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88'] +checksums = [ + 'e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88', # binutils-2.31.1.tar.gz +] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.2.2'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb index 31b94454c7b..32f34f1e824 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb @@ -8,15 +8,19 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88'] +checksums = [ + 'e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88', # binutils-2.31.1.tar.gz +] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.5'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb index 64fb2100b2e..d6fac033a36 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb @@ -2,19 +2,22 @@ name = 'binutils' version = '2.31.1' homepage = 'http://directory.fsf.org/project/binutils/' - description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88'] +checksums = [ + 'e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88', # binutils-2.31.1.tar.gz +] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.5'), - # zlib required, but being linked in statically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb index 282f81deb1e..590c08ba810 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb @@ -8,15 +8,19 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e'] +checksums = [ + '9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e', # binutils-2.32.tar.gz +] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb index 1efeca34ea5..d43378fc336 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb @@ -8,15 +8,19 @@ toolchain = {'name': 'GCCcore', 'version': '9.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e'] +checksums = [ + '9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e', # binutils-2.32.tar.gz +] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), - # zlib required, but being linked in statically, so not a runtime dep - ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] +dependencies = [ + ('zlib', '1.2.11'), +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb index aeeea2b58ea..ef960762547 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb @@ -2,19 +2,22 @@ name = 'binutils' version = '2.32' homepage = 'http://directory.fsf.org/project/binutils/' - description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e'] +checksums = [ + '9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e', # binutils-2.32.tar.gz +] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), - # zlib required, but being linked in statically, so not a runtime dep +] + +dependencies = [ ('zlib', '1.2.11'), ] From e364f86aae16794e2807919c51f4c644bedee1bf Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 16 May 2019 11:02:20 +0200 Subject: [PATCH 1654/5331] make suggested change --- easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb index c05edd4f527..cd2705d2ccd 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-7.3.0.eb @@ -14,7 +14,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v1.11/'] +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] sources = ['%(name)s-v%(version)s.tar.gz'] checksums = ['992271fef2f1ed5a477cb0a928eb650d5f1d3b9ec9cdb51816496ef8ef770f5f'] diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb index 001eb8ae8aa..3e2804d373d 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.11-GCCcore-8.2.0.eb @@ -14,7 +14,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v1.11/'] +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] sources = ['%(name)s-v%(version)s.tar.gz'] checksums = ['992271fef2f1ed5a477cb0a928eb650d5f1d3b9ec9cdb51816496ef8ef770f5f'] From 3c2aac2f8d470ce4dbb0cbbd42a63cee4f75b0ae Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 16 May 2019 11:06:18 +0200 Subject: [PATCH 1655/5331] libomp is default runtime since 2015 See https://github.com/easybuilders/easybuild-easyblocks/pull/1717#issuecomment-492983499 --- .../c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb index 43ff66c2863..2e4b2a8d3c8 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb @@ -65,7 +65,6 @@ usepolly = True build_lld = True libcxx = True enable_rtti = True -default_openmp_runtime = "libomp" skip_all_tests = True From 421dc202d0e93c65646af18e1089ce02954a4cef Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Thu, 16 May 2019 11:09:59 +0100 Subject: [PATCH 1656/5331] adding easyconfigs: Subread-1.6.4-foss-2018b.eb --- .../s/Subread/Subread-1.6.4-foss-2018b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-1.6.4-foss-2018b.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.6.4-foss-2018b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.6.4-foss-2018b.eb new file mode 100644 index 00000000000..4165d53a635 --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-1.6.4-foss-2018b.eb @@ -0,0 +1,28 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'Subread' +version = '1.6.4' + +homepage = 'http://%(namelower)s.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] +checksums = ['b7bd0ee3b0942d791aecce6454d2f3271c95a010beeeff2daf1ff71162e43969'] + +start_dir = 'src' +buildopts = '-f Makefile.Linux' + +files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] + +sanity_check_paths = { + 'files': ['LICENSE', 'README.txt'], + 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] +} + +moduleclass = 'bio' From 2374352e959c102e6ca7d58f3892c798dd3226fa Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Thu, 16 May 2019 11:19:55 +0100 Subject: [PATCH 1657/5331] Python version changed to 3.6.6 --- ...ython-3.5.2.eb => Porechop-0.2.4-foss-2018b-Python-3.6.6.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/Porechop/{Porechop-0.2.4-foss-2018b-Python-3.5.2.eb => Porechop-0.2.4-foss-2018b-Python-3.6.6.eb} (97%) diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.5.2.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb similarity index 97% rename from easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.5.2.eb rename to easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb index 4356f1b35b7..8e3aa77eb06 100644 --- a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb @@ -22,7 +22,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'] dependencies = [ - ('Python', '3.5.2'), + ('Python', '3.6.6'), ] sanity_check_paths = { From dcb8d0776fae60430ced4f30dc5ffbc2d992bcfd Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 May 2019 17:46:28 +0200 Subject: [PATCH 1658/5331] Revert back changes to binutils built with dummy and versions older than 2.28 -- they cause conflicts --- .../binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 11 +++-------- .../b/binutils/binutils-2.25-GCC-4.9.2.eb | 9 ++------- .../binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 11 +++-------- .../b/binutils/binutils-2.25-GCC-4.9.3.eb | 9 ++------- .../binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 11 +++-------- .../b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 11 +++-------- .../b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 11 +++-------- .../b/binutils/binutils-2.25-GCCcore-4.9.4.eb | 11 +++-------- easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb | 9 ++------- easybuild/easyconfigs/b/binutils/binutils-2.25.eb | 9 ++------- .../b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 11 +++-------- .../b/binutils/binutils-2.26-GCCcore-5.4.0.eb | 10 +++------- .../b/binutils/binutils-2.26-GCCcore-5.5.0.eb | 10 +++------- .../b/binutils/binutils-2.26-GCCcore-6.3.0.eb | 13 ++++--------- easybuild/easyconfigs/b/binutils/binutils-2.26.eb | 4 +--- .../b/binutils/binutils-2.27-GCCcore-6.1.0.eb | 11 +++-------- .../b/binutils/binutils-2.27-GCCcore-6.2.0.eb | 11 +++-------- .../b/binutils/binutils-2.27-GCCcore-6.3.0.eb | 11 +++-------- easybuild/easyconfigs/b/binutils/binutils-2.27.eb | 9 ++------- easybuild/easyconfigs/b/binutils/binutils-2.28.eb | 9 +++------ easybuild/easyconfigs/b/binutils/binutils-2.29.eb | 9 +++------ easybuild/easyconfigs/b/binutils/binutils-2.30.eb | 5 ++--- easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb | 9 +++------ easybuild/easyconfigs/b/binutils/binutils-2.32.eb | 9 +++------ 24 files changed, 65 insertions(+), 168 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 8d99a6addde..08e10d150ca 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -6,21 +6,16 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-%s' % version} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.8'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index ca83eb6fa7c..ea9a13974b4 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -6,18 +6,13 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCC', 'version': '4.9.2'} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), -] - -dependencies = [ + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 4370f97620b..9709696cf5d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -6,21 +6,16 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-%s' % version} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.8'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb index 6e45ced018a..7ccace85015 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb @@ -6,18 +6,13 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCC', 'version': '4.9.3'} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), -] - -dependencies = [ + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index 9fb2cfbe865..d6e68008e5b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -6,21 +6,16 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-%s' % version} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.8'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb index 6cd1a30c201..9ec7a3f3f32 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -6,22 +6,17 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '4.9.2'} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.8'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index 3fc5d09536a..f411442d121 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -6,22 +6,17 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '4.9.3'} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.8'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb index f457102034d..4eee9df8fa2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb @@ -6,22 +6,17 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '4.9.4'} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('M4', '1.4.17'), ('flex', '2.6.0'), ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.8'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb index 333e277670e..e3f5b15724b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -6,18 +6,13 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '82a40a37b13a12facb36ac7e87846475a1d80f2e63467b1b8d63ec8b6a2b63fc', # binutils-2.25.1.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), -] - -dependencies = [ + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index 60fcc2a7de2..e08cd975ad8 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -6,19 +6,14 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cccf377168b41a52a76f46df18feb8f7285654b3c1bd69fc8265cb0fc6902f2d', # binutils-2.25.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('M4', '1.4.17'), ('flex', '2.5.39'), ('Bison', '3.0.4'), -] - -dependencies = [ + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb index da0fa5b924c..d7c829040f2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -6,21 +6,16 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '5.3.0'} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1', # binutils-2.26.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.8'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb index ee88b84916b..2ae6ba18a54 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb @@ -8,19 +8,15 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1', # binutils-2.26.tar.gz -] +checksums = ['9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1'] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.8'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb index 4b70b533cc7..2d41305b4cf 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb @@ -8,19 +8,15 @@ toolchain = {'name': 'GCCcore', 'version': '5.5.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1', # binutils-2.26.tar.gz -] +checksums = ['9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1'] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.11'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb index 62f6f0bddfa..d95c058f0c8 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb @@ -6,23 +6,18 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] +checksums = ['9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1'] patches = ['binutils-%(version)s_build-with-GCCcore-6.3.0.patch'] -checksums = [ - '9615feddaeedc214d1a1ecd77b6697449c952eab69d79ab2125ea050e944bcc1', # binutils-2.26.tar.gz - 'eb766886ae76be046ec217c70afd1627db845891c4c7418311c10af21e7850e5', # binutils-2.26_build-with-GCCcore-6.3.0.patch -] builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.11'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb index ec85dfe32e5..8cc66cacab0 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb @@ -20,9 +20,7 @@ configopts = ' --disable-werror' builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), -] - -dependencies = [ + # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb index 4ea09a9ed9f..215aaf0cb28 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb @@ -6,21 +6,16 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '6.1.0'} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '26253bf0f360ceeba1d9ab6965c57c6a48a01a8343382130d1ed47c468a3094f', # binutils-2.27.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.8'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb index c5851cc3a42..88e16771dff 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb @@ -6,21 +6,16 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '6.2.0'} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '26253bf0f360ceeba1d9ab6965c57c6a48a01a8343382130d1ed47c468a3094f', # binutils-2.27.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.8'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb index b7437fbc909..9346ceba7e7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb @@ -6,21 +6,16 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'GCCcore', 'version': '6.3.0'} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '26253bf0f360ceeba1d9ab6965c57c6a48a01a8343382130d1ed47c468a3094f', # binutils-2.27.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] -dependencies = [ - ('zlib', '1.2.11'), -] - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb index f36edacc493..6011a780095 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb @@ -6,18 +6,13 @@ description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} -source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '26253bf0f360ceeba1d9ab6965c57c6a48a01a8343382130d1ed47c468a3094f', # binutils-2.27.tar.gz -] +source_urls = [GNU_SOURCE] builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), -] - -dependencies = [ + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb index c06f4780fec..a50c4f25ca1 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb @@ -2,22 +2,19 @@ name = 'binutils' version = '2.28' homepage = 'http://directory.fsf.org/project/binutils/' + description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf', # binutils-2.28.tar.gz -] +checksums = ['cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf'] builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), -] - -dependencies = [ + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29.eb index 7a35e6c14b9..6efb559b8a6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29.eb @@ -2,22 +2,19 @@ name = 'binutils' version = '2.29' homepage = 'http://directory.fsf.org/project/binutils/' + description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4', # binutils-2.29.tar.gz -] +checksums = ['172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4'] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), -] - -dependencies = [ + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb index a5ac0d7694c..12fa985a5f4 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb @@ -2,6 +2,7 @@ name = 'binutils' version = '2.30' homepage = 'http://directory.fsf.org/project/binutils/' + description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} @@ -17,9 +18,7 @@ checksums = [ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), -] - -dependencies = [ + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb index d6fac033a36..64fb2100b2e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb @@ -2,22 +2,19 @@ name = 'binutils' version = '2.31.1' homepage = 'http://directory.fsf.org/project/binutils/' + description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88', # binutils-2.31.1.tar.gz -] +checksums = ['e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88'] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.5'), -] - -dependencies = [ + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb index ef960762547..aeeea2b58ea 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb @@ -2,22 +2,19 @@ name = 'binutils' version = '2.32' homepage = 'http://directory.fsf.org/project/binutils/' + description = "binutils: GNU binary utilities" toolchain = {'name': 'dummy', 'version': ''} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e', # binutils-2.32.tar.gz -] +checksums = ['9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e'] builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), -] - -dependencies = [ + # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] From 779dba96bb1a702fc4313c7c1e23290dc41d9017 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Thu, 16 May 2019 17:48:21 +0200 Subject: [PATCH 1659/5331] Adjust format of specifying checksums --- .../easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb | 4 +--- .../easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb | 4 +--- .../easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb | 4 +--- .../easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb | 4 +--- .../easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb | 4 +--- .../easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb | 4 +--- .../easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb | 4 +--- .../easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb | 4 +--- .../easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb | 4 +--- 9 files changed, 9 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb index 57eb8122dc0..89306784b4b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb @@ -8,9 +8,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf', # binutils-2.28.tar.gz -] +checksums = ['cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf'] builddependencies = [ ('flex', '2.6.3'), diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb index 9bf3a9cc18d..287f55750d4 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb @@ -8,9 +8,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf', # binutils-2.28.tar.gz -] +checksums = ['cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf'] builddependencies = [ ('flex', '2.6.4'), diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb index 4df97f98f0c..7028a7abfca 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb @@ -8,9 +8,7 @@ toolchain = {'name': 'GCCcore', 'version': '7.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf', # binutils-2.28.tar.gz -] +checksums = ['cd717966fc761d840d451dbd58d44e1e5b92949d2073d75b73fccb476d772fcf'] builddependencies = [ ('flex', '2.6.3'), diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb index d33d5d9a717..2ef76220355 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb @@ -8,9 +8,7 @@ toolchain = {'name': 'GCCcore', 'version': '7.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4', # binutils-2.29.tar.gz -] +checksums = ['172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4'] builddependencies = [ ('flex', '2.6.4'), diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb index 07b9f5e1750..8bc61397f2c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb @@ -8,9 +8,7 @@ toolchain = {'name': 'GCCcore', 'version': 'system'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4', # binutils-2.29.tar.gz -] +checksums = ['172e8c89472cf52712fd23a9f14e9bca6182727fb45b0f8f482652a83d5a11b4'] builddependencies = [ ('flex', '2.6.4'), diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb index fc5d1ff6b6b..e23a2091e87 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb @@ -8,9 +8,7 @@ toolchain = {'name': 'GCCcore', 'version': '7.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88', # binutils-2.31.1.tar.gz -] +checksums = ['e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88'] builddependencies = [ ('flex', '2.6.4'), diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb index 32f34f1e824..9b016bae249 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb @@ -8,9 +8,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - 'e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88', # binutils-2.31.1.tar.gz -] +checksums = ['e88f8d36bd0a75d3765a4ad088d819e35f8d7ac6288049780e2fefcad18dde88'] builddependencies = [ ('flex', '2.6.4'), diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb index 590c08ba810..9de271d38b2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb @@ -8,9 +8,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e', # binutils-2.32.tar.gz -] +checksums = ['9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e'] builddependencies = [ ('flex', '2.6.4'), diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb index d43378fc336..8483b2d3adb 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb @@ -8,9 +8,7 @@ toolchain = {'name': 'GCCcore', 'version': '9.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = [ - '9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e', # binutils-2.32.tar.gz -] +checksums = ['9b0d97b3d30df184d302bced12f976aa1e5fbf4b0be696cdebc6cca30411a46e'] builddependencies = [ ('flex', '2.6.4'), From feb2288ddf2d758428ee1e3133717bec36ea6187 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 16 May 2019 19:04:14 +0200 Subject: [PATCH 1660/5331] Remove libomp as it's already the default runtime --- easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb index 3ffbb977e43..3fc09222b68 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb @@ -61,7 +61,6 @@ usepolly = True build_lld = True libcxx = True enable_rtti = True -default_openmp_runtime = 'libomp' skip_all_tests = True From 40d6f04e19202c6e1f5ead47dd4c0dcc7b627d53 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 May 2019 21:58:58 +0200 Subject: [PATCH 1661/5331] move ANTLR to GCCcore --- ...ANTLR-2.7.7-intel-2018b.eb => ANTLR-2.7.7-GCCcore-7.3.0.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/a/ANTLR/{ANTLR-2.7.7-intel-2018b.eb => ANTLR-2.7.7-GCCcore-7.3.0.eb} (90%) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb similarity index 90% rename from easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018b.eb rename to easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb index 472b977829e..8b3f8a98607 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb @@ -9,7 +9,7 @@ description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions.""" -toolchain = {'name': 'intel', 'version': '2018b'} +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = ['http://www.antlr2.org/download/'] sources = [SOURCELOWER_TAR_GZ] @@ -19,6 +19,7 @@ checksums = [ 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch ] +builddependencies = [('binutils', '2.30')] dependencies = [('Java', '1.8', '', True)] configopts = '--disable-examples --disable-csharp --disable-python' From c86b85269205f505e2c93d875aef4f82330ae956 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 16 May 2019 14:25:33 -0700 Subject: [PATCH 1662/5331] GDAL 3.0 foss-2019a --- .../GDAL-3.0.0-foss-2019a-Python-3.7.2.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..40ef018bc1c --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '3.7.2'), + ('netCDF', '4.6.2'), + ('expat', '2.2.6'), + ('GEOS', '3.7.2', '-Python-%(pyver)s'), + ('SQLite', '3.27.2'), + ('libxml2', '2.9.8'), + ('libpng', '1.6.36'), + ('libjpeg-turbo', '2.0.2'), + ('JasPer', '2.0.14'), + ('LibTIFF', '4.0.10'), + ('zlib', '1.2.11'), + ('cURL', '7.63.0'), + ('PCRE', '8.43'), + ('PROJ', '6.0.0'), + ('libgeotiff', '1.5.1'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' From a28fe01ce52454d62c5dd550c1b317d900c266a9 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 17 May 2019 09:04:06 +0200 Subject: [PATCH 1663/5331] Add comment referencing https://github.com/easybuilders/easybuild-easyblocks/issues/1350 --- easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb | 1 + .../easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb | 1 + .../easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb | 1 + 11 files changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb index 89306784b4b..9bbbbbfddf8 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb index 287f55750d4..8cb5fc489c2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb @@ -19,6 +19,7 @@ builddependencies = [ ] dependencies = [ + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb index 7028a7abfca..01135f41375 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb index 2ef76220355..2e55f487dfe 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb index 8bc61397f2c..584baf2a4ec 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb @@ -16,6 +16,7 @@ builddependencies = [ ] dependencies = [ + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb index f27b731fc30..93f0c7a2805 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb @@ -22,6 +22,7 @@ builddependencies = [ ] dependencies = [ + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb index 577322b830c..773c6f2a761 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb @@ -22,6 +22,7 @@ builddependencies = [ ] dependencies = [ + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb index e23a2091e87..d3dd29010eb 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb index 9b016bae249..5a3ac8e5023 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb index 9de271d38b2..c7e93e68ba9 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb index 8483b2d3adb..1bcb65d8a8a 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] From 45449acbf610852573e144dae397661fd32201c7 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Fri, 17 May 2019 10:49:58 +0100 Subject: [PATCH 1664/5331] First OpenBLAS easyconfig using new easyblock --- .../o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb index a6985ac7ae7..4449dd4645d 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'OpenBLAS' version = '0.3.1' @@ -27,19 +25,7 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] -skipsteps = ['configure'] - -buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' -installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" - # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' -sanity_check_paths = { - 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', - 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', - 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], - 'dirs': [], -} - moduleclass = 'numlib' From 1878d1b6923a0fb0bdbf2c1f76edb807409dd4e6 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Fri, 17 May 2019 10:58:21 +0100 Subject: [PATCH 1665/5331] Pushing eb changes out to all OpenBLAS easyconfigs for 0.3.0 and later --- .../o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb | 14 -------------- .../o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb | 14 -------------- .../o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb | 14 -------------- .../o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb | 14 -------------- .../o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb | 14 -------------- 5 files changed, 70 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb index 5d837040002..5216c5d4f3c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-6.4.0-2.28.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'OpenBLAS' version = '0.3.0' @@ -27,19 +25,7 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] -skipsteps = ['configure'] - -buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' -installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" - # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' -sanity_check_paths = { - 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', - 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', - 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], - 'dirs': [], -} - moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb index 9d5f65a1e35..29ca07ed753 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.0-GCC-7.3.0-2.30.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'OpenBLAS' version = '0.3.0' @@ -27,19 +25,7 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] -skipsteps = ['configure'] - -buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' -installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" - # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' -sanity_check_paths = { - 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', - 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', - 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], - 'dirs': [], -} - moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb index c2a8ad8469f..5bf04fcaec4 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'OpenBLAS' version = '0.3.3' @@ -27,19 +25,7 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] -skipsteps = ['configure'] - -buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' -installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" - # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' -sanity_check_paths = { - 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', - 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', - 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], - 'dirs': [], -} - moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb index 52547937c39..9827f159010 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'OpenBLAS' version = '0.3.4' @@ -27,19 +25,7 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] -skipsteps = ['configure'] - -buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$F77"' -installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" - # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' -sanity_check_paths = { - 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', - 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', - 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], - 'dirs': [], -} - moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb index dcdbeec6bd4..b9155e2755b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'OpenBLAS' version = '0.3.5' @@ -30,19 +28,7 @@ checksums = [ '56d5034869ebd7b63c7af23eadd0935280d4d57ac3b0d35956c64015a3103da9', ] -skipsteps = ['configure'] - -buildopts = 'BINARY=64 USE_THREAD=1 USE_OPENMP=1 CC="$CC" FC="$FC"' -installopts = "USE_THREAD=1 USE_OPENMP=1 PREFIX=%(installdir)s" - # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' -sanity_check_paths = { - 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', - 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', - 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], - 'dirs': [], -} - moduleclass = 'numlib' From 982551e24e2c8dfbceba7f404bbd22a94098fa08 Mon Sep 17 00:00:00 2001 From: Fotis Georgatos Date: Fri, 17 May 2019 15:16:54 +0200 Subject: [PATCH 1666/5331] Update GroopM-0.3.4-foss-2016b-Python-2.7.12.eb --- .../g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb index 03b1e223bf0..acfefb56b98 100644 --- a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb @@ -16,9 +16,9 @@ version = '0.3.4' versionsuffix = '-Python-%(pyver)s' homepage = 'http://ecogenomics.github.io/GroopM/' -description = """ GroopM is a metagenomic binning toolset. It leverages spatio-temoral -dynamics (differential coverage) to accurately (and almost automatically) -extract population genomes from multi-sample metagenomic datasets. +description = """ GroopM is a metagenomic binning toolset. It leverages spatio-temporal + dynamics (differential coverage) to accurately (and almost automatically) + extract population genomes from multi-sample metagenomic datasets. """ toolchain = {'name': 'foss', 'version': '2016b'} From 90956c0eddbade6e29a9586164b1ea4720f340da Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Fri, 17 May 2019 16:41:42 +0200 Subject: [PATCH 1667/5331] Clarify comment --- easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb | 1 + .../easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb | 1 + .../easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb | 1 + easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb | 1 + 11 files changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb index 9bbbbbfddf8..93b20c17e20 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb index 8cb5fc489c2..3cdec71af84 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb @@ -19,6 +19,7 @@ builddependencies = [ ] dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb index 01135f41375..7b12c3e7b9b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb index 2e55f487dfe..c35f4248bb2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb index 584baf2a4ec..46f269e7301 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-system.eb @@ -16,6 +16,7 @@ builddependencies = [ ] dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb index 93f0c7a2805..ed6a58e814e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb @@ -22,6 +22,7 @@ builddependencies = [ ] dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb index 773c6f2a761..f9766dc94cc 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb @@ -22,6 +22,7 @@ builddependencies = [ ] dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb index d3dd29010eb..0cfde702315 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb index 5a3ac8e5023..a2e0ca79598 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb index c7e93e68ba9..16f5d5fb70c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb index 1bcb65d8a8a..de5c0dc0615 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 ('zlib', '1.2.11'), ] From 975cbfe42a13eb2fdfd11a2e9edc695acd5b8ef1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 May 2019 18:18:15 +0200 Subject: [PATCH 1668/5331] download latest commit for SMARTdenovo as tarball rather than using git --- .../SMARTdenovo-20180219-foss-2018b.eb | 19 +++++++------------ 1 file changed, 7 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb index 451a308de9f..303a82bc2bc 100644 --- a/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb +++ b/easybuild/easyconfigs/s/SMARTdenovo/SMARTdenovo-20180219-foss-2018b.eb @@ -1,6 +1,7 @@ -easyblock = "ConfigureMake" +easyblock = 'ConfigureMake' name = 'SMARTdenovo' +commit = '5cc1356' version = '20180219' homepage = 'https://github.com/ruanjue/smartdenovo' @@ -13,23 +14,17 @@ for ONT) are still required for higher accuracy.""" toolchain = {'name': 'foss', 'version': '2018b'} -commit = '5cc1356bffb87197b0fb9b835cfe1adc5a764dc6' +source_urls = ['https://github.com/ruanjue/smartdenovo/archive/'] sources = [{ - 'filename': '%%(name)s-master-20190215-%s.tar.gz' % commit, - 'git_config': { - 'url': 'https://github.com/ruanjue', - 'repo_name': 'smartdenovo', - 'commit': commit, - } + 'download_filename': '%s.tar.gz' % commit, + 'filename': SOURCE_TAR_GZ, }] patches = [ '%(name)s-%(version)s_fix_build_flags_and_install.patch', '%(name)s-%(version)s_use_env_perl_for_startup.patch', ] checksums = [ - # Checksum will not match since the tar file is generated on the fly. - # SMARTdenovo-master-20190215-5cc1356bffb87197b0fb9b835cfe1adc5a764dc6.tar.gz - 'd1dc8b0f1ba19cbdf2572f29c91d57d4b7b75508ad6ef4eca39ecc7db049c544', + '315a1a9ef96e993dd101b34b626c1eab9c58e59c24848598eb0a6fa38e0b49cd', # SMARTdenovo-20180219.tar.gz # SMARTdenovo-20180219_fix_build_flags_and_install.patch '6138fb6db730372ee50a5cc87cadf2d99f11b48165e45832eb985804910d2420', # SMARTdenovo-20180219_use_env_perl_for_startup.patch @@ -40,7 +35,7 @@ dependencies = [('Perl', '5.28.0')] skipsteps = ['configure'] -installopts = ' INSTALLDIR=%(installdir)s ' +installopts = 'INSTALLDIR=%(installdir)s' sanity_check_paths = { 'files': ['bin/%s' % x for x in ['dbm_index_fa.pl', 'dbm_read_fa.pl', From 5687dcd5ba8bb83861f5f49de19a907e5addbd11 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 17 May 2019 10:35:39 -0700 Subject: [PATCH 1669/5331] GDAL 3.0.0 add checksum --- .../easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb index 40ef018bc1c..ca8fe406d24 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb @@ -15,6 +15,7 @@ toolchainopts = {'usempi': True} source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] sources = [SOURCELOWER_TAR_XZ] +checksums = ['ad316fa052d94d9606e90b20a514b92b2dd64e3142dfdbd8f10981a5fcd5c43e'] dependencies = [ ('Python', '3.7.2'), From 77f18d424942debe4391f4eabbf49598ea866055 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 May 2019 23:35:16 +0200 Subject: [PATCH 1670/5331] set $XDG_CACHE_HOME to $TMPDIR before 'pip install' in Arrow 0.12.0 easyconfigs --- .../a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb | 2 +- .../a/Arrow/Arrow-0.12.0-intel-2018b-Python-3.6.6.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb index 3ec7f57a41a..03dbd7b374e 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb @@ -55,7 +55,7 @@ exts_list = [ install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " install_pyarrow_cmds += " cd %(builddir)s/*arrow-%(version)s/python && " -install_pyarrow_cmds += " pip install --prefix %(installdir)s ." +install_pyarrow_cmds += " export XDG_CACHE_HOME=$TMPDIR && pip install --prefix %(installdir)s ." postinstallcmds = [install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-3.6.6.eb index 2f0beab7a70..45646286ff0 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-3.6.6.eb @@ -40,7 +40,7 @@ configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DCMAKE_INSTALL_LIBDI install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " install_pyarrow_cmds += " cd %(builddir)s/*arrow-%(version)s/python && " -install_pyarrow_cmds += " pip install --prefix %(installdir)s ." +install_pyarrow_cmds += " export XDG_CACHE_HOME=$TMPDIR && pip install --prefix %(installdir)s ." postinstallcmds = [install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 2f8b24e97023d3a4cbd0a7b41dd4086bafff7fd4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 20 May 2019 08:26:31 +0200 Subject: [PATCH 1671/5331] switch to GCC toolchain --- ...2.16.0-GCCcore-7.3.0.eb => Arb-2.16.0-GCC-7.3.0-2.30.eb} | 6 +----- ...2.5.2-GCCcore-7.3.0.eb => FLINT-2.5.2-GCC-7.3.0-2.30.eb} | 6 +----- 2 files changed, 2 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/a/Arb/{Arb-2.16.0-GCCcore-7.3.0.eb => Arb-2.16.0-GCC-7.3.0-2.30.eb} (89%) rename easybuild/easyconfigs/f/FLINT/{FLINT-2.5.2-GCCcore-7.3.0.eb => FLINT-2.5.2-GCC-7.3.0-2.30.eb} (90%) diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCC-7.3.0-2.30.eb similarity index 89% rename from easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCCcore-7.3.0.eb rename to easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCC-7.3.0-2.30.eb index 723f110c18b..d81b252cc86 100644 --- a/easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/a/Arb/Arb-2.16.0-GCC-7.3.0-2.30.eb @@ -9,17 +9,13 @@ description = """Arb is a C library for arbitrary-precision interval arithmetic. It has full support for both real and complex numbers. The library is thread-safe, portable, and extensively tested.""" -toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} github_account = 'fredrik-johansson' source_urls = [GITHUB_LOWER_SOURCE] sources = ['%(version)s.tar.gz'] checksums = ['77464be4d34a511bb004457f862fec857ff934b0ed58d56d6f52d76ebadd4daf'] -builddependencies = [ - ('binutils', '2.30'), -] - dependencies = [ ('FLINT', '2.5.2'), ('GMP', '6.1.2'), diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCC-7.3.0-2.30.eb similarity index 90% rename from easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCCcore-7.3.0.eb rename to easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCC-7.3.0-2.30.eb index e90fcf75ff1..567ec8b742d 100644 --- a/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-GCC-7.3.0-2.30.eb @@ -10,16 +10,12 @@ description = """FLINT (Fast Library for Number Theory) is a C library in suppor factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" -toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = ['http://www.%(namelower)slib.org'] sources = [SOURCELOWER_TAR_GZ] checksums = ['cbf1fe0034533c53c5c41761017065f85207a1b770483e98b2392315f6575e87'] -builddependencies = [ - ('binutils', '2.30'), -] - dependencies = [ ('GMP', '6.1.2'), ('MPFR', '4.0.1'), From c4330c7c922f9f9b155b9af7748c1be4253f3edb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 May 2019 09:19:53 +0200 Subject: [PATCH 1672/5331] update release notes & bump version for EasyBuild v3.9.1 release --- RELEASE_NOTES | 71 +++++++++++++++++++++++++++++++++++++++++++++++++-- setup.py | 2 +- 2 files changed, 70 insertions(+), 3 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index cb53857dc3b..ad533ed28e5 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,75 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 11,028 easyconfig files, for 1,711 different software packages, -31 different (compiler) toolchains, 13 software bundles and 1 meta-package. +The latest version of easybuild-easyconfig provides 11,416 easyconfig files, for 1,763 different software packages, +32 different (compiler) toolchains, 13 software bundles and 1 meta-package. + +v3.9.1 (May 20th 2019) +---------------------- + +update/bugfix release + +- added easyconfigs for new toolchains: + - fosscuda/2019a (#8063), gimkl/2018b (#8287), gomkl/2018b (#8216), gomkl/2019a (#8218), intelcuda/2019a (#8069) +- added example easyconfig files for 52 new software packages: + - ADDA (#8207), AMD-LibM (#7164), AMD-RNG (#7165), AMD-SecureRNG (#7165), ARGoS (#8039, #8104), ARWEN (#8213), + Canvas (#7716), cdsapi (#7970), charmm (#8202), emcee (#7989), FlexiDot (#8228, #8275), FreeImage (#8039), + Hello (#7704), HLAminer (8094), hypothesis (#8307), imgaug (#8229), INTEGRATE (#8193, #8304), INTEGRATE-Neo (#8094), + IRkernel (#8050, #8099), JiTCODE (#7148, #8327), libFLAME (#7163), libpsml (#5859), LibSoup (#8116), + libutempter (#6426), LS-PrePost (#8070), LUSCUS (#7191, #8105, #8285), memory-profiler (#8255), metaWRAP (#7896), + Net-core (#7716), netMHC (#8094), Nextflow (#8195), nvtop (#8024), openpyxl (#8121), py-cpuinfo (#8245), + pyFFTW (#8198), PyQtGraph (#7525, #8253), R-tesseract (#7933), RBFOpt (#8178), rnaQUAST (#8040), RStan (#7996), + scikit-multilearn (#8142), simpy (#8177, #8250), SMARTdenovo (#7630), socat (#8305), SymEngine (#7148, #8327), + unixODBC (#8074), VAtools (#7938), VirtualGL (#8008), WebKitGTK+ (#8118, #8241), xmlf90 (#5858), YAPS (#7976), + zingeR (#7264) +- added additional easyconfigs for various supported software packages, including: + - Boost 1.70.0, cairo 1.16.0, CGAL 4.14, Clang 8.0, cutadapt 2.1, dask 1.1.4, ELPA 2018.11.001, FFmpeg 4.1.3, + GCC 9.1.0, GEOS 3.7.2, GLib 2.60.1, gmsh 4.2.2, GROMACS 2019.2, GTK+ 3.24.8, h5py 2.9.0, hwloc 1.11.12, + Hypre 2.15.1, Mathematica 12.0.0, matplotlib 3.0.3, Mesa 19.0.1, NBO 7.0, NCL 6.6.2, NCO 4.7.9, + NiBabel 2.4.0, numba 0.43.1, OpenMPI 3.1.4, OrthoFinder 2.3.3, PCMSolver 1.2.3, PETSc 3.11.1, + PROJ 6.0.0, PyQt5 5.12.1, PyTorch 1.0.1, PyYAML 5.1, Qt5 5.12.3, QuantumESPRESSO 6.4.1, R 3.5.1 (w/ intel/2018b), + RNAIndel 1.0.0, Ruby 2.6.3, scikit-learn 0.20.3, SLEPc 3.11.0, sympy 1.4, Tkinter 3.7.2, Vim 8.1.1209, VTK 8.2.0, + wrf-python 1.3.1, wxPython 4.0.4, wxWidgets 3.0.4, xarray 0.12.1, zstd 1.4.0 +- minor enhancements, including: + - enable auto-download of VMD 1.9.3 + add patches for Surf and Stride (#7305) + - add mlegp extension in R 3.5.1 easyconfigs (#7814) + - add pkg-config file to bzip2 easyconfigs (#8200) + - allow use of 'use_pip = False' in easyconfigs if pip doesn't work (#8220) +- various bug fixes, including: + - fix checksums for nlme extensions in R easyconfigs (#7814, #8054) + - add missing XZ dependency for Pysam > 0.12 (#7971) + - define $GRACE_HOME in Grace easyconfigs, so that font dir can be located (#8048) + - $XDG_DATA_DIRS must be set for GTK+ (#8089) + - add missing FriBidi dependency for Pango 1.43.0 (#8103) + - add (back) custom sanity_check_paths in recent Pango easyconfigs (#8106) + - fix missing extensions in cutadapt 1.16 easyconfigs (#8130) + - add missing cURL dependency for recent SAMtools versions (#8131) + - add singledispatch extension to Python 2.7.15 easyconfig using GCCcore/8.2.0 toolchain (#8164) + - add missing X11 dependency for Gdk-Pixbuf 2.38.1 (#8222) + - make sure hdf5r picks up HDF5 dependency in R 3.5.1 easyconfigs (#8223) + - enable zstd compression in GRASS 7.6.0 easyconfig (#8224) + - add missing ICU dependency on ICU for Harfbuzz 2.4.0 (#8226) + - disable AVX512 DGEMM kernels in OpenBLAS 0.3.5 (#8227) + - fix homepage/description in OrthoFinder easyconfig (#8234) + - add Parallel::ForkManager extension to Perl 5.28.x easyconfigs (#8247) + - replace LibUUID dependencies with util-linux (#8258) + - add jemalloc & pkg-config as build deps for Salmon 0.12.0 (#8264) + - fix MAJIQ easyconfig by fixing order of extensions + avoid numpy test hang (#8272) + - fix shebang in GLib Python script + clarify runtime dependency on Python (#8277) + - add `pkg-config` and `expat` as (build) dependency for DBus (#8283) + - define $GI_TYPELIB_PATH in GTK+ and Pango easyconfigs (#8246, #8286) + - add pkg-config build dep to PROJ/6.0.0 (#8309) + - fix source URLS in recent libcerf easyconfigs (#8332, #8243) + - make zlib a real dependency rather than a build dep in recent binutils easyconfigs (>= 2.28) (#8340) + - add fix-ib-query patch to OpenMPI 2.1.x and 3.0.x easyconfigs (#8341) + - set $XDG_CACHE_HOME to $TMPDIR before 'pip install' in Arrow 0.12.0 easyconfigs (#8347) +- other changes: + - remove xbitmaps dependency from motif (#7530) + - require custom sanity_check_paths in easyconfigs touched in PRs when generic easyblock is used (#8101, #8123) + - use CMake built with GCCcore toolchain when installing Eigen 3.3.4+ (#8261) + - fix Python classifiers in setup.py, should be (only) Python 2.6 & 2.7 (#8299) + - use custom easyblock for OpenBLAS in OpenBLAS 0.3.x easyconfigs (#8345, #8339) + v3.9.0 (April 12th 2019) ------------------------ diff --git a/setup.py b/setup.py index b6a538e30ab..11248d267e6 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.9.1.dev0' +VERSION = '3.9.1' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) From 9cb883572d583cbcd5635b925c07e65b6e3e4911 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 May 2019 15:05:03 +0200 Subject: [PATCH 1673/5331] bump version to 3.9.2dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 11248d267e6..d3598721c43 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '3.9.1' +VERSION = '3.9.2.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) From 624ada4c7a5194fbde832bc1bf2c1116c2e9cb1e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 20 May 2019 15:48:21 +0200 Subject: [PATCH 1674/5331] add easyconfigs for iccifort toolchain --- ...16.0-iccifort-2018.3.222-GCC-7.3.0-2.30.eb | 34 +++++++++++++++++++ ....5.2-iccifort-2018.3.222-GCC-7.3.0-2.30.eb | 33 ++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arb/Arb-2.16.0-iccifort-2018.3.222-GCC-7.3.0-2.30.eb create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-iccifort-2018.3.222-GCC-7.3.0-2.30.eb diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.16.0-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/a/Arb/Arb-2.16.0-iccifort-2018.3.222-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..252d59a703c --- /dev/null +++ b/easybuild/easyconfigs/a/Arb/Arb-2.16.0-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Arb' +version = '2.16.0' + +homepage = 'http://%(namelower)slib.org' + +description = """Arb is a C library for arbitrary-precision interval arithmetic. + It has full support for both real and complex numbers. The library is thread-safe, + portable, and extensively tested.""" + +toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'} + +github_account = 'fredrik-johansson' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['77464be4d34a511bb004457f862fec857ff934b0ed58d56d6f52d76ebadd4daf'] + +dependencies = [ + ('FLINT', '2.5.2'), + ('GMP', '6.1.2'), + ('MPFR', '4.0.1'), +] + +configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpir=$EBROOTMPIR' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-iccifort-2018.3.222-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..5408a5cb274 --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.5.2-iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'FLINT' +version = '2.5.2' + +homepage = 'http://www.%(namelower)slib.org' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'iccifort', 'version': '2018.3.222-GCC-7.3.0-2.30'} + +source_urls = ['http://www.%(namelower)slib.org'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cbf1fe0034533c53c5c41761017065f85207a1b770483e98b2392315f6575e87'] + +dependencies = [ + ('GMP', '6.1.2'), + ('MPFR', '4.0.1'), +] + +configopts = '--with-gmp=$EBROOTGMP --with-mpir=$EBROOTMPIR' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' From ef30d5e6fcfdf70cc182d90699c907323628ab99 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 May 2019 17:27:52 +0200 Subject: [PATCH 1675/5331] adding easyconfigs: EasyBuild-3.9.1.eb --- .../e/EasyBuild/EasyBuild-3.9.1.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.1.eb new file mode 100644 index 00000000000..09a6b67838b --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.1.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '3.9.1' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://files.pythonhosted.org/packages/18/59/3274a58af6af84a87f7655735b452c06c769586ee73954f5ee15d303aa29/', + # vsc-base + 'https://files.pythonhosted.org/packages/48/aa/f05d350c358338d0e843835660e3993cc5eb28401f32c0c5b8bc9a9458d5/', + # easybuild-framework + 'https://files.pythonhosted.org/packages/c4/f7/21a0475eab7f7305a7c3aa1f34993ce16f6d3402bd0e5eb7336d63a29435/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/7d/e0/e10811ea63348a1780a734918d0b54bb560388424b7d8853872f12f51441/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/c6/76/12f9611915b7e0679dbd565ee4eb354ef1a0255a5c7a87bc5e172cfb7b70/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.11.3.tar.gz', + 'vsc-base-2.8.4.tar.gz', + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '8b102ba585863769d974ad117764039ac3cea21372a3baa5cdb6b93166673ad6', # vsc-install-0.11.3.tar.gz + 'a6d3ab52c9dec938d98e53860dce4aba79ca8ea4e81f6e07bf2c3787e764bc3e', # vsc-base-2.8.4.tar.gz + '332ea55b8e4b76dcc05c222bf7c35e9683145f52188ec7e3955f23811e4f8ecb', # easybuild-framework-3.9.1.tar.gz + 'cd32733faeb8baaee121aa13db7d779df4076801ef6c3f63d9bd13adbe977366', # easybuild-easyblocks-3.9.1.tar.gz + 'f3add056922d75fea487f1155577e1c0f200af8f1cb8c0400714eb173396a15c', # easybuild-easyconfigs-3.9.1.tar.gz +] + +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = 'tools' From a264d8ca9f211b28d0c79738257151b654a35b53 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 May 2019 08:42:51 +0200 Subject: [PATCH 1676/5331] use string_type rather than basestring in when checking dumped easyconfig --- test/easyconfigs/easyconfigs.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4720b19facd..9a501880674 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -53,6 +53,7 @@ from easybuild.tools.filetools import change_dir, remove_file, write_file from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool +from easybuild.tools.py2vs3 import string_type from easybuild.tools.robot import check_conflicts, resolve_dependencies from easybuild.tools.run import run_cmd from easybuild.tools.options import set_tmpdir @@ -683,7 +684,7 @@ def template_easyconfig_test(self, spec): # take into account that for some string-valued easyconfig parameters (configopts & co), # the easyblock may have injected additional values, which affects the dumped easyconfig file - elif isinstance(orig_val, basestring): + elif isinstance(orig_val, string_type): self.assertTrue(dumped_val.startswith(orig_val)) else: self.assertEqual(orig_val, dumped_val) From 35dd3e25cb32332ba930b1992f66231014a9c45f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 May 2019 11:24:38 +0200 Subject: [PATCH 1677/5331] add back sanity_check_paths for EMBOSS 6.6.0 built with GCCcore/7.3.0 + mention author in patch file --- .../easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb | 10 +++++++++- .../e/EMBOSS/EMBOSS-6.6.0_disable-embossupdate.patch | 2 ++ .../l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb | 2 +- 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb index 784aee829bf..1e20c9bdaa4 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb @@ -28,7 +28,7 @@ sources = [SOURCE_TAR_GZ] patches = ['%(name)s-%(version)s_disable-embossupdate.patch'] checksums = [ '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', # EMBOSS-6.6.0.tar.gz - 'c72977f710b3146d5880b4aff91c0565f4ab5fd8f695c77ac53a5c0b08216b25', # EMBOSS-6.6.0_disable-embossupdate.patch + '7e0a7deffd76f60093be9c5253605f2d6d2e3b0c2d3c9365035cc6bda43eb46c', # EMBOSS-6.6.0_disable-embossupdate.patch ] builddependencies = [('CMake', '3.11.4')] @@ -44,4 +44,12 @@ configopts = " --with-hpdf=$EBROOTLIBHARU " # jemboss.jar does not build in a parallel build parallel = 1 +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', + 'epcre', 'eplplot', 'ezlib', 'nucleus']] + + ['share/EMBOSS/jemboss/lib/jemboss.jar'], + 'dirs': [], +} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0_disable-embossupdate.patch b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0_disable-embossupdate.patch index eb875023028..d36fe5ed106 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0_disable-embossupdate.patch +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0_disable-embossupdate.patch @@ -1,4 +1,6 @@ remove build target embossupdate from Makefile +author: Kenneth Hoste (HPC-UGent) +see https://github.com/easybuilders/easybuild-easyconfigs/pull/963 diff -ruN EMBOSS-6.6.0.orig/Makefile.am EMBOSS-6.6.0/Makefile.am --- EMBOSS-6.6.0.orig/Makefile.am 2012-07-22 04:16:46.000000000 -0700 +++ EMBOSS-6.6.0/Makefile.am 2019-01-07 13:11:47.876782000 -0800 diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb index 88911a2c9a1..83831042bcc 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-7.3.0.eb @@ -25,7 +25,7 @@ description = """libHaru is a free, cross platform, open source library for toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -source_urls = [' https://github.com/libharu/libharu/archive/'] +source_urls = ['https://github.com/libharu/libharu/archive/'] sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] From 325ef52182fa946104aff818e04361574d2b339c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 May 2019 14:03:53 +0200 Subject: [PATCH 1678/5331] adding easyconfigs: adjustText-0.7.3-intel-2019a-Python-3.7.2.eb --- ...justText-0.7.3-intel-2019a-Python-3.7.2.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..4a0d474285c --- /dev/null +++ b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'adjustText' +version = '0.7.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Phlya/adjustText' +description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps." + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'] + +download_dep_fail = True +use_pip = True + +dependencies = [ + ('Python', '3.7.2'), + ('matplotlib', '3.0.3', versionsuffix), + ('SciPy-bundle', '2019.03'), # numpy +] + +options = {'modulename': 'adjustText'} + +moduleclass = 'tools' From af65429948d9ba81ad5ca9065bcda39ed9644a0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 May 2019 15:27:10 +0200 Subject: [PATCH 1679/5331] adding easyconfigs: PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb --- ...CMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..0274eb69923 --- /dev/null +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'PCMSolver' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pcmsolver.readthedocs.org' +description = """An API for the Polarizable Continuum Model.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +# we have to disable use of -march=native to ensure a correct build on recent Intel systems +# see also https://github.com/PCMSolver/pcmsolver/issues/159 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d1ef6bdc268a2e719b36c85125c3543df7a26e1a738daf4483f4ded0c76f5b60'] + +dependencies = [ + ('Python', '3.7.2'), + ('zlib', '1.2.11'), + ('Boost', '1.70.0'), +] + +builddependencies = [ + ('CMake', '3.13.3'), + ('Eigen', '3.3.7', '', True), +] + +configopts = '-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN' + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/run_pcm', 'lib/libpcm.a', 'lib/libpcm.%s' % SHLIB_EXT], + 'dirs': ['include/PCMSolver'] +} + +moduleclass = 'chem' From 89620b64c302efd542e753e1e814e26cfd7e8f9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 May 2019 15:27:16 +0200 Subject: [PATCH 1680/5331] adding easyconfigs: CheMPS2-1.8.9-foss-2019a.eb --- .../c/CheMPS2/CheMPS2-1.8.9-foss-2019a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2019a.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2019a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2019a.eb new file mode 100644 index 00000000000..e5fba7d2338 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-foss-2019a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.8.9' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ccd4c0d9432759d97690bf37a0333440f93513960c62d1f75842f090406a224d'] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [ + ('HDF5', '1.10.5') +] + +pretestopts = 'export OMP_NUM_THREADS=1 && ' +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' From 1eed77b56ce400442b1fa5581cdddc20d37d6e0a Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Tue, 21 May 2019 14:56:12 +0100 Subject: [PATCH 1681/5331] download_dep_fail and use_pip added as requested --- .../p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb index 8e3aa77eb06..6155c98dfcc 100644 --- a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb @@ -25,6 +25,10 @@ dependencies = [ ('Python', '3.6.6'), ] +download_dep_fail = ['none'] +use_pip = ['none'] + + sanity_check_paths = { 'files': ['bin/porechop', 'lib/python%(pyshortver)s/site-packages/porechop/porechop.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages/'] From 7117ee9cd6855f86d256af86ac59c4df3161c228 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 21 May 2019 16:24:40 +0200 Subject: [PATCH 1682/5331] adding easyconfigs: Racon-1.3.2-GCCcore-8.2.0.eb --- .../r/Racon/Racon-1.3.2-GCCcore-8.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.3.2-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.3.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.3.2-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..86fe34d5904 --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.3.2-GCCcore-8.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.3.2' + +homepage = 'https://github.com/isovic/racon' +description = """ Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. """ + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/isovic/racon/releases/download/%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['7c99380a0f1091f5ee138b559e318d7e9463d3145eac026bf236751c2c4b92c7'] + +builddependencies = [('CMake', '3.13.3')] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' From 3b9182b7150b89889a5ac1b5490b37354bcd7458 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 21 May 2019 16:25:51 +0200 Subject: [PATCH 1683/5331] adding easyconfigs: Pilon-1.23-Java-11.eb --- .../easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb new file mode 100644 index 00000000000..609be47bd1d --- /dev/null +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb @@ -0,0 +1,30 @@ +easyblock = 'JAR' + +name = 'Pilon' +version = '1.23' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/broadinstitute/pilon' +description = " Pilon is an automated genome assembly improvement and variant detection tool" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.jar'] +checksums = ['bde1d3c8da5537abbc80627f0b2a4165c2b68551690e5733a6adf62413b87185'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['pilon-%(version)s.jar'], + 'dirs': [], +} + +postinstallcmds = ['cd %(installdir)s && ln -s %(namelower)s-%(version)s.jar pilon.jar'] + +modloadmsg = """ +To execute Pilon run: java -Xmx8G -jar $EBROOTPILON/pilon.jar +Adjust the memory value according to the size of your input files +""" + +moduleclass = 'bio' From ca184ed4967208b8af56d1b003a600ea13141faa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 May 2019 16:36:44 +0200 Subject: [PATCH 1684/5331] clean up ELPA 2018.11.001 easyconfig to use custom easyblock for ELPA --- .../e/ELPA/ELPA-2018.11.001-intel-2019a.eb | 27 +------------------ 1 file changed, 1 insertion(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb index 02f8c215b7a..920a979ed3d 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb @@ -6,8 +6,6 @@ # ## -easyblock = 'ConfigureMake' - name = 'ELPA' version = '2018.11.001' @@ -15,7 +13,7 @@ homepage = 'http://elpa.rzg.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2019a'} -toolchainopts = {'usempi': True} +toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] @@ -25,27 +23,4 @@ builddependencies = [ ('Autotools', '20180311'), ] -common_configopts = 'FCFLAGS="-I$EBROOTIMKL/mkl/include/intel64/lp64 $FCFLAGS" ' -common_configopts += 'LIBS="$LIBSCALAPACK" ' - -configopts = [ - common_configopts + '--enable-openmp ', - common_configopts, # Default version last, so we can get the normal config.h/config-f90.h installed afterwards. -] - -buildopts = ' V=1 ' - -postinstallcmds = [ - # The include files and Fortran module files are identical with and - # without openmp. - 'ln -s elpa-%(version)s/elpa %(installdir)s/include', - 'ln -s elpa-%(version)s/modules %(installdir)s/include', -] - -sanity_check_paths = { - 'files': ['lib/libelpa.a', 'lib/libelpa.%s' % SHLIB_EXT, 'lib/libelpa_openmp.a', - 'lib/libelpa_openmp.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include/elpa-%(version)s/elpa', 'include/elpa-%(version)s/modules', 'lib/pkgconfig'], -} - moduleclass = 'math' From 900f4e9503198076a55e89117952ad331db7516e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 May 2019 19:16:28 +0200 Subject: [PATCH 1685/5331] use CMake rather than configure script for libxc 4.3.4 --- .../l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb | 30 ++++++++++++--- ....4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 38 +++++++++++++++---- .../l/libxc/libxc-4.3.4_lm-fix.patch | 14 +++++++ .../l/libxc/libxc-4.3.4_rename-F03.patch | 37 ++++++++++++++++++ 4 files changed, 105 insertions(+), 14 deletions(-) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.4_lm-fix.patch create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.4_rename-F03.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb index 5d662987600..d6a186dcd30 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-8.2.0-2.31.1.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' @@ -11,15 +11,33 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337'] +patches = ['libxc-%(version)s_lm-fix.patch'] +checksums = [ + 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch +] -configopts = '--enable-static --enable-shared --enable-fortran' +builddependencies = [ + ('CMake', '3.13.3'), + ('Perl', '5.28.1'), +] -runtest = 'check' +separate_build_dir = True + +common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +runtest = 'test' sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include'], + 'files': ['bin/xc-info', 'bin/xc-threshold'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], } parallel = 1 diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 5509d4ea627..779af6f229e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' @@ -11,17 +11,39 @@ toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337'] +patches = ['libxc-%(version)s_rename-F03.patch'] +checksums = [ + 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + 'e494be3ca2026998f2dd7c6b03a4e662f204fd3d963271e588f9f0d5739e76b5', # libxc-4.3.4_rename-F03.patch +] -configopts = '--enable-static --enable-shared --enable-fortran' +builddependencies = [ + ('CMake', '3.13.3'), + ('Perl', '5.28.1'), +] -runtest = 'check' +separate_build_dir = True -sanity_check_paths = { - 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include'], -} +# rename *.F03 source file since Intel Fortran compiler doesn't like that extension +# also requires patch file to rename file in CMakeLists.txt and src/Makefile.in +preconfigopts = "mv ../libxc-%(version)s/src/libxc_master.F03 ../libxc-%(version)s/src/libxc_master_F03.F90 && " + +common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] parallel = 1 +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info', 'bin/xc-threshold'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4_lm-fix.patch b/easybuild/easyconfigs/l/libxc/libxc-4.3.4_lm-fix.patch new file mode 100644 index 00000000000..1523374b72d --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4_lm-fix.patch @@ -0,0 +1,14 @@ +make sure that -lm is included when linking libxc executables +cfr. https://gitlab.com/libxc/libxc/issues/93 +author: Kenneth Hoste (HPC-UGent) +--- libxc-4.3.4/CMakeLists.txt.orig 2019-05-21 14:17:21.491272049 +0200 ++++ libxc-4.3.4/CMakeLists.txt 2019-05-21 14:16:34.301597402 +0200 +@@ -38,7 +38,7 @@ + set(PN ${PROJECT_NAME}) + + # link -lm only if necessary +-find_package(StandardMathLibraryC) ++set(STANDARD_MATH_LIBRARY "m") #find_package(StandardMathLibraryC) + # check if cbrt exists and declare HAVE_CBRT if it does + check_c_source_compiles ( + "#include diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4_rename-F03.patch b/easybuild/easyconfigs/l/libxc/libxc-4.3.4_rename-F03.patch new file mode 100644 index 00000000000..c970fca11c7 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4_rename-F03.patch @@ -0,0 +1,37 @@ +rename libxc_master.F03 to libxc_master_F03.F90, since Intel Fortran compiler doesn't like *.F03 files +cfr. https://gitlab.com/libxc/libxc/issues/85 +requires that libxc_master.F03 is renamed to libxc_master_F03.F90 via 'preconfigopts' in easyconfig file +author: Kenneth Hoste (HPC-UGent) +--- libxc-4.3.4/src/Makefile.in.orig 2019-03-05 00:43:32.000000000 +0100 ++++ libxc-4.3.4/src/Makefile.in 2019-05-21 17:56:25.140868203 +0200 +@@ -611,7 +611,7 @@ + string_f.h references.h util.h work_lda.c \ + work_gga_x.c work_gga_c.c \ + work_mgga_x.c work_mgga_c.c \ +- libxc_master.F90 libxc_master.F03 ++ libxc_master.F90 libxc_master_F03.F90 + + include_HEADERS = xc.h xc_funcs_removed.h + nodist_include_HEADERS = xc_funcs.h +@@ -1453,8 +1453,8 @@ + $(LTPREF)libxc.lo $(LTPREF)libxc.o : $(LIBFUNCMOD) + + $(XCLIBMODS) : $(LTPREF)libxc.lo +-libxcf03.f90 : libxc_master.F03 libxc_inc.f03 +- @FCCPP@ @CPPFLAGS@ $(AM_CPPFLAGS) -I$(top_builddir)/src $(srcdir)/libxc_master.F03 > $(top_builddir)/src/libxcf03.f90 ++libxcf03.f90 : libxc_master_F03.F90 libxc_inc.f03 ++ @FCCPP@ @CPPFLAGS@ $(AM_CPPFLAGS) -I$(top_builddir)/src $(srcdir)/libxc_master_F03.F90 > $(top_builddir)/src/libxcf03.f90 + @if [ "@F90_ACCEPTS_LINE_NUMBERS@" = "no" ]; then \ + grep -v "^#" $(top_builddir)/src/libxcf03.f90 > $(top_builddir)/src/libxcf03.f91; \ + mv -f $(top_builddir)/src/libxcf03.f91 $(top_builddir)/src/libxcf03.f90; \ +--- libxc-4.3.4/CMakeLists.txt.orig 2019-05-21 18:04:02.978334306 +0200 ++++ libxc-4.3.4/CMakeLists.txt 2019-05-21 18:04:34.308604175 +0200 +@@ -296,7 +296,7 @@ + gen_funcidx/libxc_funcs.f90 + ) + set(raw_sources_list_f03 +- src/libxc_master.F03 ++ src/libxc_master_F03.F90 + ) + + # when headers namespaced, xc_version include in xc.h needs to be local, not From a0f3d53ef95eb301e008f2a9a00396b472be54d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 May 2019 19:48:37 +0200 Subject: [PATCH 1686/5331] remove unused checksum for ballgown extension in Bioconductor 3.7 easyconfigs --- .../R-bundle-Bioconductor-3.7-foss-2018b-R-3.5.1.eb | 1 - .../R-bundle-Bioconductor-3.7-iomkl-2018a-R-3.5.0.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.7-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.7-foss-2018b-R-3.5.1.eb index f8e10ef9f25..f5c762f5d6d 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.7-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.7-foss-2018b-R-3.5.1.eb @@ -427,7 +427,6 @@ exts_list = [ 'checksums': ['5a142ac9faa2ffbf1030b4e5db7963d8038214abd7e1296dee325c09fec27228'], }), ('ballgown', '2.12.0', { - 'checksum': ['3e9d90b9f345d122824260c588d1d36a602a525a9daa1826190193d8c24ba483'], 'checksums': ['782a9760d27bb529238b1ecd3fa2f2c0f364ba8f861d7fad54bd127e2935a6d2'], }), ('DropletUtils', '1.0.3', { diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.7-iomkl-2018a-R-3.5.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.7-iomkl-2018a-R-3.5.0.eb index 507767a6ef8..27d3736b28b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.7-iomkl-2018a-R-3.5.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.7-iomkl-2018a-R-3.5.0.eb @@ -434,7 +434,6 @@ exts_list = [ 'checksums': ['5a142ac9faa2ffbf1030b4e5db7963d8038214abd7e1296dee325c09fec27228'], }), ('ballgown', '2.12.0', { - 'checksum': ['3e9d90b9f345d122824260c588d1d36a602a525a9daa1826190193d8c24ba483'], 'checksums': ['782a9760d27bb529238b1ecd3fa2f2c0f364ba8f861d7fad54bd127e2935a6d2'], }), ] From 51caddbdc44d3d87743f39855307cee38116a12a Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Tue, 21 May 2019 19:53:35 +0200 Subject: [PATCH 1687/5331] adding easyconfigs: OR-Tools-7.1-foss-2019a-Python-3.7.2.eb and patches: OR-Tools-7.1-fix-makefiles.patch --- .../OR-Tools/OR-Tools-7.1-fix-makefiles.patch | 81 +++++++++++++++++++ .../OR-Tools-7.1-foss-2019a-Python-3.7.2.eb | 50 ++++++++++++ 2 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch create mode 100644 easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch new file mode 100644 index 00000000000..dfa5a46f821 --- /dev/null +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch @@ -0,0 +1,81 @@ +# Use EB deps and install prefix +# wpoely86@gmail.com +diff -Nur or-tools-7.1.orig/Makefile.local.eb or-tools-7.1/Makefile.local.eb +--- or-tools-7.1.orig/Makefile.local.eb 1970-01-01 01:00:00.000000000 +0100 ++++ or-tools-7.1/Makefile.local.eb 2019-05-20 20:49:11.941360942 +0200 +@@ -0,0 +1,5 @@ ++UNIX_SWIG_BINARY = $(EBROOTSWIG)/bin/swig ++JAVA_HOME = $(EBROOTJAVA) ++UNIX_PYTHON_VER = 3.7 ++UNIX_GUROBI_DIR=$(EBROOTGUROBI) ++GUROBI_LIB_VERSION=$(shell echo $(EBVERSIONGUROBI) | sed 's:\([0-9]\+\)\.\([0-9]\+\)\..*:\1\2:') +diff --git a/Makefile b/Makefile +index c70b93c..c1d5a63 100755 +--- a/Makefile ++++ b/Makefile +@@ -55,6 +55,7 @@ OR_ROOT_FULL=$(OR_TOOLS_TOP) + + # Load local variables + include $(OR_ROOT)Makefile.local ++include $(OR_ROOT)Makefile.local.eb + + # Change the file extensions to increase diff tool friendliness. + # Then include specific system commands and definitions +diff --git a/makefiles/Makefile.python.mk b/makefiles/Makefile.python.mk +index 2b548e0..b7f72ae 100755 +--- a/makefiles/Makefile.python.mk ++++ b/makefiles/Makefile.python.mk +@@ -1113,7 +1113,8 @@ endif # ifneq ($(PYTHON_EXECUTABLE),) + + .PHONY: install_python # Install Python OR-Tools on the host system + install_python: pypi_archive +- cd "$(PYPI_ARCHIVE_TEMP_DIR)$Sortools" && "$(PYTHON_EXECUTABLE)" setup.py install --user ++ mkdir -p $(DESTDIR)/lib/python3.7/site-packages ++ cd "$(PYPI_ARCHIVE_TEMP_DIR)$Sortools" && PYTHONPATH=$(DESTDIR)/lib/python3.7/site-packages:$(PYTHONPATH) "$(PYTHON_EXECUTABLE)" setup.py install --prefix $(DESTDIR) + + .PHONY: uninstall_python # Uninstall Python OR-Tools from the host system + uninstall_python: +diff --git a/makefiles/Makefile.unix.mk b/makefiles/Makefile.unix.mk +index 354ea9e..5726fc6 100644 +--- a/makefiles/Makefile.unix.mk ++++ b/makefiles/Makefile.unix.mk +@@ -99,7 +99,7 @@ ifdef UNIX_SCIP_DIR + SCIP_SWIG = $(SCIP_INC) + endif + ifdef UNIX_GUROBI_DIR +- GUROBI_INC = -I$(UNIX_GUROBI_DIR)/$(GUROBI_PLATFORM)/include -DUSE_GUROBI ++ GUROBI_INC = -I$(UNIX_GUROBI_DIR)/include -DUSE_GUROBI + GUROBI_SWIG = $(GUROBI_INC) + endif + ifdef UNIX_CPLEX_DIR +@@ -134,13 +134,13 @@ ifeq ($(PLATFORM),LINUX) + ifdef UNIX_GUROBI_DIR + ifeq ($(PTRLENGTH),64) + GUROBI_LNK = \ +- -Wl,-rpath $(UNIX_GUROBI_DIR)/linux64/lib/ \ +- -L$(UNIX_GUROBI_DIR)/linux64/lib/ -m64 -lc -ldl -lm -lpthread \ ++ -Wl,-rpath $(UNIX_GUROBI_DIR)/lib/ \ ++ -L$(UNIX_GUROBI_DIR)/lib/ -m64 -lc -ldl -lm -lpthread \ + -lgurobi$(GUROBI_LIB_VERSION) + else + GUROBI_LNK = \ +- -Wl,-rpath $(UNIX_GUROBI_DIR)/linux32/lib/ \ +- -L$(UNIX_GUROBI_DIR)/linux32/lib/ -m32 -lc -ldl -lm -lpthread \ ++ -Wl,-rpath $(UNIX_GUROBI_DIR)/lib/ \ ++ -L$(UNIX_GUROBI_DIR)/lib/ -m32 -lc -ldl -lm -lpthread \ + -lgurobi$(GUROBI_LIB_VERSION) + endif + endif +diff --git a/ortools/linear_solver/gurobi_interface.cc b/ortools/linear_solver/gurobi_interface.cc +index dcc993e..de9adbd 100644 +--- a/ortools/linear_solver/gurobi_interface.cc ++++ b/ortools/linear_solver/gurobi_interface.cc +@@ -175,7 +175,7 @@ class GurobiInterface : public MPSolverInterface { + GRBenv* env_; + bool mip_; + int current_solution_index_; +- MPCallback* callback_ = nullptr; ++// MPCallback* callback_ = nullptr; + }; + + namespace { diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..827a304a0e0 --- /dev/null +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'OR-Tools' +version = '7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://developers.google.com/optimization/' +description = """Google Optimization Tools (a.k.a., OR-Tools) is an open-source, fast +and portable software suite for solving combinatorial optimization problems.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +github_account = 'google' + +patches = ['%(name)s-%(version)s-fix-makefiles.patch'] + +builddependencies = [ + ('SWIG', '3.0.12', versionsuffix), + ('CMake', '3.13.3'), +] + +dependencies = [ + ('Python', '3.7.2'), + ('zlib', '1.2.11'), + ('Java', '1.8', '', True), + # Gurobi is optional + ('Gurobi', '8.1.1', '', True), +] + +skipsteps = ['configure'] + +prebuildopts = 'make third_party &&' +buildopts = 'python cc' + +preinstallopts = 'prefix="" DESTDIR=%(installdir)s' +install_cmd = 'make' +installopts = 'install_python install_cc' + +runtest = 'test_python test_cc' + +sanity_check_paths = { + 'files': ['lib/libortools.%s' % SHLIB_EXT], + 'dirs': ['include/ortools', 'lib/python%(pyshortver)s/site-packages'] +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'math' From c2033427807eb49215a4c11d4de9481952ee3ca4 Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Tue, 21 May 2019 20:03:48 +0200 Subject: [PATCH 1688/5331] add checksums --- .../o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb index 827a304a0e0..ec5f78b4118 100644 --- a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb @@ -12,9 +12,13 @@ toolchain = {'name': 'foss', 'version': '2019a'} source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -github_account = 'google' - patches = ['%(name)s-%(version)s-fix-makefiles.patch'] +checksums = [ + '6118a931ffcf172c7e2371c3392f82380e9d2a29840daba7caff239ad70d4b44', # v7.1.tar.gz + '35d05c0c57f0691f7570b3560443ed7d933fc97c13dc18c2227e2a251c127414', # OR-Tools-7.1-fix-makefiles.patch +] + +github_account = 'google' builddependencies = [ ('SWIG', '3.0.12', versionsuffix), From e5c44935636469fa46cf7ee74fe7e301122e71a0 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Tue, 21 May 2019 20:48:47 +0200 Subject: [PATCH 1689/5331] Fix remarks --- .../o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch | 11 +++++++---- .../OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb | 8 +++++--- 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch index dfa5a46f821..cb4df86fdc7 100644 --- a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch @@ -1,4 +1,7 @@ -# Use EB deps and install prefix +# Changes: +# - Use EB deps +# - Use EB install prefix +# - Fix bug (unneeded line with unexisting type) # wpoely86@gmail.com diff -Nur or-tools-7.1.orig/Makefile.local.eb or-tools-7.1/Makefile.local.eb --- or-tools-7.1.orig/Makefile.local.eb 1970-01-01 01:00:00.000000000 +0100 @@ -6,7 +9,7 @@ diff -Nur or-tools-7.1.orig/Makefile.local.eb or-tools-7.1/Makefile.local.eb @@ -0,0 +1,5 @@ +UNIX_SWIG_BINARY = $(EBROOTSWIG)/bin/swig +JAVA_HOME = $(EBROOTJAVA) -+UNIX_PYTHON_VER = 3.7 ++UNIX_PYTHON_VER=$(shell echo $(EBVERSIONPYTHON) | sed 's:\([0-9]\+\)\.\([0-9]\+\)\..*:\1.\2:') +UNIX_GUROBI_DIR=$(EBROOTGUROBI) +GUROBI_LIB_VERSION=$(shell echo $(EBVERSIONGUROBI) | sed 's:\([0-9]\+\)\.\([0-9]\+\)\..*:\1\2:') diff --git a/Makefile b/Makefile @@ -30,8 +33,8 @@ index 2b548e0..b7f72ae 100755 .PHONY: install_python # Install Python OR-Tools on the host system install_python: pypi_archive - cd "$(PYPI_ARCHIVE_TEMP_DIR)$Sortools" && "$(PYTHON_EXECUTABLE)" setup.py install --user -+ mkdir -p $(DESTDIR)/lib/python3.7/site-packages -+ cd "$(PYPI_ARCHIVE_TEMP_DIR)$Sortools" && PYTHONPATH=$(DESTDIR)/lib/python3.7/site-packages:$(PYTHONPATH) "$(PYTHON_EXECUTABLE)" setup.py install --prefix $(DESTDIR) ++ mkdir -p $(DESTDIR)/lib/python$(UNIX_PYTHON_VER)/site-packages ++ cd "$(PYPI_ARCHIVE_TEMP_DIR)$Sortools" && PYTHONPATH=$(DESTDIR)/lib/python$(UNIX_PYTHON_VER)/site-packages:$(PYTHONPATH) "$(PYTHON_EXECUTABLE)" setup.py install --prefix $(DESTDIR) .PHONY: uninstall_python # Uninstall Python OR-Tools from the host system uninstall_python: diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb index ec5f78b4118..2b4cb069629 100644 --- a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb @@ -11,14 +11,14 @@ and portable software suite for solving combinatorial optimization problems.""" toolchain = {'name': 'foss', 'version': '2019a'} source_urls = [GITHUB_SOURCE] +github_account = 'google' sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s-fix-makefiles.patch'] checksums = [ '6118a931ffcf172c7e2371c3392f82380e9d2a29840daba7caff239ad70d4b44', # v7.1.tar.gz - '35d05c0c57f0691f7570b3560443ed7d933fc97c13dc18c2227e2a251c127414', # OR-Tools-7.1-fix-makefiles.patch + '81e0010d112f5a785a9eced0fa91375fd6aec5793af41354e94565f47edf1e48', # OR-Tools-7.1-fix-makefiles.patch ] -github_account = 'google' builddependencies = [ ('SWIG', '3.0.12', versionsuffix), @@ -35,10 +35,12 @@ dependencies = [ skipsteps = ['configure'] +# OR-Tools want it's own dependencies (like protobuf) prebuildopts = 'make third_party &&' buildopts = 'python cc' -preinstallopts = 'prefix="" DESTDIR=%(installdir)s' +# prefix is the subpath in DESTDIR, defaults to /usr/local +preinstallopts = "prefix='' DESTDIR=%(installdir)s" install_cmd = 'make' installopts = 'install_python install_cc' From d3fe2580826f23420c3c513b4a359fe329d0336a Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 22 May 2019 09:51:12 +0200 Subject: [PATCH 1690/5331] Adjust make lines for OR-Tools --- .../OR-Tools/OR-Tools-7.1-fix-makefiles.patch | 25 ++----------------- .../OR-Tools-7.1-foss-2019a-Python-3.7.2.eb | 12 ++++++--- 2 files changed, 10 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch index cb4df86fdc7..c5fe6c35eae 100644 --- a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch @@ -3,27 +3,6 @@ # - Use EB install prefix # - Fix bug (unneeded line with unexisting type) # wpoely86@gmail.com -diff -Nur or-tools-7.1.orig/Makefile.local.eb or-tools-7.1/Makefile.local.eb ---- or-tools-7.1.orig/Makefile.local.eb 1970-01-01 01:00:00.000000000 +0100 -+++ or-tools-7.1/Makefile.local.eb 2019-05-20 20:49:11.941360942 +0200 -@@ -0,0 +1,5 @@ -+UNIX_SWIG_BINARY = $(EBROOTSWIG)/bin/swig -+JAVA_HOME = $(EBROOTJAVA) -+UNIX_PYTHON_VER=$(shell echo $(EBVERSIONPYTHON) | sed 's:\([0-9]\+\)\.\([0-9]\+\)\..*:\1.\2:') -+UNIX_GUROBI_DIR=$(EBROOTGUROBI) -+GUROBI_LIB_VERSION=$(shell echo $(EBVERSIONGUROBI) | sed 's:\([0-9]\+\)\.\([0-9]\+\)\..*:\1\2:') -diff --git a/Makefile b/Makefile -index c70b93c..c1d5a63 100755 ---- a/Makefile -+++ b/Makefile -@@ -55,6 +55,7 @@ OR_ROOT_FULL=$(OR_TOOLS_TOP) - - # Load local variables - include $(OR_ROOT)Makefile.local -+include $(OR_ROOT)Makefile.local.eb - - # Change the file extensions to increase diff tool friendliness. - # Then include specific system commands and definitions diff --git a/makefiles/Makefile.python.mk b/makefiles/Makefile.python.mk index 2b548e0..b7f72ae 100755 --- a/makefiles/Makefile.python.mk @@ -33,8 +12,8 @@ index 2b548e0..b7f72ae 100755 .PHONY: install_python # Install Python OR-Tools on the host system install_python: pypi_archive - cd "$(PYPI_ARCHIVE_TEMP_DIR)$Sortools" && "$(PYTHON_EXECUTABLE)" setup.py install --user -+ mkdir -p $(DESTDIR)/lib/python$(UNIX_PYTHON_VER)/site-packages -+ cd "$(PYPI_ARCHIVE_TEMP_DIR)$Sortools" && PYTHONPATH=$(DESTDIR)/lib/python$(UNIX_PYTHON_VER)/site-packages:$(PYTHONPATH) "$(PYTHON_EXECUTABLE)" setup.py install --prefix $(DESTDIR) ++ mkdir -p $(DESTDIR)/lib/python3.7/site-packages ++ cd "$(PYPI_ARCHIVE_TEMP_DIR)$Sortools" && PYTHONPATH=$(DESTDIR)/lib/python3.7/site-packages:$(PYTHONPATH) "$(PYTHON_EXECUTABLE)" setup.py install --prefix $(DESTDIR) .PHONY: uninstall_python # Uninstall Python OR-Tools from the host system uninstall_python: diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb index 2b4cb069629..d9bf8e6a5dc 100644 --- a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb @@ -16,28 +16,32 @@ sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s-fix-makefiles.patch'] checksums = [ '6118a931ffcf172c7e2371c3392f82380e9d2a29840daba7caff239ad70d4b44', # v7.1.tar.gz - '81e0010d112f5a785a9eced0fa91375fd6aec5793af41354e94565f47edf1e48', # OR-Tools-7.1-fix-makefiles.patch + 'ca5040a5031a3ef42f5ce6634d27f4550e8eb435a066ad44231f7ef1c20723c7', # OR-Tools-7.1-fix-makefiles.patch ] - builddependencies = [ ('SWIG', '3.0.12', versionsuffix), ('CMake', '3.13.3'), ] +gurobiver = '8.1.1' + dependencies = [ ('Python', '3.7.2'), ('zlib', '1.2.11'), ('Java', '1.8', '', True), # Gurobi is optional - ('Gurobi', '8.1.1', '', True), + ('Gurobi', gurobiver, '', True), ] skipsteps = ['configure'] +gurobivershort = ''.join(gurobiver.split('.')[:2]) + # OR-Tools want it's own dependencies (like protobuf) prebuildopts = 'make third_party &&' -buildopts = 'python cc' +buildopts = 'python cc UNIX_SWIG_BINARY=$EBROOTSWIG/bin/swig JAVA_HOME=$EBROOTJAVA UNIX_PYTHON_VER=%%(pyshortver)s' +buildopts += ' UNIX_GUROBI_DIR=$EBROOTGUROBI GUROBI_LIB_VERSION=%s' % gurobivershort # prefix is the subpath in DESTDIR, defaults to /usr/local preinstallopts = "prefix='' DESTDIR=%(installdir)s" From 82548d8b3758aadd2e115ac3a522d9c0c34f6f51 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 22 May 2019 10:02:24 +0200 Subject: [PATCH 1691/5331] add binutils dep --- easybuild/easyconfigs/r/Racon/Racon-1.3.2-GCCcore-8.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.3.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.3.2-GCCcore-8.2.0.eb index 86fe34d5904..84dd81f8d6a 100644 --- a/easybuild/easyconfigs/r/Racon/Racon-1.3.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/r/Racon/Racon-1.3.2-GCCcore-8.2.0.eb @@ -12,7 +12,10 @@ source_urls = ['https://github.com/isovic/racon/releases/download/%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['7c99380a0f1091f5ee138b559e318d7e9463d3145eac026bf236751c2c4b92c7'] -builddependencies = [('CMake', '3.13.3')] +builddependencies = [ + ('CMake', '3.13.3'), + ('binutils', '2.31.1'), +] sanity_check_paths = { 'files': ['bin/racon'], From 56b86047405532293ec5bae24d2fd7aa55fd3aec Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 22 May 2019 10:03:39 +0200 Subject: [PATCH 1692/5331] Correct string templating --- .../o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb index d9bf8e6a5dc..a91f8b9a146 100644 --- a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb @@ -40,7 +40,7 @@ gurobivershort = ''.join(gurobiver.split('.')[:2]) # OR-Tools want it's own dependencies (like protobuf) prebuildopts = 'make third_party &&' -buildopts = 'python cc UNIX_SWIG_BINARY=$EBROOTSWIG/bin/swig JAVA_HOME=$EBROOTJAVA UNIX_PYTHON_VER=%%(pyshortver)s' +buildopts = 'python cc UNIX_SWIG_BINARY=$EBROOTSWIG/bin/swig JAVA_HOME=$EBROOTJAVA UNIX_PYTHON_VER=%(pyshortver)s' buildopts += ' UNIX_GUROBI_DIR=$EBROOTGUROBI GUROBI_LIB_VERSION=%s' % gurobivershort # prefix is the subpath in DESTDIR, defaults to /usr/local From d65379bfa518357fadc84f57b83d0a28a9cab4cb Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Wed, 22 May 2019 09:26:53 +0100 Subject: [PATCH 1693/5331] download_dep_fail and use_pip changed to True --- .../p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb index 6155c98dfcc..aa87ec0b172 100644 --- a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-foss-2018b-Python-3.6.6.eb @@ -25,8 +25,8 @@ dependencies = [ ('Python', '3.6.6'), ] -download_dep_fail = ['none'] -use_pip = ['none'] +download_dep_fail = True +use_pip = True sanity_check_paths = { From bd5bdf91d0ce9c26602c7f08ed4b29a835156241 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 22 May 2019 10:57:51 +0200 Subject: [PATCH 1694/5331] Add autotools as build dep --- .../o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb index a91f8b9a146..043f805b0f1 100644 --- a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb @@ -22,6 +22,7 @@ checksums = [ builddependencies = [ ('SWIG', '3.0.12', versionsuffix), ('CMake', '3.13.3'), + ('Autotools', '20180311'), ] gurobiver = '8.1.1' From 1a000addf47b6c7e9d448fe721cced1ad10121da Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Wed, 22 May 2019 10:43:56 +0100 Subject: [PATCH 1695/5331] optarch dropped as requested --- easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb index d4bcf5b48f6..9028591218b 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-foss-2018b.eb @@ -10,7 +10,7 @@ description = """HDF5 is a data model, library, and file format for storing and and efficient I/O and for high volume and complex data.""" toolchain = {'name': 'foss', 'version': '2018b'} -toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} +toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] From bdd5d6c01f6feee3c239c0196e8de1a14d9410b9 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Wed, 22 May 2019 12:03:34 +0100 Subject: [PATCH 1696/5331] Module class bio added --- .../easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb index acd78413445..391d6c0ac97 100644 --- a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb +++ b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb @@ -29,3 +29,5 @@ sanity_check_paths = { 'files': ['bin/correlations', 'bin/neighbors', 'bin/pgen', 'bin/tcrdists'], 'dirs': ['bin', 'db'], } + +moduleclass = 'bio' From a703e614c113aecf24d262c0416f5f2e931f2e93 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Wed, 22 May 2019 12:15:29 +0100 Subject: [PATCH 1697/5331] Acknowledgement added --- .../easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb index 391d6c0ac97..072fc187aa7 100644 --- a/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb +++ b/easybuild/easyconfigs/p/pubtcrs/pubtcrs-f30b96a-intel-2019.01.eb @@ -1,3 +1,6 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + easyblock = 'MakeCp' name = 'pubtcrs' From c4d91f50e9bd706354ab83b4c8a798737fcacc46 Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Wed, 22 May 2019 15:44:55 +0200 Subject: [PATCH 1698/5331] adding easyconfigs: vsc-mympirun-4.1.8.eb --- .../v/vsc-mympirun/vsc-mympirun-4.1.8.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb new file mode 100644 index 00000000000..0bfd27ac8f5 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'vsc-mympirun' +version = '4.1.8' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': ''} + +osdependencies = ['python-setuptools'] + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +download_dep_fail = True +use_pip = False + +exts_list = [ + ('IPy', '1.00', { + 'modulename': 'IPy', + 'source_urls': ['https://pypi.python.org/packages/source/i/IPy'], + }), + ('vsc-install', '0.12.7', { + 'modulename': 'vsc.install', + 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-install'], + }), + ('vsc-base', '2.9.2', { + 'modulename': 'vsc.utils', + 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-base'], + }), + (name, version, { + # don't check for import of vsc.mympirun, since that may fail if vsc-base is picked up from the OS + 'modulename': 'vsc', + 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-mympirun'], + }), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mympisanity'], + 'dirs': ['bin/fake'], +} +sanity_check_commands = ["mympirun --help"] + +moduleclass = 'tools' From 936f136011ffe101da2e4ac80ff8d7dae441efd4 Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Wed, 22 May 2019 16:19:07 +0200 Subject: [PATCH 1699/5331] add checksums and more deps --- .../v/vsc-mympirun/vsc-mympirun-4.1.8.eb | 26 ++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb index 0bfd27ac8f5..2c9b73a1ce7 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb @@ -17,22 +17,46 @@ download_dep_fail = True use_pip = False exts_list = [ + ('setuptools', '39.2.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['f7cddbb5f5c640311eb00eab6e849f7701fa70bf6a183fc8a2c33dd1d1672fb2'], + }), + ('future', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/future'], + 'checksums': ['67045236dcfd6816dc439556d009594abf643e5eb48992e36beac09c2ca659b8'], + }), + ('pbr', '5.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + 'checksums': ['8c361cc353d988e4f5b998555c88098b9d5964c2e11acf7b0d21925a66bb5824'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs/'], + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock/'], + 'checksums': ['b158b6df76edd239b8208d481dc46b6afd45a846b7812ff0ce58971cf5bc8bba'], + }), ('IPy', '1.00', { 'modulename': 'IPy', 'source_urls': ['https://pypi.python.org/packages/source/i/IPy'], + 'checksums': ['2f2bf658a858d43868d8a4352b3889cf78c66e2ce678b300dcf518c9149ba621'], }), ('vsc-install', '0.12.7', { 'modulename': 'vsc.install', 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-install'], + 'checksums': ['f1d0796aa6201c0d7e1c6bde591153be1b8bde2f04860494272432c1d30f18f5'], }), ('vsc-base', '2.9.2', { 'modulename': 'vsc.utils', 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-base'], + 'checksums': ['55803ce00f29bc0eb8b4e37518b21368b4c0f4cdb37c3a168912fc815fd88f15'], }), (name, version, { - # don't check for import of vsc.mympirun, since that may fail if vsc-base is picked up from the OS 'modulename': 'vsc', 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-mympirun'], + 'checksums': ['497433504860328934db5777200a2107561b83d524515418f908da77b5fec83b'], }), ] From 3cc7e197f164f3042783b0209a930432f4e0c76e Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Wed, 22 May 2019 16:59:51 +0200 Subject: [PATCH 1700/5331] fix remarks --- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb index 2c9b73a1ce7..2a18e36513e 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb @@ -9,11 +9,8 @@ description = """VSC-tools is a set of Python libraries and scripts that are com # we build this to work with every python version toolchain = {'name': 'dummy', 'version': ''} -osdependencies = ['python-setuptools'] - allow_system_deps = [('Python', SYS_PYTHON_VERSION)] -download_dep_fail = True use_pip = False exts_list = [ From 275324274a2421ba8c016f7a678008515abe2f8f Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Wed, 22 May 2019 17:41:41 +0200 Subject: [PATCH 1701/5331] re-add dropped comment --- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb index 2a18e36513e..2fa3a840087 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb @@ -51,6 +51,7 @@ exts_list = [ 'checksums': ['55803ce00f29bc0eb8b4e37518b21368b4c0f4cdb37c3a168912fc815fd88f15'], }), (name, version, { + # don't check for import of vsc.mympirun, since that may fail if vsc-base is picked up from the OS 'modulename': 'vsc', 'source_urls': ['https://pypi.python.org/packages/source/v/vsc-mympirun'], 'checksums': ['497433504860328934db5777200a2107561b83d524515418f908da77b5fec83b'], From 68ce012c0e3c4e91c3e31a2cbcd61c8ef3e2e131 Mon Sep 17 00:00:00 2001 From: Joerg Sassmannshausen Date: Wed, 22 May 2019 17:12:03 +0100 Subject: [PATCH 1702/5331] adding easyconfigs: cytosim-master-20190117-foss-2018b-mkl-3D-detachment.eb, cytosim-master-20190117-foss-2018b-mkl-3D-png-detachment.eb, cytosim-master-20190117-foss-2018bmkl-3D-png.eb, cytosim-master-20190117-foss-2018b-mkl-3D.eb, cytosim-master-20190117-foss-2018b-mkl-detachment.eb, cytosim-master-20190117-foss-2018b-mkl-detachment.eb, cytosim-master-20190117-foss-2018b-mkl-png-detachment.eb, cytosim-master-20190117-foss-2018b-mkl-png.eb, cytosim-master-20190117-foss-2018b-mkl.eb and patches: 3D.patch, detachment.patch, mkl.patch, png.patch --- easybuild/easyconfigs/c/cytosim/3D.patch | 11 +++++ ...r-20190117-foss-2018b-mkl-3D-detachment.eb | 47 +++++++++++++++++++ ...190117-foss-2018b-mkl-3D-png-detachment.eb | 47 +++++++++++++++++++ ...tosim-master-20190117-foss-2018b-mkl-3D.eb | 45 ++++++++++++++++++ ...ster-20190117-foss-2018b-mkl-detachment.eb | 45 ++++++++++++++++++ ...-20190117-foss-2018b-mkl-png-detachment.eb | 46 ++++++++++++++++++ ...osim-master-20190117-foss-2018b-mkl-png.eb | 45 ++++++++++++++++++ .../cytosim-master-20190117-foss-2018b-mkl.eb | 43 +++++++++++++++++ ...im-master-20190117-foss-2018bmkl-3D-png.eb | 46 ++++++++++++++++++ .../easyconfigs/c/cytosim/detachment.patch | 12 +++++ easybuild/easyconfigs/c/cytosim/mkl.patch | 28 +++++++++++ easybuild/easyconfigs/c/cytosim/png.patch | 21 +++++++++ 12 files changed, 436 insertions(+) create mode 100644 easybuild/easyconfigs/c/cytosim/3D.patch create mode 100644 easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D-detachment.eb create mode 100644 easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D-png-detachment.eb create mode 100644 easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D.eb create mode 100644 easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-detachment.eb create mode 100644 easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-png-detachment.eb create mode 100644 easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-png.eb create mode 100644 easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl.eb create mode 100644 easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018bmkl-3D-png.eb create mode 100644 easybuild/easyconfigs/c/cytosim/detachment.patch create mode 100644 easybuild/easyconfigs/c/cytosim/mkl.patch create mode 100644 easybuild/easyconfigs/c/cytosim/png.patch diff --git a/easybuild/easyconfigs/c/cytosim/3D.patch b/easybuild/easyconfigs/c/cytosim/3D.patch new file mode 100644 index 00000000000..9aa383e6d9f --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/3D.patch @@ -0,0 +1,11 @@ +diff -Nru cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b-orig/src/math/dim.h cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b/src/math/dim.h +--- cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b-orig/src/math/dim.h 2019-01-17 09:14:25.000000000 +0000 ++++ cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b/src/math/dim.h 2019-02-25 10:17:50.224521000 +0000 +@@ -7,6 +7,6 @@ + #ifndef DIM + + /// DIM defines the number of dimensions in space: 1, 2 or 3 +-#define DIM 2 ++#define DIM 3 + + #endif diff --git a/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D-detachment.eb b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D-detachment.eb new file mode 100644 index 00000000000..f222d4c988d --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D-detachment.eb @@ -0,0 +1,47 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'cytosim' +github_account = 'nedelec' +version = 'master-20190117' +versionsuffix = '-mkl-3D-detachment' + +homepage = 'https://github.com/nedelec/cytosim' +description = """Cytosim is a cytoskeleton simulation engine written in +C++ working on Mac OS, GNU/Linux and Windows (with Cygwin). +This version has set the new end dependant detachment to 1 and +is for 3 dimensions!""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [GITHUB_SOURCE] +sources = [{ + 'filename': '3ecab25.tar.gz', +}] + +checksums = [ + 'c5209ec9761902769299ad666d621dc3c169f8f73cce6799a99087be259fd246', # 3ecab25.tar.gz + '5d0389884862d21878c1923e71ed87185dc2e9260206c7514f339fec4c2d14d1', # mkl.patch + '20e97f788b5e712e9f15524f531985940d4a1f0758e4bdcea3d26ecd6d73c9be', # 3D.patch + 'b5b66bebefd6eb9543daaa5804ad5d8c7f155e9b204cd6fc7eee569abcf9e52e', # detachment.patch +] + +# fix makefile.inc so it is using MKL 3D and detachment +patches = ['mkl.patch', '3D.patch', 'detachment.patch', ] + +dependencies = [ + ('freeglut', '3.0.0'), + ('glew', '2.1.0'), + ('imkl', '2019.1.144-iimpi-2019.01', '', True), +] + +files_to_copy = ['bin', ] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/report', 'bin/sim', ], + 'dirs': [''] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D-png-detachment.eb b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D-png-detachment.eb new file mode 100644 index 00000000000..905e6b0cc5c --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D-png-detachment.eb @@ -0,0 +1,47 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'cytosim' +github_account = 'nedelec' +version = 'master-20190117' +versionsuffix = '-mkl-3D-png-detachment' + +homepage = 'https://github.com/nedelec/cytosim' +description = """Cytosim is a cytoskeleton simulation engine written in +C++ working on Mac OS, GNU/Linux and Windows (with Cygwin). +This version is for 3 dimensions and has png enabled!""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [GITHUB_SOURCE] +sources = [{ + 'filename': '3ecab25.tar.gz', +}] + +checksums = [ + 'c5209ec9761902769299ad666d621dc3c169f8f73cce6799a99087be259fd246', # 3ecab25.tar.gz + 'ce23989b8495d95f662d6aa5d16d1fcc7b170a4c7c69eacdb278b95082b7fd0d', # png.patch + '20e97f788b5e712e9f15524f531985940d4a1f0758e4bdcea3d26ecd6d73c9be', # 3D.patch + '5d0389884862d21878c1923e71ed87185dc2e9260206c7514f339fec4c2d14d1', # mkl.patch + 'b5b66bebefd6eb9543daaa5804ad5d8c7f155e9b204cd6fc7eee569abcf9e52e', # detachment.patch +] + +# fix makefile.inc so it is using MKL, 3D, detachment and PNG +patches = ['png.patch', '3D.patch', 'mkl.patch', 'detachment.patch'] + +dependencies = [ + ('freeglut', '3.0.0'), + ('glew', '2.1.0'), + ('imkl', '2019.1.144-iimpi-2019.01', '', True), +] + +files_to_copy = ['bin', ] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/report', 'bin/sim', ], + 'dirs': [''] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D.eb b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D.eb new file mode 100644 index 00000000000..90529df5290 --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-3D.eb @@ -0,0 +1,45 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'cytosim' +github_account = 'nedelec' +version = 'master-20190117' +versionsuffix = '-mkl-3D' + +homepage = 'https://github.com/nedelec/cytosim' +description = """Cytosim is a cytoskeleton simulation engine written in +C++ working on Mac OS, GNU/Linux and Windows (with Cygwin). +This version is for 3 dimensions!""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [GITHUB_SOURCE] +sources = [{ + 'filename': '3ecab25.tar.gz', +}] + +checksums = [ + 'c5209ec9761902769299ad666d621dc3c169f8f73cce6799a99087be259fd246', # 3ecab25.tar.gz + '5d0389884862d21878c1923e71ed87185dc2e9260206c7514f339fec4c2d14d1', # mkl.patch + '20e97f788b5e712e9f15524f531985940d4a1f0758e4bdcea3d26ecd6d73c9be', # 3D.patch +] + +# fix makefile.inc so it is using MKL and 3D +patches = ['mkl.patch', '3D.patch'] + +dependencies = [ + ('freeglut', '3.0.0'), + ('glew', '2.1.0'), + ('imkl', '2019.1.144-iimpi-2019.01', '', True), +] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/report', 'bin/sim'], + 'dirs': [''] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-detachment.eb b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-detachment.eb new file mode 100644 index 00000000000..0c77e6734a6 --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-detachment.eb @@ -0,0 +1,45 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'cytosim' +github_account = 'nedelec' +version = 'master-20190117' +versionsuffix = '-mkl-detachment' + +homepage = 'https://github.com/nedelec/cytosim' +description = """Cytosim is a cytoskeleton simulation engine written in +C++ working on Mac OS, GNU/Linux and Windows (with Cygwin). +This version is for 3 dimensions and has png enabled!""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [GITHUB_SOURCE] +sources = [{ + 'filename': '3ecab25.tar.gz', +}] + +checksums = [ + 'c5209ec9761902769299ad666d621dc3c169f8f73cce6799a99087be259fd246', # 3ecab25.tar.gz + '5d0389884862d21878c1923e71ed87185dc2e9260206c7514f339fec4c2d14d1', # mkl.patch + 'b5b66bebefd6eb9543daaa5804ad5d8c7f155e9b204cd6fc7eee569abcf9e52e', # detachment.patch +] + +# fix makefile.inc so it is using MKL, 3D, detachment and PNG +patches = ['mkl.patch', 'detachment.patch'] + +dependencies = [ + ('freeglut', '3.0.0'), + ('glew', '2.1.0'), + ('imkl', '2019.1.144-iimpi-2019.01', '', True), +] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/report', 'bin/sim'], + 'dirs': [''] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-png-detachment.eb b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-png-detachment.eb new file mode 100644 index 00000000000..b74990759f7 --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-png-detachment.eb @@ -0,0 +1,46 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'cytosim' +github_account = 'nedelec' +version = 'master-20190117' +versionsuffix = '-mkl-png-detachment' + +homepage = 'https://github.com/nedelec/cytosim' +description = """Cytosim is a cytoskeleton simulation engine written in +C++ working on Mac OS, GNU/Linux and Windows (with Cygwin). +This version is for 3 dimensions and has png enabled!""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [GITHUB_SOURCE] +sources = [{ + 'filename': '3ecab25.tar.gz', +}] + +checksums = [ + 'c5209ec9761902769299ad666d621dc3c169f8f73cce6799a99087be259fd246', # 3ecab25.tar.gz + '5d0389884862d21878c1923e71ed87185dc2e9260206c7514f339fec4c2d14d1', # mkl.patch + 'ce23989b8495d95f662d6aa5d16d1fcc7b170a4c7c69eacdb278b95082b7fd0d', # png.patch + 'b5b66bebefd6eb9543daaa5804ad5d8c7f155e9b204cd6fc7eee569abcf9e52e', # detachment.patch +] + +# fix makefile.inc so it is using MKL, 3D, detachment and PNG +patches = ['png.patch', 'mkl.patch', 'detachment.patch'] + +dependencies = [ + ('freeglut', '3.0.0'), + ('glew', '2.1.0'), + ('imkl', '2019.1.144-iimpi-2019.01', '', True), +] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/report', 'bin/sim'], + 'dirs': [''] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-png.eb b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-png.eb new file mode 100644 index 00000000000..fcab2b1bc6a --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl-png.eb @@ -0,0 +1,45 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'cytosim' +github_account = 'nedelec' +version = 'master-20190117' +versionsuffix = '-mkl-png' + +homepage = 'https://github.com/nedelec/cytosim' +description = """Cytosim is a cytoskeleton simulation engine written in +C++ working on Mac OS, GNU/Linux and Windows (with Cygwin). +This version is for 3 dimensions and has png enabled!""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [GITHUB_SOURCE] +sources = [{ + 'filename': '3ecab25.tar.gz', +}] + +checksums = [ + 'c5209ec9761902769299ad666d621dc3c169f8f73cce6799a99087be259fd246', # 3ecab25.tar.gz + 'ce23989b8495d95f662d6aa5d16d1fcc7b170a4c7c69eacdb278b95082b7fd0d', # png.patch + '5d0389884862d21878c1923e71ed87185dc2e9260206c7514f339fec4c2d14d1', # mkl.patch +] + +# fix makefile.inc so it is using MKL and PNG +patches = ['png.patch', 'mkl.patch'] + +dependencies = [ + ('freeglut', '3.0.0'), + ('glew', '2.1.0'), + ('imkl', '2019.1.144-iimpi-2019.01', '', True), +] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/report', 'bin/sim'], + 'dirs': [''] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl.eb b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl.eb new file mode 100644 index 00000000000..5fb131b083b --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018b-mkl.eb @@ -0,0 +1,43 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'cytosim' +github_account = 'nedelec' +version = 'master-20190117' +versionsuffix = '-mkl' + +homepage = 'https://github.com/nedelec/cytosim' +description = """Cytosim is a cytoskeleton simulation engine written in +C++ working on Mac OS, GNU/Linux and Windows (with Cygwin).""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [GITHUB_SOURCE] +sources = [{ + 'filename': '3ecab25.tar.gz', +}] + +checksums = [ + 'c5209ec9761902769299ad666d621dc3c169f8f73cce6799a99087be259fd246', # 3ecab25.tar.gz + '5d0389884862d21878c1923e71ed87185dc2e9260206c7514f339fec4c2d14d1', # mkl.patch +] + +# fix makefile.inc so it is using MKL +patches = ['mkl.patch'] + +dependencies = [ + ('freeglut', '3.0.0'), + ('glew', '2.1.0'), + ('imkl', '2019.1.144-iimpi-2019.01', '', True), +] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/report', 'bin/sim'], + 'dirs': [''] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018bmkl-3D-png.eb b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018bmkl-3D-png.eb new file mode 100644 index 00000000000..3d1ace98e17 --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/cytosim-master-20190117-foss-2018bmkl-3D-png.eb @@ -0,0 +1,46 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'cytosim' +github_account = 'nedelec' +version = 'master-20190117' +versionsuffix = 'mkl-3D-png' + +homepage = 'https://github.com/nedelec/cytosim' +description = """Cytosim is a cytoskeleton simulation engine written in +C++ working on Mac OS, GNU/Linux and Windows (with Cygwin). +This version is for 3 dimensions and has png enabled!""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [GITHUB_SOURCE] +sources = [{ + 'filename': '3ecab25.tar.gz', +}] + +checksums = [ + 'c5209ec9761902769299ad666d621dc3c169f8f73cce6799a99087be259fd246', # 3ecab25.tar.gz + 'ce23989b8495d95f662d6aa5d16d1fcc7b170a4c7c69eacdb278b95082b7fd0d', # png.patch + '20e97f788b5e712e9f15524f531985940d4a1f0758e4bdcea3d26ecd6d73c9be', # 3D.patch + '5d0389884862d21878c1923e71ed87185dc2e9260206c7514f339fec4c2d14d1', # mkl.patch +] + +# fix makefile.inc so it is using MKL, 3D and PNG +patches = ['png.patch', '3D.patch', 'mkl.patch'] + +dependencies = [ + ('freeglut', '3.0.0'), + ('glew', '2.1.0'), + ('imkl', '2019.1.144-iimpi-2019.01', '', True), +] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/report', 'bin/sim'], + 'dirs': [''] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cytosim/detachment.patch b/easybuild/easyconfigs/c/cytosim/detachment.patch new file mode 100644 index 00000000000..e009d74ea01 --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/detachment.patch @@ -0,0 +1,12 @@ +diff -Nru cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b-orig/src/sim/hand_prop.h cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b/src/sim/hand_prop.h +--- cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b-orig/src/sim/hand_prop.h 2019-01-17 09:14:25.000000000 +0000 ++++ cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b/src/sim/hand_prop.h 2019-03-07 09:03:53.027352000 +0000 +@@ -21,7 +21,7 @@ + of dynamic microtubules and mitotic motors" published in 2018 + By J. Roostalu, J. Rickman, C. Thomas, F. Nedelec and T. Surrey + */ +-#define NEW_END_DEPENDENT_DETACHMENT 0 ++#define NEW_END_DEPENDENT_DETACHMENT 1 + + + /// Property for Hand diff --git a/easybuild/easyconfigs/c/cytosim/mkl.patch b/easybuild/easyconfigs/c/cytosim/mkl.patch new file mode 100644 index 00000000000..05352da624e --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/mkl.patch @@ -0,0 +1,28 @@ +diff -Nru cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b-orig/makefile.inc cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b/makefile.inc +--- cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b-orig/makefile.inc 2019-01-17 09:14:25.000000000 +0000 ++++ cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b/makefile.inc 2019-03-13 11:11:44.649196000 +0000 +@@ -21,7 +21,7 @@ + # HAS_MKL = 2 for static linking + # otherwise, use HAS_MKL = 0; + +-HAS_MKL := 0 ++HAS_MKL := 1 + + #---------------- PNG image export support + # `libpng` needs to be installed to save PNG images: +@@ -246,13 +246,13 @@ + ifeq ($(HAS_MKL),1) + + # sequential dynamic linking: +- MKL_LIBS := -lmkl_intel$(MKL_EXT) -lmkl_sequential -lmkl_core ++ MKL_LIBS := -Wl,--no-as-needed -lmkl_intel$(MKL_EXT) -lmkl_sequential -lmkl_core + + # threaded dynamic linking: + #MKL_LIBS := -lmkl_intel$(MKL_EXT) -lmkl_intel_thread -lmkl_core -liomp5 + + # modify the linking command: +- LINK := -L$(MKL_PATH) $(MKL_LIBS) -lpthread ++ LINK := -L$(MKL_PATH) $(MKL_LIBS) -lpthread -lm + + endif + diff --git a/easybuild/easyconfigs/c/cytosim/png.patch b/easybuild/easyconfigs/c/cytosim/png.patch new file mode 100644 index 00000000000..660a42bca95 --- /dev/null +++ b/easybuild/easyconfigs/c/cytosim/png.patch @@ -0,0 +1,21 @@ +diff -Nru cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b-orig/makefile.inc cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b/makefile.inc +--- cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b-orig/makefile.inc 2019-01-17 09:14:25.000000000 +0000 ++++ cytosim-3ecab2584958081f0bbb42642e849c84f7d34c0b/makefile.inc 2019-03-13 11:11:44.649196000 +0000 +@@ -38,7 +38,7 @@ + # 1 : macport installation + # 2 : homebrew installation + +-HAS_PNG := 0 ++HAS_PNG := 1 + + #------------------------------------------------------------------------------- + #--------------------------- Platform Detection ------------------------------ +@@ -155,7 +153,7 @@ + + ifneq ($(HAS_PNG), 0) + +- LIB_PNG := $(USRLIB)/libpng.a $(USRLIB)/libz.a ++ LIB_PNG := -L$(USRLIB) -lpng + ING_PNG := + + endif From b9107261a93ec2a1cf00ca269e07564e3d38d970 Mon Sep 17 00:00:00 2001 From: vsc10042 Date: Wed, 22 May 2019 19:10:04 +0200 Subject: [PATCH 1703/5331] change description --- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb index 2fa3a840087..4d89f8f2f0f 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.8.eb @@ -4,7 +4,8 @@ name = 'vsc-mympirun' version = '4.1.8' homepage = 'https://github.com/hpcugent/vsc-mympirun' -description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" +description = """mympirun is a tool to make it easier for users of HPC clusters to +run MPI programs with good performance.""" # we build this to work with every python version toolchain = {'name': 'dummy', 'version': ''} From 97ce70484eac8257d3b23b4e85f962ff61fc2dc3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 May 2019 19:40:49 +0200 Subject: [PATCH 1704/5331] replace use of deprecated 'dummy' toolchain with 'toolchain = SYSTEM' + check for use of 'dummy' toolchain in tests --- easybuild/easyconfigs/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb | 2 +- easybuild/easyconfigs/a/ABAQUS/ABAQUS-2018-hotfix-1806.eb | 2 +- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb | 2 +- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb | 2 +- easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb | 2 +- .../easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb | 2 +- .../easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb | 2 +- .../easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb | 2 +- .../easyconfigs/a/ACML/ACML-4.4.0-gfortran-64bit-int64.eb | 2 +- easybuild/easyconfigs/a/ACML/ACML-4.4.0-gfortran-64bit.eb | 2 +- easybuild/easyconfigs/a/ACML/ACML-4.4.0-ifort-64bit-int64.eb | 2 +- easybuild/easyconfigs/a/ACML/ACML-4.4.0-ifort-64bit.eb | 2 +- .../easyconfigs/a/ACML/ACML-5.2.0-gfortran-64bit-int64.eb | 2 +- easybuild/easyconfigs/a/ACML/ACML-5.2.0-gfortran-64bit.eb | 2 +- easybuild/easyconfigs/a/ACML/ACML-5.2.0-ifort-64bit-int64.eb | 2 +- easybuild/easyconfigs/a/ACML/ACML-5.2.0-ifort-64bit.eb | 2 +- easybuild/easyconfigs/a/ACML/ACML-5.3.0-ifort-64bit.eb | 2 +- easybuild/easyconfigs/a/ACML/ACML-5.3.1-ifort-64bit.eb | 2 +- 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easybuild/easyconfigs/s/Spark/Spark-2.0.0.eb | 2 +- easybuild/easyconfigs/s/Spark/Spark-2.0.2.eb | 2 +- .../s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_144.eb | 2 +- .../s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_152.eb | 2 +- .../s/Spark/Spark-2.3.0-Hadoop-2.7-Java-1.8.0_162.eb | 2 +- .../easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb | 2 +- easybuild/easyconfigs/s/Stata/Stata-15.eb | 2 +- easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb | 2 +- easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb | 2 +- easybuild/easyconfigs/s/snappy/snappy-1.1.6.eb | 2 +- easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb | 2 +- easybuild/easyconfigs/s/supernova/supernova-2.0.1.eb | 2 +- easybuild/easyconfigs/s/supernova/supernova-2.1.1.eb | 2 +- easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb | 2 +- easybuild/easyconfigs/t/TRF/TRF-4.09-linux64.eb | 2 +- easybuild/easyconfigs/t/Tika/Tika-1.16.eb | 2 +- .../t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb | 2 +- .../t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb | 2 +- .../t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb | 2 +- easybuild/easyconfigs/t/Transrate/Transrate-1.0.3.eb | 2 +- .../t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb | 2 +- .../t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb | 2 +- .../t/Trimmomatic/Trimmomatic-0.38-Java-1.8.0_162.eb | 2 +- .../easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb | 2 +- easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb | 2 +- easybuild/easyconfigs/t/tbl2asn/tbl2asn-20180227-linux64.eb | 2 +- easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb | 2 +- easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb | 2 +- easybuild/easyconfigs/t/time/time-1.7.eb | 2 +- easybuild/easyconfigs/t/tmux/tmux-2.3.eb | 2 +- easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb | 2 +- easybuild/easyconfigs/t/travis/travis-1.8.4-Ruby-2.3.3.eb | 2 +- easybuild/easyconfigs/u/UCLUST/UCLUST-1.2.22q-i86linux64.eb | 2 +- .../u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb | 2 +- easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb | 2 +- easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb | 2 +- easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2013_update10.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2013_update11.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2013_update12.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2013_update6.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2013_update8.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2013_update9.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2016_update3.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2017.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2017_update1.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2017_update3.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2018_update1.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2018_update2.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2019_update2.eb | 2 +- easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb | 2 +- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb | 2 +- easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb | 2 +- .../easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb | 2 +- .../easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb | 2 +- easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb | 2 +- easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb | 2 +- easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb | 2 +- easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.2.eb | 2 +- easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1.eb | 2 +- easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb | 2 +- easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.0.eb | 2 +- easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.1.eb | 2 +- easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.3.eb | 2 +- easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb | 2 +- easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb | 2 +- easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6.eb | 2 +- easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.1.eb | 2 +- easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.2.eb | 2 +- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb | 2 +- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb | 2 +- .../v/vsc-mympirun/vsc-mympirun-3.4.2-vsc-base-2.4.2.eb | 2 +- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb | 2 +- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb | 2 +- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb | 2 +- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb | 2 +- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb | 2 +- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.4.eb | 2 +- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.5.eb | 2 +- easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.6.eb | 2 +- .../vsc-processcontrol-1.0-vsc-base-2.1.2.eb | 2 +- .../v/vsc-processcontrol/vsc-processcontrol-1.0.eb | 2 +- easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb | 2 +- easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb | 2 +- .../w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb | 2 +- easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb | 2 +- easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb | 2 +- easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb | 2 +- easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb | 2 +- easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb | 2 +- easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.2.eb | 2 +- easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb | 2 +- test/easyconfigs/easyconfigs.py | 4 ++++ 1287 files changed, 1290 insertions(+), 1286 deletions(-) diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb index c0357522cc1..3d12a106d1a 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb @@ -7,7 +7,7 @@ homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [ '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-6.tar', diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2018-hotfix-1806.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2018-hotfix-1806.eb index 43f697575ff..57629dd37e7 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2018-hotfix-1806.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2018-hotfix-1806.eb @@ -7,7 +7,7 @@ homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [ '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-4.tar', diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb index 1b2933e3cad..07032bdb679 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb @@ -6,7 +6,7 @@ homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TGZ] diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb index e7d7f8108ea..4499967864c 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb @@ -6,7 +6,7 @@ homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TGZ] diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb index 77fcbc5c082..7987d1a4045 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb @@ -6,7 +6,7 @@ homepage = 'http://www.simulia.com/products/abaqus_fea.html' description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TGZ] diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb index 4802aa3c15b..e0ad2006394 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.3-x86_64_linux_gnu4.5.eb @@ -20,7 +20,7 @@ homepage = 'http://www.abinit.org/' description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp.abinit.org/'] sources = [{ diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb index bb745faa335..d264389404c 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.0.5-x86_64_linux_gnu4.5.eb @@ -22,7 +22,7 @@ homepage = 'http://www.abinit.org/' description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp.abinit.org/'] sources = [{ diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb index 1d942af521c..31156129313 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.2.1-x86_64_linux_gnu4.5.eb @@ -23,7 +23,7 @@ homepage = 'http://www.abinit.org/' description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic structure calculations using DFT.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp.abinit.org/'] sources = [{ diff --git a/easybuild/easyconfigs/a/ACML/ACML-4.4.0-gfortran-64bit-int64.eb b/easybuild/easyconfigs/a/ACML/ACML-4.4.0-gfortran-64bit-int64.eb index 638328d5267..3b8eb6b7842 100644 --- a/easybuild/easyconfigs/a/ACML/ACML-4.4.0-gfortran-64bit-int64.eb +++ b/easybuild/easyconfigs/a/ACML/ACML-4.4.0-gfortran-64bit-int64.eb @@ -7,7 +7,7 @@ description = """ACML provides a free set of thoroughly optimized and threaded m scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s-%s%s.tgz' % (name.lower(), '-'.join(version.split('.')), versionsuffix)] diff --git a/easybuild/easyconfigs/a/ACML/ACML-4.4.0-gfortran-64bit.eb b/easybuild/easyconfigs/a/ACML/ACML-4.4.0-gfortran-64bit.eb index cafa6411384..5b98ee4ae2c 100644 --- a/easybuild/easyconfigs/a/ACML/ACML-4.4.0-gfortran-64bit.eb +++ b/easybuild/easyconfigs/a/ACML/ACML-4.4.0-gfortran-64bit.eb @@ -7,7 +7,7 @@ description = """ACML provides a free set of thoroughly optimized and threaded m scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s-%s%s.tgz' % (name.lower(), '-'.join(version.split('.')), versionsuffix)] diff --git a/easybuild/easyconfigs/a/ACML/ACML-4.4.0-ifort-64bit-int64.eb b/easybuild/easyconfigs/a/ACML/ACML-4.4.0-ifort-64bit-int64.eb index 624d1051a0e..c1db79e1d6c 100644 --- a/easybuild/easyconfigs/a/ACML/ACML-4.4.0-ifort-64bit-int64.eb +++ b/easybuild/easyconfigs/a/ACML/ACML-4.4.0-ifort-64bit-int64.eb @@ -7,7 +7,7 @@ description = """ACML provides a free set of thoroughly optimized and threaded m scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s-%s%s.tgz' % (name.lower(), '-'.join(version.split('.')), versionsuffix)] diff --git a/easybuild/easyconfigs/a/ACML/ACML-4.4.0-ifort-64bit.eb b/easybuild/easyconfigs/a/ACML/ACML-4.4.0-ifort-64bit.eb index 36afd634e69..5aa6a61a9ed 100644 --- a/easybuild/easyconfigs/a/ACML/ACML-4.4.0-ifort-64bit.eb +++ b/easybuild/easyconfigs/a/ACML/ACML-4.4.0-ifort-64bit.eb @@ -7,7 +7,7 @@ description = """ACML provides a free set of thoroughly optimized and threaded m scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s-%s%s.tgz' % (name.lower(), '-'.join(version.split('.')), versionsuffix)] diff --git a/easybuild/easyconfigs/a/ACML/ACML-5.2.0-gfortran-64bit-int64.eb b/easybuild/easyconfigs/a/ACML/ACML-5.2.0-gfortran-64bit-int64.eb index 7369859f0cc..04820d26355 100644 --- a/easybuild/easyconfigs/a/ACML/ACML-5.2.0-gfortran-64bit-int64.eb +++ b/easybuild/easyconfigs/a/ACML/ACML-5.2.0-gfortran-64bit-int64.eb @@ -7,7 +7,7 @@ description = """ACML provides a free set of thoroughly optimized and threaded m scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s-%s%s.tgz' % (name.lower(), '-'.join(version.split('.')), versionsuffix)] diff --git a/easybuild/easyconfigs/a/ACML/ACML-5.2.0-gfortran-64bit.eb b/easybuild/easyconfigs/a/ACML/ACML-5.2.0-gfortran-64bit.eb index 5ec277dddf5..6433b1ccc99 100644 --- a/easybuild/easyconfigs/a/ACML/ACML-5.2.0-gfortran-64bit.eb +++ b/easybuild/easyconfigs/a/ACML/ACML-5.2.0-gfortran-64bit.eb @@ -7,7 +7,7 @@ description = """ACML provides a free set of thoroughly optimized and threaded m scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s-%s%s.tgz' % (name.lower(), '-'.join(version.split('.')), versionsuffix)] diff --git a/easybuild/easyconfigs/a/ACML/ACML-5.2.0-ifort-64bit-int64.eb b/easybuild/easyconfigs/a/ACML/ACML-5.2.0-ifort-64bit-int64.eb index ceb42fb7b97..447c9c6816b 100644 --- a/easybuild/easyconfigs/a/ACML/ACML-5.2.0-ifort-64bit-int64.eb +++ b/easybuild/easyconfigs/a/ACML/ACML-5.2.0-ifort-64bit-int64.eb @@ -7,7 +7,7 @@ description = """ACML provides a free set of thoroughly optimized and threaded m scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s-%s%s.tgz' % (name.lower(), '-'.join(version.split('.')), versionsuffix)] diff --git a/easybuild/easyconfigs/a/ACML/ACML-5.2.0-ifort-64bit.eb b/easybuild/easyconfigs/a/ACML/ACML-5.2.0-ifort-64bit.eb index 118517ece7a..81dfe7b71c0 100644 --- a/easybuild/easyconfigs/a/ACML/ACML-5.2.0-ifort-64bit.eb +++ b/easybuild/easyconfigs/a/ACML/ACML-5.2.0-ifort-64bit.eb @@ -7,7 +7,7 @@ description = """ACML provides a free set of thoroughly optimized and threaded m scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s-%s%s.tgz' % (name.lower(), '-'.join(version.split('.')), versionsuffix)] diff --git a/easybuild/easyconfigs/a/ACML/ACML-5.3.0-ifort-64bit.eb b/easybuild/easyconfigs/a/ACML/ACML-5.3.0-ifort-64bit.eb index f0ed6d5d00a..cb1717345db 100644 --- a/easybuild/easyconfigs/a/ACML/ACML-5.3.0-ifort-64bit.eb +++ b/easybuild/easyconfigs/a/ACML/ACML-5.3.0-ifort-64bit.eb @@ -7,7 +7,7 @@ description = """ACML provides a free set of thoroughly optimized and threaded m scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s-%s%s.tgz' % (name.lower(), '-'.join(version.split('.')), versionsuffix)] diff --git a/easybuild/easyconfigs/a/ACML/ACML-5.3.1-ifort-64bit.eb b/easybuild/easyconfigs/a/ACML/ACML-5.3.1-ifort-64bit.eb index df8e241247f..b721be9557e 100644 --- a/easybuild/easyconfigs/a/ACML/ACML-5.3.1-ifort-64bit.eb +++ b/easybuild/easyconfigs/a/ACML/ACML-5.3.1-ifort-64bit.eb @@ -7,7 +7,7 @@ description = """ACML provides a free set of thoroughly optimized and threaded m scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s-%s%s.tgz' % (name.lower(), '-'.join(version.split('.')), versionsuffix)] diff --git a/easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb b/easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb index 20c4c52dec2..0ede9d4bbab 100644 --- a/easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb +++ b/easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb @@ -10,7 +10,7 @@ description = """ ACT is a Java application for displaying pairwise comparisons and to explore conservation of synteny, in the context of the entire sequences and their annotation. It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/sanger-pathogens/Artemis/releases/download/v%(version)s/'] sources = ['artemis-unix-release-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb index 107e9cc6684..e5741451f14 100755 --- a/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb @@ -6,7 +6,7 @@ version = '2009.01a.pc64_linux.intelmpi' homepage = 'http://www.scm.com/' description = "ADF is a premium-quality quantum chemistry software package based on Density Functional Theory (DFT)." -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s%(version)s.bin.tgz'] diff --git a/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb b/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb index f7098831f65..db4d733aeb1 100644 --- a/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2014.02.eb @@ -7,7 +7,7 @@ homepage = 'http://www.scm.com/ADF/' description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%(namelower)s%(version)s.pc64_linux.IntelMPI+CUDA.tgz'] diff --git a/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb b/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb index 6c3aae43602..c82ba7b1390 100644 --- a/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb +++ b/easybuild/easyconfigs/a/ADF/ADF-2016.101.eb @@ -7,7 +7,7 @@ homepage = 'http://www.scm.com/ADF/' description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['adf%(version)s.pc64_linux.intelmpi.tgz'] diff --git a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb index b21558716c7..6485dfbc593 100644 --- a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb +++ b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb @@ -8,7 +8,7 @@ description = """ADMIXTURE is a software tool for maximum likelihood estimation multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://software.genetics.ucla.edu/%(namelower)s/binaries/'] sources = ['%(namelower)s_linux-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb b/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb index 944ad05e35b..0adc6a51072 100644 --- a/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb +++ b/easybuild/easyconfigs/a/ANSYS/ANSYS-15.0.eb @@ -6,7 +6,7 @@ description = """ANSYS simulation software enables organizations to confidently how their products will operate in the real world. We believe that every product is a promise of something greater. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # create a zip file from the 3 install iso files. # make sure all files of the iso's are in the same directory. diff --git a/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb index 7497b3bc67c..9ed21392a81 100644 --- a/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb +++ b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb @@ -8,7 +8,7 @@ description = """ANSYS computational fluid dynamics (CFD) simulation software al the impact of fluid flows on your product throughout design and manufacturing as well as during end use. ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['FLUIDSTRUCTURES_162_LINX64.tar'] diff --git a/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-17.0.eb b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-17.0.eb index 0217d1be22f..7b50f3cc914 100644 --- a/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-17.0.eb +++ b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-17.0.eb @@ -8,7 +8,7 @@ description = """ANSYS computational fluid dynamics (CFD) simulation software al the impact of fluid flows on your product throughout design and manufacturing as well as during end use. ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['FLUIDSTRUCTURES_%s_LINX64.tar' % ''.join(version.split('.'))] diff --git a/easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb b/easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb index 53c47699003..1818f3d6e3b 100644 --- a/easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb +++ b/easybuild/easyconfigs/a/APBS/APBS-1.4-linux-static-x86_64.eb @@ -15,7 +15,7 @@ description = """ APBS is a software package for modeling biomolecular solvation continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb index 86e01377a66..187034be35c 100644 --- a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb +++ b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb @@ -10,7 +10,7 @@ version = 'rev103_20140612' homepage = 'https://sites.google.com/site/hipposubfields/home' description = """ Automatic Segmentation of Hippocampal Subfields (ASHS) """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # You need to create an account to download the source # from https://www.nitrc.org/frs/?group_id=370 diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb index 72a18e6d64a..3ccd42d2471 100644 --- a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.el6.x86_64.eb @@ -7,7 +7,7 @@ versionsuffix = '.el6.x86_64' homepage = 'http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html' description = """ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download via http://www.embl-hamburg.de/biosaxs/download.html sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb index 8f8ca911d7d..4e74cb6d15e 100644 --- a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.5.1-1.sl5.x86_64.eb @@ -7,7 +7,7 @@ versionsuffix = '.sl5.x86_64' homepage = 'http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html' description = """ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download via http://www.embl-hamburg.de/biosaxs/download.html sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.7.1-1.el7.x86_64.eb b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.7.1-1.el7.x86_64.eb index d2e1adc5f03..fcba32c971a 100644 --- a/easybuild/easyconfigs/a/ATSAS/ATSAS-2.7.1-1.el7.x86_64.eb +++ b/easybuild/easyconfigs/a/ATSAS/ATSAS-2.7.1-1.el7.x86_64.eb @@ -7,7 +7,7 @@ versionsuffix = '.el7.x86_64' homepage = 'http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html' description = """ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download via http://www.embl-hamburg.de/biosaxs/download.html sources = ['%(name)s-%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb index 70205ebf3a4..48d74035d13 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2016_update2.eb @@ -8,7 +8,7 @@ description = """Vectorization Optimization and Thread Prototyping - Prioritize, Prototype & Predict performance gain """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['advisor_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb index 6e2edca0dc6..a7bd64668b2 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb @@ -8,7 +8,7 @@ description = """Vectorization Optimization and Thread Prototyping - Prioritize, Prototype & Predict performance gain """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['advisor_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb index 1d58d1b0dbb..80234d38ef7 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update1.eb @@ -8,7 +8,7 @@ description = """Vectorization Optimization and Thread Prototyping - Prioritize, Prototype & Predict performance gain """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['advisor_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb index 75f8b5cc129..1f0021d4c40 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2018_update3.eb @@ -8,7 +8,7 @@ description = """Vectorization Optimization and Thread Prototyping - Prioritize, Prototype & Predict performance gain """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['advisor_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb index 423480bc2c7..6a33c20f00f 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update2.eb @@ -8,7 +8,7 @@ description = """Vectorization Optimization and Thread Prototyping - Prioritize, Prototype & Predict performance gain """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15084/'] sources = ['advisor_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb index 0df139ad774..8b427b71e14 100644 --- a/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2019_update3.eb @@ -8,7 +8,7 @@ description = """Vectorization Optimization and Thread Prototyping - Prioritize, Prototype & Predict performance gain """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15206/'] sources = ['advisor_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-5.7-x86_64.eb b/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-5.7-x86_64.eb index e3a2bc98c49..f86c990c051 100644 --- a/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-5.7-x86_64.eb +++ b/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-5.7-x86_64.eb @@ -5,7 +5,7 @@ homepage = 'http://www.allinea.com' description = """The Allinea environment is an essential toolkit for developers and computational scientists looking to get results faster.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://content.allinea.com/downloads/'] sources = ['%(namelower)s-tools-%(version)s.tar'] diff --git a/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-6.0-x86_64.eb b/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-6.0-x86_64.eb index 9b1ddba6368..da450e5d581 100644 --- a/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-6.0-x86_64.eb +++ b/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-6.0-x86_64.eb @@ -5,7 +5,7 @@ homepage = 'http://www.allinea.com' description = """The Allinea environment is an essential toolkit for developers and computational scientists looking to get results faster.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://content.allinea.com/downloads/'] sources = ['%(namelower)s-tools-%(version)s.tar'] diff --git a/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb b/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb index 5f9521e1fef..50e76aa563b 100644 --- a/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb +++ b/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb @@ -5,7 +5,7 @@ homepage = 'http://www.allinea.com' description = """The Allinea environment is an essential toolkit for developers and computational scientists looking to get results faster.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://content.allinea.com/downloads/'] sources = ['%(namelower)s-forge-%(version)s.tar'] diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2018.12.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2018.12.eb index a804888dfde..50a52ff7451 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2018.12.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2018.12.eb @@ -11,7 +11,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.03.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.03.eb index 7f36c2c856a..4cfd20f5f5b 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.03.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-2019.03.eb @@ -12,7 +12,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb index c0ff978ea57..40093b893a8 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb @@ -10,7 +10,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.2.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.2.0.eb index 9db109fa47b..0df488151ba 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.2.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.2.0.eb @@ -10,7 +10,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.4.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.4.0.eb index 26980fb5a78..1c0946094b0 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.4.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.4.0.eb @@ -11,7 +11,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.0.1.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.0.1.eb index b911e87119f..8694cf6cf32 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.0.1.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.0.1.eb @@ -11,7 +11,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.1.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.1.0.eb index 598b64655a1..708d8274d08 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.1.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.1.0.eb @@ -11,7 +11,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.3.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.3.0.eb index eba49bfe7da..1a53a13371a 100644 --- a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.3.0.eb +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-5.3.0.eb @@ -11,7 +11,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2018.12.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2018.12.eb index 4150b7c6935..45b2a5a337b 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2018.12.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2018.12.eb @@ -12,7 +12,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.03.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.03.eb index ad7d7c70a14..1d8e6fc4956 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.03.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2019.03.eb @@ -13,7 +13,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb index 87325e0a063..cbeb1802a5b 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.0.0.eb @@ -10,7 +10,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.2.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.2.0.eb index a29b70702bc..f6a0c5681ff 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.2.0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.2.0.eb @@ -10,7 +10,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.4.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.4.0.eb index 8e373b97307..6e5900e8565 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.4.0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-4.4.0.eb @@ -11,7 +11,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.0.1.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.0.1.eb index 8e170767034..79e82ef5d25 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.0.1.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.0.1.eb @@ -11,7 +11,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.1.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.1.0.eb index 7ea9f7c2406..494b5852d1d 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.1.0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.1.0.eb @@ -12,7 +12,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.3.0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.3.0.eb index c6be7588de4..4549e080cd8 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.3.0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-5.3.0.eb @@ -12,7 +12,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/archive/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb index 4f0e52ebffa..54fcefea731 100644 --- a/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb +++ b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.7.2.354.010c3b8.eb @@ -16,7 +16,7 @@ a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Aspera CLI install script includes tarball inline and installs to a # fixed location. Need to include custom extract command to pull diff --git a/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.9.0.1326.6985b21.eb b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.9.0.1326.6985b21.eb index bc4e764e663..19d050e4662 100644 --- a/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.9.0.1326.6985b21.eb +++ b/easybuild/easyconfigs/a/Aspera-CLI/Aspera-CLI-3.9.0.1326.6985b21.eb @@ -21,7 +21,7 @@ a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Aspera CLI install script includes tarball inline and installs to a # fixed location. Need to include custom extract command to pull diff --git a/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb b/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb index d5fdd133768..65411d301c6 100644 --- a/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb +++ b/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb @@ -7,7 +7,7 @@ homepage = 'http://downloads.asperasoft.com/connect2/' description = """Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://download.asperasoft.com/download/sw/connect/%(version)s/'] sources = ['%(namelower)s-%(version)s.110647-linux-64.tar.gz'] diff --git a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb index e4f561f6242..01717004821 100644 --- a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb +++ b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb @@ -12,7 +12,7 @@ versionsuffix = '_linux_x86' homepage = 'http://vina.scripps.edu/index.html' description = """ AutoDock Vina is an open-source program for doing molecular docking. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://vina.scripps.edu/download/'] sources = ['%s_%s%s.tgz' % (name.lower(), version.replace('.', '_'), versionsuffix)] diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb index 4f5b87c86e4..14c838921e6 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69.eb @@ -10,7 +10,7 @@ description = """Autoconf is an extensible package of M4 macros that produce she creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15.eb index 4d0af0a11b2..08c8f75b22a 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15.eb @@ -18,7 +18,7 @@ version = "1.15" homepage = 'http://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb index af33b5e0232..9d0879cff97 100644 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215.eb @@ -6,7 +6,7 @@ version = '20150215' # date of the most recent change homepage = 'http://autotools.io' description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('Autoconf', '2.69'), # 20120424 diff --git a/easybuild/easyconfigs/a/ack/ack-2.14.eb b/easybuild/easyconfigs/a/ack/ack-2.14.eb index 2fd715d5725..30ffbef35ca 100644 --- a/easybuild/easyconfigs/a/ack/ack-2.14.eb +++ b/easybuild/easyconfigs/a/ack/ack-2.14.eb @@ -6,7 +6,7 @@ version = '2.14' homepage = 'http://beyondgrep.com/' description = "ack is a tool like grep, optimized for programmers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [homepage] # use 'cp' as 'unpack' command diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb index d2ebd371892..3ba64d002a6 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.0-Java-1.8.0_112.eb @@ -7,7 +7,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%(name)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb index 42ed3e61966..c8ba6e44d0b 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_121.eb @@ -7,7 +7,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%(name)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_144.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_144.eb index 77159ab0f19..c3144993a2b 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_144.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_144.eb @@ -7,7 +7,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] sources = ['apache-%(name)s-%(version)s-src.tar.gz'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_152.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_152.eb index d989b5bca76..dde813abb00 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_152.eb @@ -7,7 +7,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] sources = ['apache-%(name)s-%(version)s-src.tar.gz'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_162.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_162.eb index 5728369f31c..96d3988c772 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.0_162.eb @@ -7,7 +7,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] sources = ['apache-%(name)s-%(version)s-src.tar.gz'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb index dc2a62675eb..1ffd386831a 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb @@ -10,7 +10,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] sources = ['apache-%(name)s-%(version)s-src.tar.gz'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.5-Java-1.8.eb b/easybuild/easyconfigs/a/ant/ant-1.10.5-Java-1.8.eb index 28ac5f4338c..226d87849e4 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.5-Java-1.8.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.5-Java-1.8.eb @@ -9,7 +9,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://apache.cu.be//ant/binaries'] sources = ['apache-%(name)s-%(version)s-bin.tar.gz'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb index ffe0aa3aaf4..f4f905a4ed3 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_10.eb @@ -6,7 +6,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%s-%s-src.tar.gz' % (name, version)] source_urls = ['http://archive.apache.org/dist/%s/source/' % name] diff --git a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb index f37d535fe6b..c19d66998e9 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.8.4-Java-1.7.0_21.eb @@ -6,7 +6,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%s-%s-src.tar.gz' % (name, version)] source_urls = ['http://archive.apache.org/dist/%s/source/' % name] diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb index 7a79bafbc3f..d8c6f42666a 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_15.eb @@ -6,7 +6,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%s-%s-src.tar.gz' % (name, version)] source_urls = ['http://archive.apache.org/dist/%s/source/' % name] diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb index ab777254e94..660f76f1aa4 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.0-Java-1.7.0_21.eb @@ -6,7 +6,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%s-%s-src.tar.gz' % (name, version)] source_urls = ['http://archive.apache.org/dist/%s/source/' % name] diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb index 03ba48168e7..4cb788cfe7e 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_60.eb @@ -6,7 +6,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%(name)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb index 986e3e5a6f6..d6a6de94865 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb @@ -6,7 +6,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%(name)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb index 6036bb0be83..d36f87c7c4a 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_75.eb @@ -6,7 +6,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%(name)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb index d51a118fba3..9ca8ede0f3b 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb @@ -7,7 +7,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%(name)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb index 0e7df6fdf18..b20f64aced3 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_80.eb @@ -7,7 +7,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%(name)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb index 33aa30131b0..ad491befafc 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_66.eb @@ -6,7 +6,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%(name)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb index 0f10c1689bc..4231ec383ec 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb @@ -7,7 +7,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%(name)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb index f22f0e01b79..42eb7490e43 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb @@ -7,7 +7,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%(name)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb index 4c6e292088e..56d1149b215 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb @@ -7,7 +7,7 @@ description = """Apache Ant is a Java library and command-line tool whose missio build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['apache-%(name)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] diff --git a/easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb b/easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb index 4a078913f57..1c56d559ad8 100644 --- a/easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb +++ b/easybuild/easyconfigs/b/BCEL/BCEL-5.2-Java-1.8.eb @@ -14,7 +14,7 @@ description = """ files (those ending with .class). """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [('http://archive.apache.org/dist/jakarta/bcel/binaries/')] sources = ['%(namelower)s-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31.eb index 4f50e7cd657..1a1472df680 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31.eb @@ -20,7 +20,7 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] sources = ['ncbi-blast-%(version)s+-x64-linux.tar.gz'] diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb index 98748d456d2..18a95c65a3f 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb @@ -14,7 +14,7 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast//executables/legacy/%(version)s/'] sources = ['%(namelower)s-%(version)s-x64-linux.tar.gz'] diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb index 22a6c7cda85..9166123641a 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.8.1-Linux_x86_64.eb @@ -13,7 +13,7 @@ homepage = 'http://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST'] sources = ['ncbi-%(namelower)s-%(version)s+-x64-linux.tar.gz'] diff --git a/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb index 1584cea2970..ac656c0c29d 100644 --- a/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb +++ b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb @@ -14,7 +14,7 @@ encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://www.nitrc.org/frs/download.php/7384/'] sources = ['bxh_xcede_tools-%(version)s-lsb30.x86_64.tgz'] diff --git a/easybuild/easyconfigs/b/Bandage/Bandage-0.8.1_Centos.eb b/easybuild/easyconfigs/b/Bandage/Bandage-0.8.1_Centos.eb index d4eff96c871..bb849099332 100644 --- a/easybuild/easyconfigs/b/Bandage/Bandage-0.8.1_Centos.eb +++ b/easybuild/easyconfigs/b/Bandage/Bandage-0.8.1_Centos.eb @@ -12,7 +12,7 @@ versionsuffix = '_Centos' homepage = 'http://rrwick.github.io/Bandage/' description = "Bandage is a program for visualising de novo assembly graphs" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/rrwick/Bandage/releases/download/v%(version)s/'] sources = ['%s%s_static_v%s.zip' % (name, versionsuffix, version.replace(".", "_"))] diff --git a/easybuild/easyconfigs/b/Bandage/Bandage-0.8.1_Ubuntu.eb b/easybuild/easyconfigs/b/Bandage/Bandage-0.8.1_Ubuntu.eb index 197edc804d5..64a56b101cc 100644 --- a/easybuild/easyconfigs/b/Bandage/Bandage-0.8.1_Ubuntu.eb +++ b/easybuild/easyconfigs/b/Bandage/Bandage-0.8.1_Ubuntu.eb @@ -12,7 +12,7 @@ versionsuffix = '_Ubuntu' homepage = 'http://rrwick.github.io/Bandage/' description = "Bandage is a program for visualising de novo assembly graphs" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/rrwick/Bandage/releases/download/v%(version)s/'] sources = ['%s%s_static_v%s.zip' % (name, versionsuffix, version.replace(".", "_"))] diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb index d034b7c154b..b3117ad37c4 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-1.0-linux32.eb @@ -17,7 +17,7 @@ description = """ BayesTraits is a computer package for performing analyses of t Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://www.evolution.reading.ac.uk/Files/'] sources = ['BayesTraits-Linux-Intel-V1.0.tar.gz'] diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb index a7199d6201c..5fae3e913c2 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-2.0-Beta-Linux64.eb @@ -18,7 +18,7 @@ description = """ BayesTraits is a computer package for performing analyses of t Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://www.evolution.reading.ac.uk/Files/'] sources = ['%(name)sV%(version_major)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb index 5bfa2535aa2..2f63e5cfd55 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.4.4.eb @@ -10,7 +10,7 @@ homepage = 'http://bazel.io/' description = """Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-dist.zip'] source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb index c94bcc0b40d..8b901156428 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb @@ -16,7 +16,7 @@ description = """ BEAST is a cross-platform program for Bayesian MCMC analysis o tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/'] sources = ['BEASTv%(version)s.tgz'] diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb b/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb index 512e98ad2ae..099d660e005 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.1.3.eb @@ -16,7 +16,7 @@ description = """ BEAST is a cross-platform program for Bayesian MCMC analysis o tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://github.com/CompEvol/beast2/releases/download/v%(version)s/'] sources = ['BEAST.v%(version)s.tgz'] diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7.eb index 137d2f967e1..9d6496f082d 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-2.7.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/bison' description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb index 790a47263e4..2ad4bbddce0 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb @@ -11,7 +11,7 @@ description = """ employing LALR(1) parser tables. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5.eb index fdfcad357a5..6ed7994f402 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5.eb @@ -11,7 +11,7 @@ description = """ employing LALR(1) parser tables. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2.eb index 5f3d4865db8..1d99944195d 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2.eb @@ -11,7 +11,7 @@ description = """ employing LALR(1) parser tables. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0.eb index 9e85b84df70..cf5ecc79e63 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.55.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0.eb @@ -4,7 +4,7 @@ version = '1.55.0' homepage = 'http://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb b/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb index 4779d17ea88..417607e2865 100644 --- a/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb +++ b/easybuild/easyconfigs/b/bbcp/bbcp-12.01.30.00.0-amd64_linux26.eb @@ -23,7 +23,7 @@ description = """BBCP is an alternative to Gridftp when transferring large amoun See details at http://pcbunn.cithep.caltech.edu/bbcp/using_bbcp.htm or http://www.nics.tennessee.edu/computing-resources/data-transfer/bbcp""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # fi. http://www.slac.stanford.edu/~abh/bbcp/bin/amd64_linux26/bbcp # VERY poor way of distributing software sources = [name] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb index e3f5b15724b..b118c8caae4 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.1.eb @@ -4,7 +4,7 @@ version = '2.25.1' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb index e08cd975ad8..b2873665ea2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -4,7 +4,7 @@ version = '2.25' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb index 8cc66cacab0..6f0d57b692f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26.eb @@ -4,7 +4,7 @@ version = '2.26' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb index 6011a780095..fceb6f61363 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb @@ -4,7 +4,7 @@ version = '2.27' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb index a50c4f25ca1..6cc53f407ef 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28.eb @@ -5,7 +5,7 @@ homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29.eb index 6efb559b8a6..4f28075083b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29.eb @@ -5,7 +5,7 @@ homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb index 12fa985a5f4..38a49858892 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb @@ -5,7 +5,7 @@ homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb index 64fb2100b2e..d5f0f629751 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1.eb @@ -5,7 +5,7 @@ homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb index aeeea2b58ea..79e1be6c009 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32.eb @@ -5,7 +5,7 @@ homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb b/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb index d9d9591bf7b..4fee97322e6 100644 --- a/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb +++ b/easybuild/easyconfigs/b/bwakit/bwakit-0.7.15_x64-linux.eb @@ -13,7 +13,7 @@ homepage = 'https://github.com/lh3/bwa/tree/master/bwakit' description = """Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://sourceforge.net/projects/bio-bwa/files/bwakit/'] sources = ['%(name)s-%(version)s%(versionsuffix)s.tar.bz2'] diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb index 1110fd72bcf..7b519b889e3 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6.eb @@ -6,7 +6,7 @@ description = """bzip2 is a freely available, patent free, high-quality data com compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM toolchainopts = {'pic': True} source_urls = ['https://fossies.org/linux/misc/'] diff --git a/easybuild/easyconfigs/c/C3D/C3D-1.0.0.eb b/easybuild/easyconfigs/c/C3D/C3D-1.0.0.eb index 11ec02b9c52..99b8a3fc4be 100644 --- a/easybuild/easyconfigs/c/C3D/C3D-1.0.0.eb +++ b/easybuild/easyconfigs/c/C3D/C3D-1.0.0.eb @@ -6,7 +6,7 @@ version = '1.0.0' homepage = 'https://sourceforge.net/projects/c3d/' description = "Convert3D Medical Image Processing Tool" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = ['c3d-%(version)s-Linux-x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb index de682d1d50f..a753dc41af5 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86.eb @@ -12,7 +12,7 @@ easyblock = 'PackedBinary' homepage = 'http://seq.cs.iastate.edu/' description = """CAP3 assembly program """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [('http://seq.cs.iastate.edu/CAP3/')] sources = ['cap3.linux.tar'] diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb index ceeb82f27dd..a6e8797d8db 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-intel-x86_64.eb @@ -12,7 +12,7 @@ easyblock = 'PackedBinary' homepage = 'http://seq.cs.iastate.edu/' description = """CAP3 assembly program """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [('http://seq.cs.iastate.edu/CAP3/')] sources = ['cap3.linux.x86_64.tar'] diff --git a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb index 4747b56abdb..a1a93c2cdc9 100644 --- a/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb +++ b/easybuild/easyconfigs/c/CAP3/CAP3-20071221-opteron.eb @@ -12,7 +12,7 @@ easyblock = 'PackedBinary' homepage = 'http://seq.cs.iastate.edu/' description = """CAP3 assembly program """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [('http://seq.cs.iastate.edu/CAP3/')] sources = ['cap3.linux.opteron64.tar'] diff --git a/easybuild/easyconfigs/c/CCL/CCL-1.11.5.eb b/easybuild/easyconfigs/c/CCL/CCL-1.11.5.eb index 880a69d6ee7..6873bf80d5e 100644 --- a/easybuild/easyconfigs/c/CCL/CCL-1.11.5.eb +++ b/easybuild/easyconfigs/c/CCL/CCL-1.11.5.eb @@ -8,7 +8,7 @@ description = """Clozure CL (often called CCL for short) is a free Common Lisp include fast compilation speed, native threads, a precise, generational, compacting garbage collector, and a convenient foreign-function interface.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [' https://github.com/Clozure/ccl/releases/download/v%(version)s'] sources = ['ccl-%(version)s-linuxx86.tar.gz'] diff --git a/easybuild/easyconfigs/c/CHASE/CHASE-20130626.eb b/easybuild/easyconfigs/c/CHASE/CHASE-20130626.eb index a951a89a48e..7075cd25a59 100644 --- a/easybuild/easyconfigs/c/CHASE/CHASE-20130626.eb +++ b/easybuild/easyconfigs/c/CHASE/CHASE-20130626.eb @@ -11,7 +11,7 @@ homepage = 'http://people.duke.edu/~asallen/Software.html' description = """Case-control HAplotype Sharing analyses. Haplotype sharing analyses for genome-wide association studies.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://people.duke.edu/~asallen/Software_files/'] sources = ['chase_64bit_linux.tar.gz'] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb index 873f4f2f725..0897dc0c562 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.1.3.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb index fa2ba9a1738..d122346d10b 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.12.1.eb @@ -11,7 +11,7 @@ description = """ """ # note: requires C++ compiler that supports C++11, which is not the case in older OSs like CentOS 6... -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb index fea9079c88e..151b1f33306 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb index 701830e8719..0d0b35f0b3e 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb index b69bcb6ac0b..5808143c4e5 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb index 30e7eabb0ca..f6d16d18754 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.1.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb b/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb index b0776d7c054..0f1e52cc09a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.9.6.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org' description = """CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.4.eb b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.4.eb index 128e2f2ae34..55ee7e26cc5 100644 --- a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.4.eb +++ b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.4.eb @@ -6,7 +6,7 @@ description = """IBM ILOG CPLEX Optimizer's mathematical programming technology analytical decision support for improving efficiency, reducing costs, and increasing profitability.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # the Academic Initiative version (as used in this file) can be downloaded as described on # https://www.ibm.com/developerworks/community/blogs/jfp/entry/cplex_studio_in_ibm_academic_initiative?lang=en diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb index 34d683a4dba..722568ad18c 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.0.130.eb @@ -9,7 +9,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] sources = ['%(namelower)s_%(version)s_410.48_linux'] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb index 5653d0295c0..f08bbfd51f6 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-10.1.105.eb @@ -10,7 +10,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] sources = ['%(namelower)s_%(version)s_418.39_linux.run'] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22.eb b/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22.eb index bf2df9790e1..69a64f39cfa 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-5.5.22.eb @@ -19,7 +19,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # eg. http://developer.download.nvidia.com/compute/cuda/5_5/rel/installers/cuda_5.5.22_linux_64.run source_urls = ['http://developer.download.nvidia.com/compute/cuda/5_5/rel/installers/'] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb index 009755e0fb8..3b25b94b058 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb @@ -19,7 +19,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # http://developer.download.nvidia.com/compute/cuda/6_0/rel/installers/cuda_6.0.37_linux_64.run source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/rel/installers/'] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb index d2a841d6691..68f5d8d923a 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb @@ -19,7 +19,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # eg. http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run source_urls = ['http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/'] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb index ab24e09cd3a..306737125e0 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.0.28.eb @@ -7,7 +7,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/Prod/local_installers/', diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18.eb b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18.eb index 51cc9d1f81c..4088d33b9b7 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-7.5.18.eb @@ -7,7 +7,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb index 8a34ad1f5e2..38dfccd11cd 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb @@ -7,7 +7,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/prod/local_installers/'] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb index b3ad585f708..4010b500a5e 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.61.eb @@ -7,7 +7,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod2/local_installers/'] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-9.0.176.eb b/easybuild/easyconfigs/c/CUDA/CUDA-9.0.176.eb index 921a1d653ae..0f3d2a375ae 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-9.0.176.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-9.0.176.eb @@ -7,7 +7,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] sources = ['cuda_%(version)s_384.81_linux-run'] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-9.1.85.eb b/easybuild/easyconfigs/c/CUDA/CUDA-9.1.85.eb index a20bdac3fb8..f4a43e3b9fa 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-9.1.85.eb @@ -9,7 +9,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] sources = ['%(namelower)s_%(version)s_387.26_linux'] diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-9.2.148.1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-9.2.148.1.eb index 24f26665b1d..16b8178f0a0 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-9.2.148.1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-9.2.148.1.eb @@ -12,7 +12,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod2/local_installers/', diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88.eb b/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88.eb index bf6c87a638a..068c8afa6c8 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-9.2.88.eb @@ -9,7 +9,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://developer.nvidia.com/compute/%(namelower)s/%(version_major_minor)s/Prod/local_installers/'] sources = ['%(namelower)s_%(version)s_396.26_linux'] diff --git a/easybuild/easyconfigs/c/Canvas/Canvas-1.39.0.1598.eb b/easybuild/easyconfigs/c/Canvas/Canvas-1.39.0.1598.eb index d5ba0a34d90..eafcf2c0df3 100644 --- a/easybuild/easyconfigs/c/Canvas/Canvas-1.39.0.1598.eb +++ b/easybuild/easyconfigs/c/Canvas/Canvas-1.39.0.1598.eb @@ -11,7 +11,7 @@ version = '1.39.0.1598' homepage = 'https://github.com/Illumina/canvas' description = "Copy number variant (CNV) calling from DNA sequencing data" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/Illumina/canvas/releases/download/%(version)s%2Bmaster/'] sources = ['Canvas-%(version)s.master_x64.tar.gz'] diff --git a/easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.0.eb b/easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.0.eb index ad680e6ac7b..267743701de 100644 --- a/easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.0.eb +++ b/easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.0.eb @@ -11,7 +11,7 @@ description = """Cell Ranger is a set of analysis pipelines that process Chromiu single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.2.eb b/easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.2.eb index ff29a375024..97285bde637 100644 --- a/easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.2.eb +++ b/easybuild/easyconfigs/c/CellRanger/CellRanger-3.0.2.eb @@ -11,7 +11,7 @@ description = """Cell Ranger is a set of analysis pipelines that process Chromiu single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb b/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb index 509561f0766..73ffc2035ae 100644 --- a/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb +++ b/easybuild/easyconfigs/c/Chimera/Chimera-1.10-linux_x86_64.eb @@ -12,7 +12,7 @@ description = """ UCSF Chimera is a highly extensible program for interactive vi and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # no public download URL. Go to https://www.cgl.ucsf.edu/chimera/download.html sources = ['%(namelower)s-%(version)s%(versionsuffix)s.bin'] diff --git a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb index 26131a57649..4b8eddf099b 100644 --- a/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb +++ b/easybuild/easyconfigs/c/ClusterShell/ClusterShell-1.7.3.eb @@ -7,7 +7,7 @@ homepage = 'http://cea-hpc.github.io/clustershell/' description = """ClusterShell is an event-driven open source Python library, designed to run local or distant commands in parallel on server farms or on large Linux clusters.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb index 1b697a0fc2e..b538c66edff 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.2.2.eb @@ -15,7 +15,7 @@ a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://ftp.humanconnectome.org/workbench/'] sources = ['workbench-rh_linux64-v%(version)s.zip'] diff --git a/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb b/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb index c89dad88b78..4a00f26fe95 100644 --- a/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb +++ b/easybuild/easyconfigs/c/Coot/Coot-0.8.1-binary-Linux-x86_64-rhel-6-python-gtk2.eb @@ -13,7 +13,7 @@ homepage = 'http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot' description = """Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release'] sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb index da34dc3b821..330602eae5f 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.06.eb @@ -6,7 +6,7 @@ version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module (PE release: November 2015).\n""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb index f6426373ddc..a4c09300c3b 100644 --- a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-2015.11.eb @@ -6,7 +6,7 @@ version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module (PE release: November 2015).\n""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb index af4314daa96..572ac525360 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.06.eb @@ -6,7 +6,7 @@ version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1506' description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2015).\n""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb index fdcd8836c8e..0e6a5c2553f 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2015.11.eb @@ -6,7 +6,7 @@ version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: November 2015).\n""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.03.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.03.eb index eeedf98b762..817e5af6722 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.03.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.03.eb @@ -6,7 +6,7 @@ version = '2016.03' homepage = 'http://docs.cray.com/books/S-9408-1603/' description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: March 2016).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.04.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.04.eb index 19027f6d871..3225949472c 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.04.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.04.eb @@ -6,7 +6,7 @@ version = '2016.04' homepage = 'http://docs.cray.com/books/S-9408-1604/' description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: April 2016).\n""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.06.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.06.eb index 306310f5af2..ac3224eaa1c 100644 --- a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.06.eb +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.06.eb @@ -6,7 +6,7 @@ version = '2016.06' homepage = 'http://docs.cray.com/books/S-9408-1606/' description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2016).\n""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb index 5d9b4c1609a..c16cb736aaa 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.06.eb @@ -6,7 +6,7 @@ version = '2015.06' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: November 2015).\n""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb index 8632b007b7c..f293b619e2e 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2015.11.eb @@ -6,7 +6,7 @@ version = '2015.11' homepage = 'http://docs.cray.com/books/S-9407-1511' description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: November 2015).\n""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2016.06.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2016.06.eb index bb3bd926dab..c1b499d5de0 100644 --- a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2016.06.eb +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2016.06.eb @@ -6,7 +6,7 @@ version = '2016.06' homepage = 'http://docs.cray.com/books/S-9407-1606' description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: June 2016).\n""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version diff --git a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb index 8f554a1eb2f..a5e1ba06e50 100644 --- a/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb +++ b/easybuild/easyconfigs/c/CrayPGI/CrayPGI-2016.04.eb @@ -6,7 +6,7 @@ version = '2016.04' homepage = 'http://www.pgroup.com/' description = """Toolchain using Cray compiler wrapper, using PrgEnv-pgi module.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.2.5.eb b/easybuild/easyconfigs/c/ccache/ccache-3.2.5.eb index 1db87d30570..9221fc7e1af 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.2.5.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.2.5.eb @@ -14,7 +14,7 @@ version = '3.2.5' homepage = 'http://ccache.samba.org/' description = """ccache-3.1.9: Cache for C/C++ compilers""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM toolchainopts = {'static': True} source_urls = ['https://github.com/ccache/ccache/archive/'] diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb b/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb index f857d10d3a7..391c444279f 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.3.1.eb @@ -14,7 +14,7 @@ version = '3.3.1' homepage = 'http://ccache.samba.org/' description = """ccache-3.1.9: Cache for C/C++ compilers""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM toolchainopts = {'static': True} source_urls = ['https://github.com/ccache/ccache/archive/'] diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.3.3.eb b/easybuild/easyconfigs/c/ccache/ccache-3.3.3.eb index 66d52c698cf..4ba6846b7f8 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.3.3.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.3.3.eb @@ -14,7 +14,7 @@ version = '3.3.3' homepage = 'http://ccache.samba.org/' description = """ccache-3.1.9: Cache for C/C++ compilers""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM toolchainopts = {'static': True} source_urls = ['https://github.com/ccache/ccache/archive/'] diff --git a/easybuild/easyconfigs/c/ccache/ccache-3.3.4-f90.eb b/easybuild/easyconfigs/c/ccache/ccache-3.3.4-f90.eb index 609100b0d35..7844fc1c53b 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-3.3.4-f90.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-3.3.4-f90.eb @@ -15,7 +15,7 @@ versionsuffix = '-f90' homepage = 'http://ccache.samba.org/' description = "Cache for C/C++ compilers" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM toolchainopts = {'static': True} source_urls = ['https://github.com/ccache/ccache/archive/'] diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb index 5f652c0c865..5de680ccb2c 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb @@ -9,7 +9,7 @@ read data. Although this is intended as a stable version the code is released as early access. Parts of the CRAMTools are experimental and may not be supported in the future.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/enasequence/%(name)s/archive/'] diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb index a560b37abe7..282255a99e1 100644 --- a/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/c/cramtools/cramtools-3.0-Java-1.7.0_80.eb @@ -10,7 +10,7 @@ read data. Although this is intended as a stable version the code is released as early access. Parts of the CRAMTools are experimental and may not be supported in the future.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/enasequence/%(name)s/archive/'] diff --git a/easybuild/easyconfigs/c/cscope/cscope-15.9.eb b/easybuild/easyconfigs/c/cscope/cscope-15.9.eb index e4816d79cd4..50eec2bb566 100644 --- a/easybuild/easyconfigs/c/cscope/cscope-15.9.eb +++ b/easybuild/easyconfigs/c/cscope/cscope-15.9.eb @@ -6,7 +6,7 @@ version = '15.9' homepage = 'http://cscope.sourceforge.net/' description = "Cscope is a developer's tool for browsing source code." -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/c/ctags/ctags-5.8.eb b/easybuild/easyconfigs/c/ctags/ctags-5.8.eb index d6a175dbc3d..c23280f54ba 100644 --- a/easybuild/easyconfigs/c/ctags/ctags-5.8.eb +++ b/easybuild/easyconfigs/c/ctags/ctags-5.8.eb @@ -7,7 +7,7 @@ homepage = 'http://ctags.sourceforge.net/' description = """Ctags generates an index (or tag) file of language objects found in source files that allows these items to be quickly and easily located by a text editor or other utility.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb index ccc5cdbff90..0e78f0b18df 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-4.0.eb @@ -12,7 +12,7 @@ homepage = 'https://developer.nvidia.com/cudnn' description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-CUDA-7.5.18.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-CUDA-7.5.18.eb index 1c8da2633c2..32b2c7f4537 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-CUDA-7.5.18.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-CUDA-7.5.18.eb @@ -15,7 +15,7 @@ homepage = 'https://developer.nvidia.com/cudnn' description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb index 97236ec5ffb..b3ca95090ba 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-rc.eb @@ -12,7 +12,7 @@ homepage = 'https://developer.nvidia.com/cudnn' description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb index 655063d1790..82104ee440d 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb @@ -15,7 +15,7 @@ homepage = 'https://developer.nvidia.com/cudnn' description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb index 29bbebe51b3..e97571c5553 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0-CUDA-8.0.61.eb @@ -15,7 +15,7 @@ homepage = 'https://developer.nvidia.com/cudnn' description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.2-CUDA-9.0.176.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.2-CUDA-9.0.176.eb index 47cab328d3b..98c36351dd8 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.2-CUDA-9.0.176.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.2-CUDA-9.0.176.eb @@ -17,7 +17,7 @@ homepage = 'https://developer.nvidia.com/cudnn' description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb index 6318c9eeb44..b4a0c8b2f56 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb @@ -17,7 +17,7 @@ homepage = 'https://developer.nvidia.com/cudnn' description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-CUDA-10.0.130.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-CUDA-10.0.130.eb index 6048ccf2d21..1e185e98fac 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-CUDA-10.0.130.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.4.2.24-CUDA-10.0.130.eb @@ -17,7 +17,7 @@ homepage = 'https://developer.nvidia.com/cudnn' description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb index 27c3a7d1efa..a6e9f59d091 100644 --- a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb @@ -12,7 +12,7 @@ description = """DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space -- with no modifications to user code or to the O/S.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.1.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.1.eb index f789025bd2f..2c6fe51913c 100644 --- a/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.1.eb +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.5.1.eb @@ -8,7 +8,7 @@ description = """DMTCP (Distributed MultiThreaded Checkpointing) transparently c distributed computation in user-space -- with no modifications to user code or to the O/S. It works on most Linux applications, including Python, Matlab, R, GUI desktops, MPI, etc.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb index 2a945fa40d6..e4dbcfab5e7 100644 --- a/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb +++ b/easybuild/easyconfigs/d/DSRC/DSRC-2.0rc-linux-64-bit.eb @@ -19,7 +19,7 @@ description = """DNA Sequence Reads Compression is an application designed for c (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%(namelower)s'] source_urls = ['http://sun.aei.polsl.pl/dsrc/download/%(version)s/'] diff --git a/easybuild/easyconfigs/d/Delly/Delly-0.7.8-linux_x86_64.eb b/easybuild/easyconfigs/d/Delly/Delly-0.7.8-linux_x86_64.eb index 2e4dd6e4542..c338289ac3a 100644 --- a/easybuild/easyconfigs/d/Delly/Delly-0.7.8-linux_x86_64.eb +++ b/easybuild/easyconfigs/d/Delly/Delly-0.7.8-linux_x86_64.eb @@ -17,7 +17,7 @@ description = """Delly is an integrated structural variant (SV) prediction inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://github.com/dellytools/%(namelower)s/releases/download/v%(version)s/'] sources = [{ diff --git a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb index e27f766c81a..5077e846a5f 100644 --- a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb @@ -12,7 +12,7 @@ versionsuffix = "-Java-%(javaver)s" homepage = 'http://nrg.wustl.edu/software/dicom-browser/' description = """DicomBrowser is an application for inspecting and modifying DICOM metadata in many files at once.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://bitbucket.org/nrg/dicombrowser/downloads/'] sources = ['%(name)s-%(version)s-bin-with-dependencies.jar'] diff --git a/easybuild/easyconfigs/d/Drake/Drake-1.0.3-Java-1.8.eb b/easybuild/easyconfigs/d/Drake/Drake-1.0.3-Java-1.8.eb index 1a415da8014..0c573b000c4 100644 --- a/easybuild/easyconfigs/d/Drake/Drake-1.0.3-Java-1.8.eb +++ b/easybuild/easyconfigs/d/Drake/Drake-1.0.3-Java-1.8.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/Factual/drake' description = """Drake is a simple-to-use, extensible, text-based data workflow tool that organizes command execution around data and its dependencies.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/Factual/drake/releases/download/%(version)s'] sources = ['%(namelower)s.jar'] diff --git a/easybuild/easyconfigs/e/EPD/EPD-7.3-2-rh5.eb b/easybuild/easyconfigs/e/EPD/EPD-7.3-2-rh5.eb index 49e5c9059ac..6bc2357e5c7 100644 --- a/easybuild/easyconfigs/e/EPD/EPD-7.3-2-rh5.eb +++ b/easybuild/easyconfigs/e/EPD/EPD-7.3-2-rh5.eb @@ -8,7 +8,7 @@ description = """The Enthought Python Distribution provides scientists with a co EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s_free-%s-x86_64.sh' % (name.lower(), version)] source_urls = ['http://epd-free.enthought.com/'] diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb index 9b67e772905..cd0d2f9a893 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb index f6e48794a2d..4da2042d2d0 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb index f65e4d33b76..ffe75dac446 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb index b404084816b..e57c844679a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb index 6d0b6bbd58f..9a29eb0fd70 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb index 09d7412e21e..b97f0e0b6fc 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb index 3e0b4775515..686d7c89d57 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb index fda0eaa230f..77988ee84b9 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb index e8bc1709592..e8718f6028f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb index 148881ec177..d67c4972075 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb index a573ff7efb3..06cfbe58b67 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb index 017904a16a8..87e76ccafa6 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb index 4b605cc4743..067fc8ba9c5 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb index 71ca7c902db..82407591317 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb index d694c3a975b..ea4fcd2ac7a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb index 777f78e3ada..9e6707bfcda 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb index 5c38c0a9838..0018039fe09 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb index ee0fb34daf6..b584c0b03bd 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb index 0249a90b8dd..bdfc6b019c3 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb index 58e8279a68d..d93d711afdb 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb index 1b589199e10..defea617a7b 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb index 95539b250fb..94f5a87252a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb index 3caeb8de82c..900f305fa7e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb index 63848ea26b7..46abc15c347 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb index a99feae3bc2..2246b750601 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb index f835d8df774..4b9204aab5f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb index 74d11b79a17..f2db44b1c5e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/e/easybuild-framework/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb index 2fb2c7bbce3..a79758cbef2 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/v/vsc-base/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb index b20ff4070be..f35fdb83001 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/v/vsc-base/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb index 1f6796bb5aa..a9cba16997e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/v/vsc-base/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb index e49097cb3fb..01d7bd86c06 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/v/vsc-base/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb index 3e1199f516f..0e504525d59 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/v/vsc-base/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb index 0f1a2dfaa8a..0ff5d92d80e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.4.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/v/vsc-base/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb index d04e3a4e315..ae328309336 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.5.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/v/vsc-base/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb index c7485aea5fc..5720cb0e56d 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.6.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/v/vsc-base/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb index fcefd777787..a8600bddf6f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.7.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/source/v/vsc-base/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb index ee8f725ccc7..4c0cb1e68cf 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://pypi.python.org/packages/1d/9e/9a69f54d7bdb4a75e78530d1ccdd66be5fd61e31ef289f167cf007e11089/', diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb index 5785d7ac7a0..d1f3a9cadbf 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb index ef3430f3ded..091bfdd1f39 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb index 1660b8e4a18..c5c5708b29c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.9.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb index 70b18de5102..b78bae87ff2 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb index f26a42f0014..687f66af7e2 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb index f26040b3c7e..163dd0dbe48 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.0.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb index e385b6fbbeb..d029f1e5f88 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb index 94e497613d3..86a2ac5c79d 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb index ce2ab0cb59d..9ea423e594b 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.1.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb index 3ee48d069a5..206acad1003 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb index 176c9217f3e..432ef560899 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.2.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb index 5f1753bce3f..5aa57c2d2ee 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.1.eb index 38ca592d16d..0d6f71620f4 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.3.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.0.eb index 581ed37dc0e..9dcebf89daf 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.1.eb index b668956c7f2..a7bd5a00480 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.4.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.0.eb index e74b64f3978..43ef6a6fe46 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.1.eb index 96fbd42e3c9..abca8313440 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.2.eb index de4bd1ab979..eee35717e1a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.3.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.3.eb index 4e5af26e6cd..9e5cd57bf8a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.3.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.5.3.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.0.eb index 3b52bbec57c..db2771386cc 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.1.eb index ca8b235edc4..df607c13644 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.2.eb index e39ab61e731..8b9918765b1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.6.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.7.0.eb index 2f3937a5924..21b57c94074 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.7.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.7.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.7.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.7.1.eb index d667ed927fe..7e6fe574186 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.7.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.7.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.0.eb index e75d03b32c7..ba87a4b87ed 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.1.eb index 9c444dc3b0b..b6c8f2964f7 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.8.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.0.eb index 6140b7de208..2b711e97572 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb index 8648dbd440c..22a253aaa02 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.5.eb @@ -5,7 +5,7 @@ homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb index d79ef2b7af3..364dac71d6d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.6.eb @@ -5,7 +5,7 @@ homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8.eb index 34ee5e6ea49..7421b53f826 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8.eb @@ -5,7 +5,7 @@ homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb index b00d99847c9..f3c06d21ec3 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb @@ -9,7 +9,7 @@ description = """ """ # only includes header files, so no need for a non-dummy toolchain -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb index 549c7213223..a4dda7d7d95 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb @@ -9,7 +9,7 @@ description = """ """ # only includes header files, so no need for a non-dummy toolchain -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb index 9ff7967ddbf..9fdc827300d 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.7.eb @@ -9,7 +9,7 @@ description = """Eigen is a C++ template library for linear algebra: matrices, v and related algorithms.""" # only includes header files, so no need for a non-dummy toolchain -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [BITBUCKET_SOURCE] sources = ['%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/f/FCM/FCM-2.3.1.eb b/easybuild/easyconfigs/f/FCM/FCM-2.3.1.eb index a6fc678d74e..9621d9339ad 100644 --- a/easybuild/easyconfigs/f/FCM/FCM-2.3.1.eb +++ b/easybuild/easyconfigs/f/FCM/FCM-2.3.1.eb @@ -6,7 +6,7 @@ version = '2.3.1' homepage = 'http://www.metoffice.gov.uk/research/collaboration/fcm' description = """FCM is a set of tools for managing and building source code.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s.tar.gz' % '-'.join(version.split('.'))] source_urls = ['https://github.com/metomi/fcm/archive/'] diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb index f79371e678d..c1230769b3e 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb @@ -9,7 +9,7 @@ description = """ Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download .sh from https://bintray.com/nist-fire-research/releases/FDS-SMV/6.0.1/view/files to create tarball sources = ['FDS_6.0.1-SMV_6.1.5_linux64.tar.gz'] diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.11.337.eb b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.11.337.eb index ddfd8fc85df..f77a591751d 100644 --- a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.11.337.eb +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.11.337.eb @@ -5,7 +5,7 @@ homepage = 'http://www.lumerical.com/tcad-products/fdtd/' description = """High performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb index b90f9315a5e..1c7e0c8dd74 100644 --- a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.16.982.eb @@ -5,7 +5,7 @@ homepage = 'http://www.lumerical.com/tcad-products/fdtd/' description = """High performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb index 719fbe2f436..b6c6156a0ce 100644 --- a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.20.1731.eb @@ -5,7 +5,7 @@ homepage = 'http://www.lumerical.com/tcad-products/fdtd/' description = """High performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] patches = [ diff --git a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.6.2.eb b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.6.2.eb index cbc167c5817..38ed2880aee 100644 --- a/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.6.2.eb +++ b/easybuild/easyconfigs/f/FDTD_Solutions/FDTD_Solutions-8.6.2.eb @@ -5,7 +5,7 @@ homepage = 'http://www.lumerical.com/tcad-products/fdtd/' description = """High performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-14.5.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-14.5.eb index a981a478ad8..71803e5e4fa 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-14.5.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-14.5.eb @@ -7,7 +7,7 @@ description = """ANSYS FLUENT software contains the broad physical modeling capa air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['CFX%s%s_LINX64-without_helpfiles.tar' % (name, ''.join(version.split('.')))] diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-15.0.7.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-15.0.7.eb index 0079337b80d..5a9ab69cd28 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-15.0.7.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-15.0.7.eb @@ -7,7 +7,7 @@ to model flow, turbulence, heat transfer, and reactions for industrial applicati air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['CFXFLUENT1507_LINX64.tar'] diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb index 0d42136505f..3974e92a831 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-16.0.eb @@ -7,7 +7,7 @@ to model flow, turbulence, heat transfer, and reactions for industrial applicati air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['FLUIDS_160_LINX64.tar'] diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb index c1ec088d35e..d1a9764bcf1 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-17.1.eb @@ -7,7 +7,7 @@ to model flow, turbulence, heat transfer, and reactions for industrial applicati air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['FLUIDS_171_LINX64.tar'] diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.0.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.0.eb index 7feeec83d45..1db7f7b3db1 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.0.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.0.eb @@ -7,7 +7,7 @@ to model flow, turbulence, heat transfer, and reactions for industrial applicati air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['FLUIDSTRUCTURES_%(version_major)s%(version_minor)s_LINX64.tar'] diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.1.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.1.eb index adedc0b4440..f243ca631a9 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.1.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.1.eb @@ -7,7 +7,7 @@ to model flow, turbulence, heat transfer, and reactions for industrial applicati air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['FLUIDSTRUCTURES_%(version_major)s%(version_minor)s_LINX64.tar'] diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb index 52783b2be41..2e5a9ebe66e 100644 --- a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb +++ b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb @@ -10,7 +10,7 @@ homepage = 'https://github.com/jordansissel/fpm' description = """Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease and sanity.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://rubygems.org/downloads/'] sources = ['%(namelower)s-%(version)s.gem'] diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-centos6_64.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-centos6_64.eb index a98d2244dbe..bc2687bb7cb 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-5.0.9-centos6_64.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-centos6_64.eb @@ -7,7 +7,7 @@ versionsuffix = '-centos6_64' homepage = 'http://www.fmrib.ox.ac.uk/fsl/' description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://fsl.fmrib.ox.ac.uk/fsldownloads/'] sources = ['fsl-%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb index 602621d4aa4..9804ed65151 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-Java-1.7.0_80.eb @@ -17,7 +17,7 @@ description = """FastQC is a quality control application for high throughput seq application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s_v%(version)s.zip'] source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb index 89f6650b3ca..2267230369c 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.2-Java-1.7.0_60.eb @@ -9,7 +9,7 @@ description = """FastQC is a quality control application for high throughput seq application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb index fd7fff1b162..30ef0da8b08 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.3-Java-1.7.0_80.eb @@ -9,7 +9,7 @@ description = """FastQC is a quality control application for high throughput seq application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb index 7c531942b3f..b93d0fe61e9 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_66.eb @@ -9,7 +9,7 @@ description = """FastQC is a quality control application for high throughput seq application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb index 5b6a4d51e97..87b6a80dd6d 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.4-Java-1.8.0_74.eb @@ -9,7 +9,7 @@ description = """FastQC is a quality control application for high throughput seq application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb index f6dbacc9e2a..2cc7d0d386c 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.7.0_80.eb @@ -10,7 +10,7 @@ description = """FastQC is a quality control application for high throughput seq application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb index 46332ee18ad..80e39544263 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_144.eb @@ -10,7 +10,7 @@ description = """FastQC is a quality control application for high throughput seq application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb index 7b8be6500dd..e62b02cefb1 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.5-Java-1.8.0_74.eb @@ -10,7 +10,7 @@ description = """FastQC is a quality control application for high throughput seq application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.7-Java-1.8.0_162.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.7-Java-1.8.0_162.eb index 08b99fe3db6..612ff213a12 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.7-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.7-Java-1.8.0_162.eb @@ -10,7 +10,7 @@ description = """FastQC is a quality control application for high throughput seq application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb index cc59c878ea9..9251dd40828 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb @@ -11,7 +11,7 @@ provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] sources = ['%(namelower)s_v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb index 5f3c9ec3261..e0bbb3a890c 100644 --- a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb +++ b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb @@ -13,7 +13,7 @@ description = """Firefox is a free, open source Web browser for Windows, Linux a Mozilla code base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://ftp.mozilla.org/pub/firefox/releases/%(version)s/linux-x86_64/en-US/'] sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/f/FoldX/FoldX-2.5.2.eb b/easybuild/easyconfigs/f/FoldX/FoldX-2.5.2.eb index fc612da0cbb..16363c05b28 100644 --- a/easybuild/easyconfigs/f/FoldX/FoldX-2.5.2.eb +++ b/easybuild/easyconfigs/f/FoldX/FoldX-2.5.2.eb @@ -5,7 +5,7 @@ homepage = 'http://foldx.crg.es/' description = """FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # no source URLs because registration is required to obtain sources sources = ['%(namelower)s_%(version)s.linux.zip'] diff --git a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta5.1.eb b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta5.1.eb index 64799c2a131..7d3e2c89832 100644 --- a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta5.1.eb +++ b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta5.1.eb @@ -5,7 +5,7 @@ homepage = 'http://foldx.crg.es/' description = """FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # no source URLs because registration is required to obtain sources sources = ['%(name)s_30b5.1_linux64.zip'] diff --git a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb index 264a1ea82dd..6dbd25a42db 100644 --- a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb +++ b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb @@ -5,7 +5,7 @@ homepage = 'http://foldx.crg.es/' description = """FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # no source URLs because registration is required to obtain sources # same name as zip file for 3.0 beta 6 >_< diff --git a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb index 4eedd88eaa6..12c730cfdfb 100644 --- a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb +++ b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb @@ -5,7 +5,7 @@ homepage = 'http://foldx.crg.es/' description = """FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # no source URLs because registration is required to obtain sources # same name as zip file for 3.0 beta 6.1 >_< diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-centos4_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-centos4_x86_64.eb index 7aa7d0a82ec..1d5111f9d0f 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-centos4_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-centos4_x86_64.eb @@ -6,7 +6,7 @@ homepage = 'http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki' description = """FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%(namelower)s-Linux%(versionsuffix)s-stable-pub-v%(version)s.tar.gz'] source_urls = ['ftp://surfer.nmr.mgh.harvard.edu/pub/dist/%(namelower)s/%(version)s'] diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-centos6_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-centos6_x86_64.eb index 8d5cb684a59..175f49be855 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-centos6_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-centos6_x86_64.eb @@ -7,7 +7,7 @@ description = """FreeSurfer is a software package for the analysis and visualiza neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%(namelower)s-Linux%(versionsuffix)s-stable-pub-v%(version)s.tar.gz'] source_urls = ['ftp://surfer.nmr.mgh.harvard.edu/pub/dist/%(namelower)s/%(version)s'] diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-6.0.0-centos6_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-6.0.0-centos6_x86_64.eb index 1e2fc9061d6..a447630d1c8 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-6.0.0-centos6_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-6.0.0-centos6_x86_64.eb @@ -6,7 +6,7 @@ homepage = 'http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki' description = """FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'ftp://surfer.nmr.mgh.harvard.edu/pub/dist/%(namelower)s/%(version)s', diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-6.0.1-centos6_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-6.0.1-centos6_x86_64.eb index d10e025c5e6..2f780b5d6a6 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-6.0.1-centos6_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-6.0.1-centos6_x86_64.eb @@ -6,7 +6,7 @@ homepage = 'https://surfer.nmr.mgh.harvard.edu/' description = """FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', diff --git a/easybuild/easyconfigs/f/f90cache/f90cache-0.96.eb b/easybuild/easyconfigs/f/f90cache/f90cache-0.96.eb index e0fc7d99c55..d1bbc4badfd 100644 --- a/easybuild/easyconfigs/f/f90cache/f90cache-0.96.eb +++ b/easybuild/easyconfigs/f/f90cache/f90cache-0.96.eb @@ -8,7 +8,7 @@ description = """f90cache is a compiler cache. It acts as a caching pre-processo using the -E compiler switch and a hash to detect when a compilation can be satisfied from cache. This often results in a great speedup in common compilations.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://people.irisa.fr/Edouard.Canot/f90cache/'] sources = [SOURCE_TAR_BZ2] diff --git a/easybuild/easyconfigs/f/fast5/fast5-0.6.5.eb b/easybuild/easyconfigs/f/fast5/fast5-0.6.5.eb index a91f73454e2..9d8696ab4a6 100644 --- a/easybuild/easyconfigs/f/fast5/fast5-0.6.5.eb +++ b/easybuild/easyconfigs/f/fast5/fast5-0.6.5.eb @@ -12,7 +12,7 @@ homepage = 'http://simpsonlab.github.io/2017/02/27/packing_fast5/' description = """A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://github.com/mateidavid/fast5/archive'] sources = ['v%(version)s.zip'] diff --git a/easybuild/easyconfigs/f/fastPHASE/fastPHASE-1.4.8.eb b/easybuild/easyconfigs/f/fastPHASE/fastPHASE-1.4.8.eb index f17bac6c215..34442f2dc98 100644 --- a/easybuild/easyconfigs/f/fastPHASE/fastPHASE-1.4.8.eb +++ b/easybuild/easyconfigs/f/fastPHASE/fastPHASE-1.4.8.eb @@ -12,7 +12,7 @@ description = """ fastPHASE: software for haplotype reconstruction, and estimating missing genotypes from population data Documentation: http://scheet.org/code/fastphase_doc_1.4.pdf""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://scheet.org/code/'] sources = ['Linuxfp.tar.gz'] diff --git a/easybuild/easyconfigs/f/findhap/findhap-4.eb b/easybuild/easyconfigs/f/findhap/findhap-4.eb index 732e2ab92d2..e9afd928a46 100644 --- a/easybuild/easyconfigs/f/findhap/findhap-4.eb +++ b/easybuild/easyconfigs/f/findhap/findhap-4.eb @@ -9,7 +9,7 @@ version = '4' homepage = 'http://aipl.arsusda.gov/software/findhap/' description = """Find haplotypes and impute genotypes using multiple chip sets and sequence data""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%(name)sV%(version)s.zip'] source_urls = ['http://aipl.arsusda.gov/software/%(name)s/'] diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.35.eb b/easybuild/easyconfigs/f/flex/flex-2.5.35.eb index 6831986cc0f..3488012d4a7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.35.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.35.eb @@ -5,7 +5,7 @@ homepage = 'http://flex.sourceforge.net/' description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39.eb index 797f2faa4fd..5073f012764 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39.eb @@ -5,7 +5,7 @@ homepage = 'http://flex.sourceforge.net/' description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb index 853b81ad96d..dceb346d3bd 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0.eb @@ -5,7 +5,7 @@ homepage = 'http://flex.sourceforge.net/' description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb index f920a0f965d..ab3d8511d39 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb @@ -9,7 +9,7 @@ description = """ in text. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM toolchainopts = {'pic': True} source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb index 98a7f69e4cd..9fc7b3acbde 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb @@ -9,7 +9,7 @@ description = """ in text. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM toolchainopts = {'pic': True} source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] diff --git a/easybuild/easyconfigs/f/foss/foss-2014b.eb b/easybuild/easyconfigs/f/foss/foss-2014b.eb index aa3f30546c8..82a7ece124c 100644 --- a/easybuild/easyconfigs/f/foss/foss-2014b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2014b.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_version = '4.8.3' diff --git a/easybuild/easyconfigs/f/foss/foss-2015.05.eb b/easybuild/easyconfigs/f/foss/foss-2015.05.eb index 67dfaafb82a..471b1446812 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015.05.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015.05.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '4.9.2' binutilsver = '2.25' diff --git a/easybuild/easyconfigs/f/foss/foss-2015a.eb b/easybuild/easyconfigs/f/foss/foss-2015a.eb index 467e3e3b84d..5527a0e07c9 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015a.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015a.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_version = '4.9.2' diff --git a/easybuild/easyconfigs/f/foss/foss-2015b.eb b/easybuild/easyconfigs/f/foss/foss-2015b.eb index c0ff6816c77..d28d199a5c9 100644 --- a/easybuild/easyconfigs/f/foss/foss-2015b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2015b.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '4.9.3' binutilsver = '2.25' diff --git a/easybuild/easyconfigs/f/foss/foss-2016.04.eb b/easybuild/easyconfigs/f/foss/foss-2016.04.eb index b798c1a0056..540a02cc3c2 100644 --- a/easybuild/easyconfigs/f/foss/foss-2016.04.eb +++ b/easybuild/easyconfigs/f/foss/foss-2016.04.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '5.3.0-2.26' diff --git a/easybuild/easyconfigs/f/foss/foss-2016.06.eb b/easybuild/easyconfigs/f/foss/foss-2016.06.eb index 94b361db691..48ac1de09da 100644 --- a/easybuild/easyconfigs/f/foss/foss-2016.06.eb +++ b/easybuild/easyconfigs/f/foss/foss-2016.06.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/f/foss/foss-2016.07.eb b/easybuild/easyconfigs/f/foss/foss-2016.07.eb index a3df9581369..2f4d7eed1f4 100644 --- a/easybuild/easyconfigs/f/foss/foss-2016.07.eb +++ b/easybuild/easyconfigs/f/foss/foss-2016.07.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.1.0' binutilsver = '2.27' diff --git a/easybuild/easyconfigs/f/foss/foss-2016.09.eb b/easybuild/easyconfigs/f/foss/foss-2016.09.eb index 4092325a36a..58185ae53d1 100644 --- a/easybuild/easyconfigs/f/foss/foss-2016.09.eb +++ b/easybuild/easyconfigs/f/foss/foss-2016.09.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.2.0-2.27' diff --git a/easybuild/easyconfigs/f/foss/foss-2016a.eb b/easybuild/easyconfigs/f/foss/foss-2016a.eb index 6128fe5952d..2f56ccaae0b 100644 --- a/easybuild/easyconfigs/f/foss/foss-2016a.eb +++ b/easybuild/easyconfigs/f/foss/foss-2016a.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '4.9.3-2.25' diff --git a/easybuild/easyconfigs/f/foss/foss-2016b.eb b/easybuild/easyconfigs/f/foss/foss-2016b.eb index d4d59e08aaa..189dc1ab962 100644 --- a/easybuild/easyconfigs/f/foss/foss-2016b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2016b.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/f/foss/foss-2017a.eb b/easybuild/easyconfigs/f/foss/foss-2017a.eb index ac1c78408f7..31b73cd65e3 100644 --- a/easybuild/easyconfigs/f/foss/foss-2017a.eb +++ b/easybuild/easyconfigs/f/foss/foss-2017a.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.3.0-2.27' diff --git a/easybuild/easyconfigs/f/foss/foss-2017b.eb b/easybuild/easyconfigs/f/foss/foss-2017b.eb index 8c70f8464d2..0e583902e4f 100644 --- a/easybuild/easyconfigs/f/foss/foss-2017b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2017b.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/f/foss/foss-2018.08.eb b/easybuild/easyconfigs/f/foss/foss-2018.08.eb index 38f06e433fd..2e534242539 100644 --- a/easybuild/easyconfigs/f/foss/foss-2018.08.eb +++ b/easybuild/easyconfigs/f/foss/foss-2018.08.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '8.2.0-2.31.1' diff --git a/easybuild/easyconfigs/f/foss/foss-2018a.eb b/easybuild/easyconfigs/f/foss/foss-2018a.eb index 83a20bbf22e..137e5cacb80 100644 --- a/easybuild/easyconfigs/f/foss/foss-2018a.eb +++ b/easybuild/easyconfigs/f/foss/foss-2018a.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/f/foss/foss-2018b.eb b/easybuild/easyconfigs/f/foss/foss-2018b.eb index cf5e9768bbc..378c6dc57b9 100644 --- a/easybuild/easyconfigs/f/foss/foss-2018b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2018b.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '7.3.0-2.30' diff --git a/easybuild/easyconfigs/f/foss/foss-2019a.eb b/easybuild/easyconfigs/f/foss/foss-2019a.eb index 2a5e5bb7d87..9f6759ea515 100644 --- a/easybuild/easyconfigs/f/foss/foss-2019a.eb +++ b/easybuild/easyconfigs/f/foss/foss-2019a.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#fo description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '8.2.0-2.31.1' diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2017b.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2017b.eb index f5fdce0c03a..b58428025a5 100644 --- a/easybuild/easyconfigs/f/fosscuda/fosscuda-2017b.eb +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2017b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2018a.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2018a.eb index 189e8d499b3..c37742f5b88 100644 --- a/easybuild/easyconfigs/f/fosscuda/fosscuda-2018a.eb +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2018a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb index 1de9a43aa60..66a12279271 100644 --- a/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2018b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '7.3.0-2.30' diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb index d5450aaae14..81134ada981 100644 --- a/easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2019a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '8.2.0-2.31.1' diff --git a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb index 15da25496f9..ec1c8e1fb1e 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-1.0.5083.eb @@ -9,7 +9,7 @@ description = """The GATK is a structured software library that makes writing ef medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb index b64688b618c..5c93916499e 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.5-2-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb index 1b89f6c6ecc..8c8252deab7 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.6-5-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb index 1969cdc702b..c4f48bc7372 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb index 272836da198..b5f5c1489ed 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.7-4.eb @@ -9,7 +9,7 @@ description = """The GATK is a structured software library that makes writing ef medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb index df931a819c3..aabd4494550 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-2.8-1-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb index afaf5a587ac..c416baa255e 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb @@ -22,7 +22,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb index fd5122e871a..f312d728758 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_21.eb @@ -23,7 +23,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb index f3b21831fe6..a55ce7b507e 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb @@ -23,7 +23,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb index 8dd25ea92a3..8904f8653d4 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.8.0_66.eb @@ -23,7 +23,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb index 598a86e9b2d..8b9fe5eaa2b 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_66.eb @@ -23,7 +23,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb index 06ec8c03a74..631986879ad 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.5-Java-1.8.0_74.eb @@ -24,7 +24,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb index bd6fea5ef5d..81dea19c49e 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb @@ -26,7 +26,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb index bc0c66d4fe6..d3321a6b45c 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.7-Java-1.8.0_112.eb @@ -26,7 +26,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.8-0-Java-1.8.0_144.eb b/easybuild/easyconfigs/g/GATK/GATK-3.8-0-Java-1.8.0_144.eb index 443c272e9d2..c958726570c 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-3.8-0-Java-1.8.0_144.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-3.8-0-Java-1.8.0_144.eb @@ -26,7 +26,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download manually from http://www.broadinstitute.org/gatk/download sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb index b9d6b8121d2..4444a58b164 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.1.2-Java-1.8.eb @@ -16,7 +16,7 @@ description = """The Genome Analysis Toolkit or GATK is a software package devel data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] sources = ['%(namelower)s-%(version)s.zip'] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index cac38108835..53e2ff2549b 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -7,7 +7,7 @@ homepage = 'https://gc3pie.readthedocs.org' description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM osdependencies = [('python-devel', 'python-dev')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index 998be90954d..0eff44a892a 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -7,7 +7,7 @@ homepage = 'https://gc3pie.readthedocs.org' description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM osdependencies = [('python-devel', 'python-dev')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index 0c8648ce0dc..0a8ac7a577d 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -7,7 +7,7 @@ homepage = 'https://gc3pie.readthedocs.org' description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM osdependencies = [('python-devel', 'python-dev')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index 3fa03bbcc06..fda459ae303 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -7,7 +7,7 @@ homepage = 'https://gc3pie.readthedocs.org' description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM osdependencies = [('python-devel', 'python-dev')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index 835ea3dee6f..148f1edcfd2 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -7,7 +7,7 @@ homepage = 'https://gc3pie.readthedocs.org' description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM osdependencies = [('python-devel', 'python-dev')] diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.0.eb index 32535e5262d..eaa7d4c9c8e 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.5.0.eb @@ -7,7 +7,7 @@ homepage = 'https://gc3pie.readthedocs.org' description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM osdependencies = [('python-devel', 'python-dev')] diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb index 3353304539c..ee46a3a5ffa 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.1.2.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dependencies are loaded +toolchain = SYSTEM # empty version to ensure that dependencies are loaded source_urls = ['http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb index 2315380a64e..4bf5e668782 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.2.4.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dependencies are loaded +toolchain = SYSTEM # empty version to ensure that dependencies are loaded source_urls = ['http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb b/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb index 49e488fc5da..409cef1b46c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.3.6.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dependencies are loaded +toolchain = SYSTEM # empty version to ensure that dependencies are loaded source_urls = ['http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb b/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb index 9a6e1777a23..fd3cf319ba9 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.4.7.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} # empty version to ensure that dependencies are loaded +toolchain = SYSTEM # empty version to ensure that dependencies are loaded source_urls = ['http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb index ad60232e289..b9d82bae824 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb index 019d19eb56b..f1d8e765544 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.3-CLooG-PPL.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM pplver = '0.11' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb index 88319148198..d62b4a5f696 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.3.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb index 9403935bdb2..a1bcd7bba4f 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb index df6c38b9505..ed181e7d6c4 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.3-CLooG-PPL.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM pplver = '0.12' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb index a488c39f16c..ac8a50e61f5 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.3.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb index 86485150dc1..2c60a9a2a19 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.4.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb index 918a15feda4..2da8bd96b6a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.0-CLooG-PPL.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM pplver = '0.12' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb index 6411cf28588..331b66a1a4f 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.0.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb index 46f9b7d21ae..cae768a4e6c 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.1-CLooG-PPL.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM pplver = '0.12' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb index c4dfce1f205..126f74f452a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.1.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb index e447e159cd5..d262b97d044 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.2.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb index e786a6b52eb..94d92ba0efd 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.3-CLooG-PPL.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM pplver = '0.12.1' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb index 1ece419969b..083996a1652 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.3.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb index f31e548fa6f..0f91e8e62c4 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.4-CLooG-PPL.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM pplver = '0.12.1' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb index 41fe3fb4570..6b6c9d76622 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.7.4.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb index 173739849ff..702e9cb06ab 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1-CLooG.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb index 05ab87dd628..fe6ceebcb18 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.1.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb index 388636b216d..5cc25832b98 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG-multilib.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb index 19854b76387..40334320a43 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-CLooG.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb index 7161e91a0ef..07cca804195 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2-multilib.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb index 78a7feb6b9b..d1859757c5f 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.2.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb index 71ae570cb51..c4273ac8941 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3-CLooG-multilib.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb index cb03c433d10..358a5076c79 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.3.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb index b9b542a87a2..bcba4df21a6 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG-multilib.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb index ed1babfeb30..7b7ae189960 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4-CLooG.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb index b82b0b4649e..e5f7a85cf2d 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.4.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb index 8885142c5d2..a3781b8b84e 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'http://ftpmirror.gnu.org/gnu/%(namelower)s/%(namelower)s-%(version)s', # GCC auto-resolving HTTP mirror diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb index 8e94f1851e1..ebabb919eab 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG-multilib.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb index 0c6e3232959..373e266326e 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0-CLooG.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb index ed67f96825f..b05e36a8f43 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.0.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb index 7aee9e3804d..aa957b9c8a4 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG-multilib.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb index dcaae075337..562433c61d2 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1-CLooG.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb index 67c04bb38f2..3b80ed3163a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.1.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb index ceae6c78f69..81600614fa6 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG-multilib.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb index 16245d7d88b..672ba0942e8 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-CLooG.eb @@ -6,7 +6,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb index 97cf5d65ab2..e440bf7f7b1 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb @@ -8,7 +8,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb index 6cafb451e54..a3ec9930812 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-2.25.eb index 1c861989160..e49d416f4f1 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-2.25.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb index 71608b174f8..3b3fc6317a7 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb @@ -8,7 +8,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb index a187fe01363..670090b3326 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.9.4-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.4-2.25.eb index cb99659c2bb..45bf1fb8748 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-4.9.4-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.4-2.25.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb index b476ba706ed..ff42cba2f83 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -8,7 +8,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 904d9c485f5..fa96986bb48 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb index 4de09f9e430..cf282ccebd4 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.3' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb index 34bf1f36a8e..99f9117397d 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0-2.26.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb index b313db1f7bf..007695c837d 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.3.0.eb @@ -5,7 +5,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.3' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/g/GCC/GCC-5.4.0-2.26.eb index 5be824a1d7d..89aba8da951 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.4.0-2.26.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.5.0-2.26.eb b/easybuild/easyconfigs/g/GCC/GCC-5.5.0-2.26.eb index c6a6ea3541b..fa71220cffb 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.5.0-2.26.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.5.0-2.26.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb index 4faa0a48e88..d87a6f5dbef 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/g/GCC/GCC-6.2.0-2.27.eb index 645cbb03144..80b94e26491 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-6.2.0-2.27.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-6.2.0-2.27.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.27.eb index 93f922e6d08..f9a545c6c5b 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.27.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb index bac0785b8cb..ff3d1319ee2 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-6.3.0-2.28.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb index f5f6e4e49d2..a671ddf3b1a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-6.4.0-2.28.eb @@ -14,7 +14,7 @@ description = """ libgcj,...). [NOTE: This module does not include Objective-C, Java or Ada] """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb b/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb index 870e7eab317..e1ccd253a25 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-7.1.0-2.28.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/g/GCC/GCC-7.2.0-2.29.eb index 8e1f8bd6161..35e9efaeb58 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-7.2.0-2.29.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-7.2.0-2.29.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/g/GCC/GCC-7.3.0-2.30.eb index 6cb853472c0..21485b78daa 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-7.3.0-2.30.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-7.4.0-2.31.1.eb b/easybuild/easyconfigs/g/GCC/GCC-7.4.0-2.31.1.eb index 71d6b40bab0..2084ff97f4a 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-7.4.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-7.4.0-2.31.1.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-8.1.0-2.30.eb b/easybuild/easyconfigs/g/GCC/GCC-8.1.0-2.30.eb index 9f586d06175..bf91d571af9 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-8.1.0-2.30.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-8.1.0-2.30.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GCC/GCC-8.2.0-2.31.1.eb index 4475af1f8dc..c1f02b0a4d4 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-8.2.0-2.31.1.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/g/GCC/GCC-8.3.0-2.32.eb index 5111e6b2eb5..706035d09ca 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-8.3.0-2.32.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb b/easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb index e68c767c1d9..e89f6f886aa 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-9.1.0-2.32.eb @@ -10,7 +10,7 @@ homepage = 'https://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-system-2.29.eb b/easybuild/easyconfigs/g/GCC/GCC-system-2.29.eb index d9def23009a..644fc3379f7 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-system-2.29.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-system-2.29.eb @@ -10,7 +10,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM dependencies = [ ('GCCcore', version), diff --git a/easybuild/easyconfigs/g/GCC/GCC-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb index cff7cc3f076..7b76cf04651 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-system.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -18,6 +18,6 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb index 446f8e6ce56..7b23e9dd0f6 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.2.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.2' gcc_name = 'GCC' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb index f954772aab6..f37c7438dcd 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.3.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.2' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb index 31daf390a1b..17ce11a1974 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.4' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index 34214dd770e..7f0d7dd287e 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.3' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb index 758f19910b3..8bae81a79ec 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.4' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.5.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.5.0.eb index 2a7017d824f..b94f4f7ba35 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.5.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.6' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index f98e0557e6f..fb25db8dc97 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.4' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index 7d03a6a483c..d4cf4f45f60 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.4' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb index 7da4ea086ce..739618bfbb7 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.5' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb index 7042bee242d..e3713770cf0 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb @@ -11,7 +11,7 @@ description = """ libgcj,...). [NOTE: This module does not include Objective-C, Java or Ada] """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.5' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.5.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.5.0.eb index 47e5032eae1..5334b2ca481 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.5.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.5.0.eb @@ -11,7 +11,7 @@ description = """ libgcj,...). [NOTE: This module does not include Objective-C, Java or Ada] """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.6' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb index c099f821a75..8e39405fdb1 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.5' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb index 135f61dcc07..99e21f6bf41 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '3.1.5' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.3.0.eb index 0e438f8e46c..01c7de146bc 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.3.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '4.0.1' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.4.0.eb index 39a811b1e1c..18235e5f6f1 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.4.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '4.0.1' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb index dcbcf2c72a7..39798fd4a25 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '4.0.1' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb index 1c70f153c5c..f02dec54e1e 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '4.0.1' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb index 23e2b9335ac..c1894e08326 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb @@ -7,7 +7,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '4.0.2' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb index eb7c39ad3f0..6e5d240ebcd 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb @@ -7,7 +7,7 @@ homepage = 'https://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM mpfr_version = '4.0.2' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-system.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-system.eb index 78b16dd345d..a470eb30a28 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-system.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-system.eb @@ -18,7 +18,7 @@ homepage = 'http://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM generate_standalone_module = True diff --git a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb index 62ae81e4f08..7e4da1c11d0 100644 --- a/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb +++ b/easybuild/easyconfigs/g/GEM-library/GEM-library-20130406-045632_pre-release-3_Linux-x86_64.eb @@ -20,7 +20,7 @@ description = """ Next-generation sequencing platforms (Illumina/Solexa, ABI/SOL Many high-performance standalone programs (mapper, splice mapper, etc.) are provided along with the library; in general, new algorithms and tools can be easily implemented on the top of it. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [('http://sourceforge.net/projects/gemlibrary/files/gem-library/Binary%20pre-release%203/', 'download')] # core_i3 is the recommended version by developers. Better performance diff --git a/easybuild/easyconfigs/g/GHC/GHC-6.12.3.eb b/easybuild/easyconfigs/g/GHC/GHC-6.12.3.eb index 125cb4abdd7..92c62f1887b 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-6.12.3.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-6.12.3.eb @@ -4,7 +4,7 @@ version = '6.12.3' homepage = 'http://haskell.org/ghc/' description = """The Glorious/Glasgow Haskell Compiler""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-x86_64-unknown-linux-n.tar.bz2'] source_urls = ['http://www.haskell.org/ghc/dist/%(version)s/'] diff --git a/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279.linux64.eb b/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279.linux64.eb index 271972fd7f8..37947e5987c 100644 --- a/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279.linux64.eb +++ b/easybuild/easyconfigs/g/GIMPS/GIMPS-p95v279.linux64.eb @@ -16,7 +16,7 @@ homepage = 'http://www.mersenne.org/' description = """GIMPS: Great Internet Mersenne Prime Search; it can be useful for limited stress testing of nodes, in user space""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%(version)s.tar.gz'] source_urls = ['http://www.mersenne.info/%(namelower)s'] diff --git a/easybuild/easyconfigs/g/GMP/GMP-4.3.2.eb b/easybuild/easyconfigs/g/GMP/GMP-4.3.2.eb index 83a58f1b101..5388fbb4bff 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-4.3.2.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-4.3.2.eb @@ -7,7 +7,7 @@ homepage = 'http://gmplib.org/' description = """GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCELOWER_TAR_BZ2] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb index 61b0e08a72c..d328ecddce9 100644 --- a/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/g/GNU/GNU-4.9.2-2.25.eb @@ -8,7 +8,7 @@ version = '%s-%s' % (gccver, binutilsver) homepage = 'http://www.gnu.org/software/' description = "Compiler-only toolchain with GCC and binutils." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # GCC built on top of (dummy-built) binutils diff --git a/easybuild/easyconfigs/g/GNU/GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GNU/GNU-4.9.3-2.25.eb index e9a60222d5d..5214378c267 100644 --- a/easybuild/easyconfigs/g/GNU/GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/GNU/GNU-4.9.3-2.25.eb @@ -8,7 +8,7 @@ version = '%s-%s' % (gccver, binutilsver) homepage = 'http://www.gnu.org/software/' description = "Compiler-only toolchain with GCC and binutils." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # GCC built on top of (dummy-built) binutils diff --git a/easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb index 684b3462cf3..4775e34b644 100644 --- a/easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb +++ b/easybuild/easyconfigs/g/GNU/GNU-5.1.0-2.25.eb @@ -8,7 +8,7 @@ version = '%s-%s' % (gccver, binutilsver) homepage = 'http://www.gnu.org/software/' description = "Compiler-only toolchain with GCC and binutils." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ # GCC built on top of (dummy-built) binutils diff --git a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.8.7929.eb b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.8.7929.eb index 96448f6cf14..9b244272da9 100644 --- a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.8.7929.eb +++ b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.8.7929.eb @@ -8,7 +8,7 @@ description = """PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://wiki.fysik.dtu.dk/gpaw-files/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['fa18f24ee523ed537f21f621a87796d76f48a8fa5e76f3b3fd4fe3cfe466df63'] diff --git a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.11271.eb b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.11271.eb index 7ae659a7de1..469b0a0c0a0 100644 --- a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.11271.eb +++ b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.11271.eb @@ -8,7 +8,7 @@ description = """PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://wiki.fysik.dtu.dk/gpaw-files/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['71083327cee250fc61e9a5f5b3907e55b457857b54629563509464cb54b02a97'] diff --git a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.20000.eb b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.20000.eb index 95b53a1e60f..392f24e6e5d 100644 --- a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.20000.eb +++ b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.20000.eb @@ -8,7 +8,7 @@ description = """PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://wiki.fysik.dtu.dk/gpaw-files/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['6c71682be12a41e17909f65fd7c1a2e4a6a7becb63fbeed2f0f3a1616d6fd41f'] diff --git a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.9672.eb b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.9672.eb index a613fa8d0a4..35fa8da7035 100644 --- a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.9672.eb +++ b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-0.9.9672.eb @@ -8,7 +8,7 @@ description = """PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://wiki.fysik.dtu.dk/gpaw-files/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['f0907195df141365cbcc76159b78870e33e45688ac6886640990e153430712ce'] diff --git a/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb index df06c730095..3ca2fb6a228 100644 --- a/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb +++ b/easybuild/easyconfigs/g/GTOOL/GTOOL-0.7.5.eb @@ -11,7 +11,7 @@ homepage = 'http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html' description = """ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://www.well.ox.ac.uk/~cfreeman/software/gwas/'] sources = ['gtool_v%(version)s_x86_64.tgz'] diff --git a/easybuild/easyconfigs/g/Gblocks/Gblocks-0.91b.eb b/easybuild/easyconfigs/g/Gblocks/Gblocks-0.91b.eb index eb7ee6a0e65..5d312cd7f3e 100644 --- a/easybuild/easyconfigs/g/Gblocks/Gblocks-0.91b.eb +++ b/easybuild/easyconfigs/g/Gblocks/Gblocks-0.91b.eb @@ -6,7 +6,7 @@ version = '0.91b' homepage = 'http://molevol.cmima.csic.es/castresana/Gblocks.html' description = "Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://molevol.cmima.csic.es/castresana/Gblocks/'] sources = [('Gblocks_Linux64_%(version)s.tar.Z', "tar xfz %s")] diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb index 935c3f665fc..cce041c25ce 100644 --- a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM java = 'Java' javaver = '1.7.0_80' diff --git a/easybuild/easyconfigs/g/GlobusConnectPersonal/GlobusConnectPersonal-2.3.6.eb b/easybuild/easyconfigs/g/GlobusConnectPersonal/GlobusConnectPersonal-2.3.6.eb index 26773f31a1b..e075cb48dcb 100644 --- a/easybuild/easyconfigs/g/GlobusConnectPersonal/GlobusConnectPersonal-2.3.6.eb +++ b/easybuild/easyconfigs/g/GlobusConnectPersonal/GlobusConnectPersonal-2.3.6.eb @@ -12,7 +12,7 @@ or laptop—even if it's behind a firewall and you don't have administrator privileges. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://downloads.globus.org/globus-connect-personal/linux/stable/'] sources = [SOURCELOWER_TGZ] diff --git a/easybuild/easyconfigs/g/Go/Go-1.11.5.eb b/easybuild/easyconfigs/g/Go/Go-1.11.5.eb index 90c7d94cf1a..ef3f583d7db 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.11.5.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.11.5.eb @@ -7,7 +7,7 @@ homepage = 'http://www.golang.org' description = """Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://storage.googleapis.com/golang/'] sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] diff --git a/easybuild/easyconfigs/g/Go/Go-1.12.eb b/easybuild/easyconfigs/g/Go/Go-1.12.eb index c43fcce0469..8cfed92cb1d 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.12.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.12.eb @@ -7,7 +7,7 @@ homepage = 'http://www.golang.org' description = """Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://storage.googleapis.com/golang/'] sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] diff --git a/easybuild/easyconfigs/g/Go/Go-1.8.1.eb b/easybuild/easyconfigs/g/Go/Go-1.8.1.eb index 07ab4f25c48..b9028008879 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.8.1.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.8.1.eb @@ -7,7 +7,7 @@ homepage = 'http://www.golang.org' description = """Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] source_urls = ['https://storage.googleapis.com/golang/'] diff --git a/easybuild/easyconfigs/g/Gradle/Gradle-4.5.1.eb b/easybuild/easyconfigs/g/Gradle/Gradle-4.5.1.eb index a4cfdc686c9..0c1026f63f1 100644 --- a/easybuild/easyconfigs/g/Gradle/Gradle-4.5.1.eb +++ b/easybuild/easyconfigs/g/Gradle/Gradle-4.5.1.eb @@ -9,7 +9,7 @@ From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://services.gradle.org/distributions'] sources = ['gradle-%(version)s-all.zip'] diff --git a/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb b/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb index aff38f5ddf3..5cbbfde4eed 100644 --- a/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb +++ b/easybuild/easyconfigs/g/GroIMP/GroIMP-1.5.eb @@ -6,7 +6,7 @@ version = '1.5' homepage = 'http://www.grogra.de/software/groimp' description = "GroIMP (Growth Grammar-related Interactive Modelling Platform) is a 3D-modelling platform." -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = ['GroIMP-%(version)s-src.zip'] diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb index b39d4408171..4381b1f84d9 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb @@ -7,7 +7,7 @@ The solvers in the Gurobi Optimizer were designed from the ground up to exploit architectures and multi-core processors, using the most advanced implementations of the latest algorithms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # registration is required # source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb index fdd1e676cad..079ed26d62d 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.2.eb @@ -7,7 +7,7 @@ The solvers in the Gurobi Optimizer were designed from the ground up to exploit architectures and multi-core processors, using the most advanced implementations of the latest algorithms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # registration is required # source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb index 758e95aed3d..e5528b03f3f 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-7.0.1.eb @@ -7,7 +7,7 @@ The solvers in the Gurobi Optimizer were designed from the ground up to exploit architectures and multi-core processors, using the most advanced implementations of the latest algorithms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # registration is required # source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-7.5.2.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-7.5.2.eb index 10787ca43cf..85dc07549dd 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-7.5.2.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-7.5.2.eb @@ -7,7 +7,7 @@ The solvers in the Gurobi Optimizer were designed from the ground up to exploit architectures and multi-core processors, using the most advanced implementations of the latest algorithms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # registration is required # source_urls = ['http://www.gurobi.com/downloads/user/gurobi-optimizer'] diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-8.1.1.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-8.1.1.eb index 4239a554559..d04d5a2b51e 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-8.1.1.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-8.1.1.eb @@ -7,7 +7,7 @@ The solvers in the Gurobi Optimizer were designed from the ground up to exploit architectures and multi-core processors, using the most advanced implementations of the latest algorithms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] sources = ['%(namelower)s%(version)s_linux64.tar.gz'] diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb index 18f71c6334b..1acd591bc1c 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.08.eb @@ -6,7 +6,7 @@ version = '2016.08' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '4.9.4-2.25' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.eb index ddfec681fb5..3275ad68b3b 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2016.10.eb @@ -6,7 +6,7 @@ version = '2016.10' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb index 1dc82058704..f74da1b65fb 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.01.eb @@ -6,7 +6,7 @@ version = '2017.01' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.02.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.02.eb index 3ae31aa6a53..73cfef30dec 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.02.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2017.02.eb @@ -6,7 +6,7 @@ version = '2017.02' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2017b.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2017b.eb index b5822bd1063..9f6bba46692 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2017b.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2017b.eb @@ -6,7 +6,7 @@ version = '2017b' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2018a.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2018a.eb index afc4a3e389f..1868c8c774a 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2018a.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2018a.eb @@ -6,7 +6,7 @@ version = '2018a' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb index 2f9c39e59c3..12e83146b98 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2018b.eb @@ -6,7 +6,7 @@ version = '2018b' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '7.3.0-2.30' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2019a.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2019a.eb index 31bb58d6d7c..81beaf31ce0 100644 --- a/easybuild/easyconfigs/g/gcccuda/gcccuda-2019a.eb +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2019a.eb @@ -6,7 +6,7 @@ version = '2019a' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '8.2.0-2.31.1' diff --git a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb index ff69d49387e..6a626a2eaa3 100644 --- a/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb +++ b/easybuild/easyconfigs/g/gencore_variant_detection/gencore_variant_detection-1.0.eb @@ -19,7 +19,7 @@ variant = "Linux-x86_64" homepage = "https://nyuad-cgsb.github.io/variant_detection/public/index.html" description = """ This is a bundled install of many software packages for doing variant detection analysis. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM builddependencies = [('Anaconda3', '4.0.0')] diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb index 7a8d3e894ec..95949dd4981 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.18.2.eb @@ -13,7 +13,7 @@ and documentation""" # It is the first step in the cyclic dependency chain of # XZ -> libxml2 -> gettext -> XZ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb index a0f60730a38..03d437952e1 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4.eb @@ -13,7 +13,7 @@ and documentation""" # It is the first step in the cyclic dependency chain of # XZ -> libxml2 -> gettext -> XZ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb index 46b4448367f..ab24e1a37dd 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.6.eb @@ -13,7 +13,7 @@ and documentation""" # It is the first step in the cyclic dependency chain of # XZ -> libxml2 -> gettext -> XZ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb index 9eaf0f0ebec..488bedec74e 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.7.eb @@ -13,7 +13,7 @@ and documentation""" # It is the first step in the cyclic dependency chain of # XZ -> libxml2 -> gettext -> XZ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb index edc2880db8e..6652fd2942b 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1.eb @@ -13,7 +13,7 @@ and documentation""" # It is the first step in the cyclic dependency chain of # XZ -> libxml2 -> gettext -> XZ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb index 214e98b5d71..255b233ef6c 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.eb @@ -13,7 +13,7 @@ and documentation""" # It is the first step in the cyclic dependency chain of # XZ -> libxml2 -> gettext -> XZ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/g/gimkl/gimkl-2.11.5.eb b/easybuild/easyconfigs/g/gimkl/gimkl-2.11.5.eb index 6a600c6a19c..4ff006dbd55 100644 --- a/easybuild/easyconfigs/g/gimkl/gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/g/gimkl/gimkl-2.11.5.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI and Intel MKL (BLAS, (Sca)LAPACK, FFTW).""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp = ('GCC', '4.9.3') diff --git a/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb b/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb index a390890a867..dd1db1c8a28 100644 --- a/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb +++ b/easybuild/easyconfigs/g/gimkl/gimkl-2017a.eb @@ -6,7 +6,7 @@ version = '2017a' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp = ('GCC', '5.4.0-2.26') diff --git a/easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb b/easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb index 470b66fd9e6..2b40387c4c9 100644 --- a/easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb +++ b/easybuild/easyconfigs/g/gimkl/gimkl-2018b.eb @@ -6,7 +6,7 @@ version = '2018b' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp = ('GCC', '7.3.0-2.30') diff --git a/easybuild/easyconfigs/g/gimpi/gimpi-2.11.5.eb b/easybuild/easyconfigs/g/gimpi/gimpi-2.11.5.eb index 2f8f5d71760..8b4e8a5e6f8 100644 --- a/easybuild/easyconfigs/g/gimpi/gimpi-2.11.5.eb +++ b/easybuild/easyconfigs/g/gimpi/gimpi-2.11.5.eb @@ -6,7 +6,7 @@ version = '2.11.5' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp = ('GCC', '4.9.3') diff --git a/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb b/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb index 93489e64154..7834eb4e6b2 100644 --- a/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb +++ b/easybuild/easyconfigs/g/gimpi/gimpi-2017a.eb @@ -6,7 +6,7 @@ version = '2017a' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp = ('GCC', '5.4.0-2.26') diff --git a/easybuild/easyconfigs/g/gimpi/gimpi-2017b.eb b/easybuild/easyconfigs/g/gimpi/gimpi-2017b.eb index 5d1bb3c4beb..3a8aa3f5f62 100644 --- a/easybuild/easyconfigs/g/gimpi/gimpi-2017b.eb +++ b/easybuild/easyconfigs/g/gimpi/gimpi-2017b.eb @@ -6,7 +6,7 @@ version = '2017b' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp = ('GCC', '6.4.0-2.28') diff --git a/easybuild/easyconfigs/g/gimpi/gimpi-2018a.eb b/easybuild/easyconfigs/g/gimpi/gimpi-2018a.eb index 9e86f64ad93..a0711237a80 100644 --- a/easybuild/easyconfigs/g/gimpi/gimpi-2018a.eb +++ b/easybuild/easyconfigs/g/gimpi/gimpi-2018a.eb @@ -6,7 +6,7 @@ version = '2018a' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, next to Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp = ('GCC', '6.4.0-2.28') diff --git a/easybuild/easyconfigs/g/gimpi/gimpi-2018b.eb b/easybuild/easyconfigs/g/gimpi/gimpi-2018b.eb index ac6227f8a6e..6e69b1bf208 100644 --- a/easybuild/easyconfigs/g/gimpi/gimpi-2018b.eb +++ b/easybuild/easyconfigs/g/gimpi/gimpi-2018b.eb @@ -6,7 +6,7 @@ version = '2018b' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp = ('GCC', '7.3.0-2.30') diff --git a/easybuild/easyconfigs/g/gimpic/gimpic-2017b.eb b/easybuild/easyconfigs/g/gimpic/gimpic-2017b.eb index 82c8372145c..eda1b27b2c1 100644 --- a/easybuild/easyconfigs/g/gimpic/gimpic-2017b.eb +++ b/easybuild/easyconfigs/g/gimpic/gimpic-2017b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including IntelMPI for MPI support with CUDA features enabled.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/giolf/giolf-2017b.eb b/easybuild/easyconfigs/g/giolf/giolf-2017b.eb index baba7c38417..7297fa41bab 100644 --- a/easybuild/easyconfigs/g/giolf/giolf-2017b.eb +++ b/easybuild/easyconfigs/g/giolf/giolf-2017b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/giolf/giolf-2018a.eb b/easybuild/easyconfigs/g/giolf/giolf-2018a.eb index cda8b43b329..bd0be2a39d9 100644 --- a/easybuild/easyconfigs/g/giolf/giolf-2018a.eb +++ b/easybuild/easyconfigs/g/giolf/giolf-2018a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/giolfc/giolfc-2017b.eb b/easybuild/easyconfigs/g/giolfc/giolfc-2017b.eb index 9cab8f58cfd..e4a0058a075 100644 --- a/easybuild/easyconfigs/g/giolfc/giolfc-2017b.eb +++ b/easybuild/easyconfigs/g/giolfc/giolfc-2017b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb index 449b40c4aac..85968c4196d 100755 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-1.1.1.eb @@ -13,7 +13,7 @@ description = """Git Large File Storage (LFS) replaces large files such as audio datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com or GitHub Enterprise.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/github/git-lfs/releases/download/v%(version)s/'] sources = ['%(name)s-linux-amd64-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb index dd2cc50c158..977899c8538 100644 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-2.7.1.eb @@ -8,7 +8,7 @@ description = """Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/git-lfs/git-lfs/archive/'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb index 45cf27aa8b3..5329613de19 100644 --- a/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb +++ b/easybuild/easyconfigs/g/gmpich/gmpich-2016a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """gcc and GFortran based compiler toolchain, including MPICH for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compname = 'GCC' compver = '4.9.3-2.25' diff --git a/easybuild/easyconfigs/g/gmpich/gmpich-2017.08.eb b/easybuild/easyconfigs/g/gmpich/gmpich-2017.08.eb index 5c5839df5cc..416fea505e9 100644 --- a/easybuild/easyconfigs/g/gmpich/gmpich-2017.08.eb +++ b/easybuild/easyconfigs/g/gmpich/gmpich-2017.08.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """gcc and GFortran based compiler toolchain, including MPICH for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compname = 'GCC' compver = '7.2.0-2.29' diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb index d81b50276db..ec0aa196307 100644 --- a/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb +++ b/easybuild/easyconfigs/g/gmpolf/gmpolf-2016a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """gcc and GFortran based compiler toolchain, MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '4.9.3-2.25' diff --git a/easybuild/easyconfigs/g/gmpolf/gmpolf-2017.10.eb b/easybuild/easyconfigs/g/gmpolf/gmpolf-2017.10.eb index 138e8545765..a42c5a5bc78 100644 --- a/easybuild/easyconfigs/g/gmpolf/gmpolf-2017.10.eb +++ b/easybuild/easyconfigs/g/gmpolf/gmpolf-2017.10.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """gcc and GFortran based compiler toolchain, MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '7.2.0-2.29' diff --git a/easybuild/easyconfigs/g/gmvapich2/gmvapich2-1.7.20.eb b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-1.7.20.eb index 22b6c5bfc39..f7406ecc1dd 100644 --- a/easybuild/easyconfigs/g/gmvapich2/gmvapich2-1.7.20.eb +++ b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-1.7.20.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compname = 'GCC' compver = '4.8.4' diff --git a/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb index 80a9588d018..db8f42bd788 100644 --- a/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb +++ b/easybuild/easyconfigs/g/gmvapich2/gmvapich2-2016a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compname = 'GCC' compver = '4.9.3-2.25' diff --git a/easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.20.eb b/easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.20.eb index 5c496f8a679..38dfd3abc16 100644 --- a/easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/gmvolf/gmvolf-1.7.20.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_version = '4.8.4' diff --git a/easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb b/easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb index b9a63b2c7c9..8b62dc05787 100644 --- a/easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb +++ b/easybuild/easyconfigs/g/gmvolf/gmvolf-2016a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '4.9.3-2.25' diff --git a/easybuild/easyconfigs/g/golf/golf-2018a.eb b/easybuild/easyconfigs/g/golf/golf-2018a.eb index b67118d792a..f97641085bc 100644 --- a/easybuild/easyconfigs/g/golf/golf-2018a.eb +++ b/easybuild/easyconfigs/g/golf/golf-2018a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenBLAS (BLAS and LAPACK support) and FFTW.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2018b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2018b.eb index e98ea3e910d..3d09d5a3a6a 100644 --- a/easybuild/easyconfigs/g/gomkl/gomkl-2018b.eb +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2018b.eb @@ -6,7 +6,7 @@ version = '2018b' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp = ('GCC', '7.3.0-2.30') diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2019a.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2019a.eb index 4781ecb3865..1fe6db56a47 100644 --- a/easybuild/easyconfigs/g/gomkl/gomkl-2019a.eb +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2019a.eb @@ -6,7 +6,7 @@ version = '2019a' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp = ('GCC', '8.2.0-2.31.1') diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.4.10.eb b/easybuild/easyconfigs/g/gompi/gompi-1.4.10.eb index f6a0e78bc96..9df7b98d183 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-1.4.10.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-1.4.10.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compname = 'GCC' compver = '4.7.2' diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.5.14.eb b/easybuild/easyconfigs/g/gompi/gompi-1.5.14.eb index aa4b516b969..e07afe604d3 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-1.5.14.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-1.5.14.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compname = 'GCC' compver = '4.8.2' diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb b/easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb index 14f67f765f8..79cc75e6369 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-1.5.16.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compname = 'GCC' compver = '4.8.3' diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.6.10.eb b/easybuild/easyconfigs/g/gompi/gompi-1.6.10.eb index b129e96e3e2..8c0334c5484 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-1.6.10.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-1.6.10.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compname = 'GCC' compver = '4.8.2' diff --git a/easybuild/easyconfigs/g/gompi/gompi-1.7.20.eb b/easybuild/easyconfigs/g/gompi/gompi-1.7.20.eb index 487b9b45ace..52284eb6891 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-1.7.20.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-1.7.20.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compname = 'GCC' compver = '4.8.4' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2014b.eb b/easybuild/easyconfigs/g/gompi/gompi-2014b.eb index ebe311c4104..4ad9c46527e 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2014b.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2014b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compname = 'GCC' compver = '4.8.3' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb index a9acbdd507e..9b9fb3a6c16 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '4.9.2' binutilsver = '2.25' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015a.eb b/easybuild/easyconfigs/g/gompi/gompi-2015a.eb index 149ce234a69..2c95116480d 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2015a.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2015a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compname = 'GCC' compver = '4.9.2' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015b.eb b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb index dd242ab2546..e653b770a01 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2015b.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '4.9.3' binutilsver = '2.25' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb index b978fd902aa..0d0b644764a 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.04.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '5.3.0-2.26' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.06.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.06.eb index c1a2b47b81b..b4bad76a662 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.06.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.06.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb index eec2b277ee8..06eb92c94e6 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.07.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.1.0' binutilsver = '2.27' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb index 7e7b36e6030..8f9b96d1a73 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.09.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.2.0-2.27' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016a.eb b/easybuild/easyconfigs/g/gompi/gompi-2016a.eb index 793e78b5ef1..d7890527c30 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016a.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '4.9.3-2.25' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2016b.eb b/easybuild/easyconfigs/g/gompi/gompi-2016b.eb index 1a6033a5a73..0a8be98581a 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2016b.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2016b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2017a.eb b/easybuild/easyconfigs/g/gompi/gompi-2017a.eb index 7022e6111ef..46b649bfddc 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2017a.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2017a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.3.0-2.27' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2017b.eb b/easybuild/easyconfigs/g/gompi/gompi-2017b.eb index acba6f51d98..38e3be1d383 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2017b.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2017b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2018.08.eb b/easybuild/easyconfigs/g/gompi/gompi-2018.08.eb index 7a5edb5095c..73cc7039db1 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2018.08.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2018.08.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '8.2.0-2.31.1' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2018a.eb b/easybuild/easyconfigs/g/gompi/gompi-2018a.eb index fb6ca69beb4..2cbe2138615 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2018a.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2018a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2018b.eb b/easybuild/easyconfigs/g/gompi/gompi-2018b.eb index 63e4e296fe4..8facd860085 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2018b.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2018b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '7.3.0-2.30' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2019a.eb b/easybuild/easyconfigs/g/gompi/gompi-2019a.eb index b9b88613ce2..52af9c7f651 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2019a.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2019a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '8.2.0-2.31.1' diff --git a/easybuild/easyconfigs/g/gompi/gompi-system-2.29.eb b/easybuild/easyconfigs/g/gompi/gompi-system-2.29.eb index 0ec55da014e..31a1dd6d85d 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-system-2.29.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-system-2.29.eb @@ -10,7 +10,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '%s%s' % (version, versionsuffix) diff --git a/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb b/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb index 0b3a7841da2..fee88c88790 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2016.08.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '4.9.4-2.25' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2016.10.eb b/easybuild/easyconfigs/g/gompic/gompic-2016.10.eb index 17119787dd2..43e61ff429b 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2016.10.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2016.10.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2017.01.eb b/easybuild/easyconfigs/g/gompic/gompic-2017.01.eb index 4978d8e04f2..133a5fdac21 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2017.01.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2017.01.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2017.02.eb b/easybuild/easyconfigs/g/gompic/gompic-2017.02.eb index aacbdca1b3f..0908b64a0a1 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2017.02.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2017.02.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2017b.eb b/easybuild/easyconfigs/g/gompic/gompic-2017b.eb index 85f98a735ad..f89fcbd0c5d 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2017b.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2017b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2018a.eb b/easybuild/easyconfigs/g/gompic/gompic-2018a.eb index 82e4a72f279..3a58fa97a57 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2018a.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2018a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2018b.eb b/easybuild/easyconfigs/g/gompic/gompic-2018b.eb index d855fd56301..c8a35bdcbf5 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2018b.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2018b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '7.3.0-2.30' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2019a.eb b/easybuild/easyconfigs/g/gompic/gompic-2019a.eb index c6d17476287..b7b10d61d4b 100644 --- a/easybuild/easyconfigs/g/gompic/gompic-2019a.eb +++ b/easybuild/easyconfigs/g/gompic/gompic-2019a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM gccver = '8.2.0-2.31.1' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.4.10.eb b/easybuild/easyconfigs/g/goolf/goolf-1.4.10.eb index 537eee87704..35d0a6e7146 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.4.10.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_version = '4.7.2' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.5.14.eb b/easybuild/easyconfigs/g/goolf/goolf-1.5.14.eb index 347b2db1686..84fa699f860 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.5.14.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.5.14.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_version = '4.8.2' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb b/easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb index d2c9c2614aa..db11146cfc7 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_version = '4.8.3' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.6.10.eb b/easybuild/easyconfigs/g/goolf/goolf-1.6.10.eb index 5567b7cb860..9c96ecb354e 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.6.10.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.6.10.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_version = '4.8.2' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.7.20.eb b/easybuild/easyconfigs/g/goolf/goolf-1.7.20.eb index 8ad7f93a10c..ed86f9f256a 100644 --- a/easybuild/easyconfigs/g/goolf/goolf-1.7.20.eb +++ b/easybuild/easyconfigs/g/goolf/goolf-1.7.20.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_version = '4.8.4' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb index ecd555a7380..38cc40b4893 100644 --- a/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2016.08.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '4.9.4-2.25' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.eb index 93b14eb0c19..fda31ce48eb 100644 --- a/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.eb +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2016.10.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb index cd738fbfa8f..add4a766aee 100644 --- a/easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2017.01.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2017.02.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2017.02.eb index e62704eb35f..89de9d3186b 100644 --- a/easybuild/easyconfigs/g/goolfc/goolfc-2017.02.eb +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2017.02.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '5.4.0-2.26' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2017b.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2017b.eb index 3714d3a7617..a05b785ed4e 100644 --- a/easybuild/easyconfigs/g/goolfc/goolfc-2017b.eb +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2017b.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/g/goolfc/goolfc-2018a.eb b/easybuild/easyconfigs/g/goolfc/goolfc-2018a.eb index de7265ae7a9..745ae5765ee 100644 --- a/easybuild/easyconfigs/g/goolfc/goolfc-2018a.eb +++ b/easybuild/easyconfigs/g/goolfc/goolfc-2018a.eb @@ -8,7 +8,7 @@ homepage = '(none)' description = """GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'GCC' comp_ver = '6.4.0-2.28' diff --git a/easybuild/easyconfigs/h/HAPGEN2/HAPGEN2-2.2.0.eb b/easybuild/easyconfigs/h/HAPGEN2/HAPGEN2-2.2.0.eb index 9ce09554133..88f4a6814c2 100644 --- a/easybuild/easyconfigs/h/HAPGEN2/HAPGEN2-2.2.0.eb +++ b/easybuild/easyconfigs/h/HAPGEN2/HAPGEN2-2.2.0.eb @@ -10,7 +10,7 @@ version = '2.2.0' homepage = 'https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html' description = """'HAPGEN2' simulates case control datasets at SNP markers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/download/builds/x86_64/v%(version)s/'] sources = ['hapgen2_x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb index 84ff25e5342..1f33c69ebcc 100644 --- a/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb +++ b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb @@ -6,7 +6,7 @@ version = '1.0.2' homepage = 'http://hbase.apache.org/' description = """Apache HBase. is the Hadoop database, a distributed, scalable, big data store. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin.tar.gz'] source_urls = ['http://archive.apache.org/dist/hbase/hbase-%(version)s/'] diff --git a/easybuild/easyconfigs/h/HDFView/HDFView-2.14-Java-1.8.0_152-centos6.eb b/easybuild/easyconfigs/h/HDFView/HDFView-2.14-Java-1.8.0_152-centos6.eb index 108199657e5..bc5b76fad46 100644 --- a/easybuild/easyconfigs/h/HDFView/HDFView-2.14-Java-1.8.0_152-centos6.eb +++ b/easybuild/easyconfigs/h/HDFView/HDFView-2.14-Java-1.8.0_152-centos6.eb @@ -8,7 +8,7 @@ versionsuffix = '-Java-%%(javaver)s-%s' % label homepage = 'https://support.hdfgroup.org/products/java/hdfview/' description = "HDFView is a visual tool for browsing and editing HDF4 and HDF5 files." -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://support.hdfgroup.org/ftp/HDF5/hdf-java/current/bin/'] sources = ['%%(name)s-%%(version)s-%s_64.tar.gz' % label] diff --git a/easybuild/easyconfigs/h/HDFView/HDFView-2.14-Java-1.8.0_152-centos7.eb b/easybuild/easyconfigs/h/HDFView/HDFView-2.14-Java-1.8.0_152-centos7.eb index 461fc098803..3d7d8abd8ec 100644 --- a/easybuild/easyconfigs/h/HDFView/HDFView-2.14-Java-1.8.0_152-centos7.eb +++ b/easybuild/easyconfigs/h/HDFView/HDFView-2.14-Java-1.8.0_152-centos7.eb @@ -8,7 +8,7 @@ versionsuffix = '-Java-%%(javaver)s-%s' % label homepage = 'https://support.hdfgroup.org/products/java/hdfview/' description = "HDFView is a visual tool for browsing and editing HDF4 and HDF5 files." -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://support.hdfgroup.org/ftp/HDF5/hdf-java/current/bin/'] sources = ['%%(name)s-%%(version)s-%s_64.tar.gz' % label] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb index 13c43df5957..d885d2ae52b 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.4.0-seagate-722af1-native.eb @@ -6,7 +6,7 @@ versionsuffix = '-seagate-%s-native' % commit homepage = 'https://github.com/Seagate/hadoop-on-lustre2' description = """Hadoop MapReduce for Parallel File Systems as provided by Seagate""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%s.tar.gz' % commit] source_urls = ['https://github.com/Seagate/hadoop-on-lustre2/archive'] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index 0b189ca56d3..aa4c1bf9663 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -5,7 +5,7 @@ versionsuffix = '-native' homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' description = """Hadoop MapReduce by Cloudera""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.12.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.12.0-native.eb index bc2f4774b0f..85085865d94 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.12.0-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.12.0-native.eb @@ -5,7 +5,7 @@ versionsuffix = '-native' homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' description = """Hadoop MapReduce by Cloudera""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb index e848ea7c2c2..f7082ab9126 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb @@ -5,7 +5,7 @@ versionsuffix = '-native' homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' description = """Hadoop MapReduce by Cloudera""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb index b5884a562e4..6bdceac2322 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.7.0-native.eb @@ -5,7 +5,7 @@ versionsuffix = '-native' homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' description = """Hadoop MapReduce by Cloudera""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.8.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.8.0-native.eb index 66a15912e54..f91a6fcf6fe 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.8.0-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.8.0-native.eb @@ -5,7 +5,7 @@ versionsuffix = '-native' homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' description = """Hadoop MapReduce by Cloudera""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-src.tar.gz'] source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb index 5f42f6f666f..a974ab4a1b5 100644 --- a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.2-linux-x86_64-static.eb @@ -8,7 +8,7 @@ homepage = 'http://www.hdfgroup.org/h4toh5/' description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # fi. http://www.hdfgroup.org/ftp/HDF5/tools/h4toh5/bin/h4h5tools-2.2.1-linux-x86_64-static.tar.gz source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/bin' % name] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb index 75709d82143..52346888250 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.0-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb index b73eb385054..53cb823d426 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.1-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb index 06478172596..31352d991d6 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.2-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb index 627abea0f84..0da051bd2d4 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.3-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb index 99b3d7a2782..5f36662beee 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.0.4-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb index 39824e71f85..88ee1a23f1f 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.0-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb index 087ee5e6de5..07257d88953 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb index 6fcad6708ed..bf815b89e8c 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb index 199ec04704c..96ce2681cdb 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb index 42cd05d9145..9b08399c6ed 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.4-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb index 4c7fe1c8c46..01b8d95ac1f 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.0-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb index 6dc4a4e6dd9..fbc85768bd6 100644 --- a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.2.2-cli.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/hpcugent/hanythingondemand' description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb index 9dded57c017..cfc0d1f5641 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4.eb @@ -10,7 +10,7 @@ description = """ output of other commands. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_XZ] diff --git a/easybuild/easyconfigs/h/htop/htop-2.0.0.eb b/easybuild/easyconfigs/h/htop/htop-2.0.0.eb index cadc02fadc2..b43d9b2a7c5 100644 --- a/easybuild/easyconfigs/h/htop/htop-2.0.0.eb +++ b/easybuild/easyconfigs/h/htop/htop-2.0.0.eb @@ -6,7 +6,7 @@ version = '2.0.0' homepage = 'http://hisham.hm/htop/' description = """An interactive process viewer for Unix""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://hisham.hm/htop/releases/%(version)s/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/htop/htop-2.0.1.eb b/easybuild/easyconfigs/h/htop/htop-2.0.1.eb index 8c6054d0f42..fad068b9a60 100644 --- a/easybuild/easyconfigs/h/htop/htop-2.0.1.eb +++ b/easybuild/easyconfigs/h/htop/htop-2.0.1.eb @@ -7,7 +7,7 @@ homepage = 'http://hisham.hm/htop/' description = """An interactive process viewer for Unix""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://hisham.hm/htop/releases/%(version)s/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/h/hub/hub-2.2.2-linux-amd64.eb b/easybuild/easyconfigs/h/hub/hub-2.2.2-linux-amd64.eb index b96b5278710..6ca48774b28 100644 --- a/easybuild/easyconfigs/h/hub/hub-2.2.2-linux-amd64.eb +++ b/easybuild/easyconfigs/h/hub/hub-2.2.2-linux-amd64.eb @@ -10,7 +10,7 @@ description = """hub is a command-line wrapper for git that makes you better at source_urls = ['https://github.com/github/hub/releases/download/v%(version)s/'] sources = ['%(namelower)s%(versionsuffix)s-%(version)s.tgz'] -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM postinstallcmds = ['chmod -x %(installdir)s/install'] diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb index 56a8573d697..e4ccbe63a37 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.0.eb @@ -7,7 +7,7 @@ homepage = 'http://zhanglab.ccmb.med.umich.edu/I-TASSER/' description = """I-TASSER is a set of pre-compiled binaries and scripts for protein structure and function modelling and comparison.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Can't download from the web site automatically as registration is required. # The source code may be downloaded manually from http://zhanglab.ccmb.med.umich.edu. diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb index 66efa1aea5c..cd4c2ed14d4 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-4.2.eb @@ -7,7 +7,7 @@ homepage = 'http://zhanglab.ccmb.med.umich.edu/I-TASSER/' description = """I-TASSER is a set of pre-compiled binaries and scripts for protein structure and function modelling and comparison.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Can't download from the web site automatically as registration is required. # The source code may be downloaded manually from http://zhanglab.ccmb.med.umich.edu. diff --git a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-5.1.eb b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-5.1.eb index f505003e03a..faa7be8ab4b 100644 --- a/easybuild/easyconfigs/i/I-TASSER/I-TASSER-5.1.eb +++ b/easybuild/easyconfigs/i/I-TASSER/I-TASSER-5.1.eb @@ -7,7 +7,7 @@ homepage = 'http://zhanglab.ccmb.med.umich.edu/I-TASSER/' description = """I-TASSER is a set of pre-compiled binaries and scripts for protein structure and function modelling and comparison.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Can't download from the web site automatically as registration is required. # The source code may be downloaded manually from http://zhanglab.ccmb.med.umich.edu. diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb index ee79473cdf7..4cca046c53b 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.68-Java-1.7.0_80.eb @@ -13,7 +13,7 @@ description = """ The Integrative Genomics Viewer (IGV) is a high-performance vi tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] sources = ['%(name)s_%(version)s.zip'] diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb index c819155a71d..b1cd056289a 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb @@ -13,7 +13,7 @@ description = """ The Integrative Genomics Viewer (IGV) is a high-performance vi tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] sources = ['%(name)s_%(version)s.zip'] diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb index a658a7cd6b2..175e1547ee9 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb @@ -16,7 +16,7 @@ description = """This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s'] sources = ['%(name)s_%(version)s.zip'] diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb index cea60ec2332..d68a381e67a 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.68-Java-1.7.0_80.eb @@ -13,7 +13,7 @@ description = """ This package contains command line utilities for preprocessing computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] sources = ['%(namelower)s_%(version)s.zip'] diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb index 789c8136662..2a013dfdca9 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.72-Java-1.7.0_80.eb @@ -15,7 +15,7 @@ description = """ This package contains command line utilities for preprocessing computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] sources = ['%(namelower)s_%(version)s.zip'] diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb index d8d59137d03..ec76146d870 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb @@ -16,7 +16,7 @@ description = """ This package contains command line utilities for preprocessing computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] sources = ['%(namelower)s_%(version)s.zip'] diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.4.18-Java-1.8.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.4.18-Java-1.8.eb index 2acadf08862..68d53371da0 100644 --- a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.4.18-Java-1.8.eb +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.4.18-Java-1.8.eb @@ -16,7 +16,7 @@ description = """ This package contains command line utilities for preprocessing computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s/'] sources = ['%(namelower)s_%(version)s.zip'] diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb index 51f4a9d25bd..a1c29d2be56 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -16,7 +16,7 @@ data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://bio3d.colorado.edu/imod/AMD64-RHEL5/'] sources = ['%(namelower)s_%(version)s%(versionsuffix)s.csh'] diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb index 5e16612e005..2c829fd7e41 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb @@ -13,7 +13,7 @@ homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb index 3bbb6f11e46..d1187efca13 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb @@ -13,7 +13,7 @@ homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb index a3ccfb16ac3..f2920f90e04 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_dynamic.eb @@ -13,7 +13,7 @@ homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] sources = ['%s_v%%(version)s%%(versionsuffix)s.tgz' % name.lower()[:-1]] diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb index d7a1d00fa6d..1de2b41cae2 100644 --- a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.2_x86_64_static.eb @@ -13,7 +13,7 @@ homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] sources = ['%s_v%%(version)s%%(versionsuffix)s.tgz' % name.lower()[:-1]] diff --git a/easybuild/easyconfigs/i/IPy/IPy-0.83.eb b/easybuild/easyconfigs/i/IPy/IPy-0.83.eb index 661784d022f..c0603051081 100644 --- a/easybuild/easyconfigs/i/IPy/IPy-0.83.eb +++ b/easybuild/easyconfigs/i/IPy/IPy-0.83.eb @@ -7,7 +7,7 @@ homepage = 'https://pypi.python.org/pypi/IPy' description = """Class and tools for handling of IPv4 and IPv6 addresses and networks""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb index e70e5ac1e44..7d9f547d493 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb @@ -9,7 +9,7 @@ version = '1.51a' homepage = 'https://imagej.nih.gov/ij' description = "Image Processing and Analysis in Java" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://imagej.nih.gov/ij/download/src/'] sources = ['ij%(version_major)s%(version_minor)s-src.zip'] diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51i.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51i.eb index 8963988c6f5..3d44b969e3d 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51i.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51i.eb @@ -6,7 +6,7 @@ version = '1.51i' homepage = 'https://imagej.nih.gov/ij' description = "Image Processing and Analysis in Java" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://imagej.nih.gov/ij/download/src/'] sources = ['ij%(version_major)s%(version_minor)s-src.zip'] diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb index 9875b136f19..289ff4ff4c6 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb @@ -6,7 +6,7 @@ version = '1.51k' homepage = 'https://imagej.nih.gov/ij' description = "Image Processing and Analysis in Java" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'https://imagej.nih.gov/ij/download/src/', diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb index ab3458b6cb7..8e67dfe5af3 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update6.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['inspector_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb index 264e117584b..241784cccb1 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2013_update7.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['inspector_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb index 9e9351c6639..33985cc4693 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2016_update3.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['inspector_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb index 5e1233098f8..7762dc1a82e 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update1.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb index 9ea21d95ae2..1981fe14e8a 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2017_update2.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] checksums = ['d85a3bbd699b0fc77967fcd5e923ad35'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb index 6ce8e805908..a7b0f1c2a92 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update1.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] checksums = ['af99624f1b6ea1b71a28b066fa3e1eea568eb2604fedbfc2cf8c7ea7ac8ab425'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb index df0b0a12292..e3e48669178 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update2.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] checksums = ['201e29c9b177d21eae619eec090ee1ec703bb7398716377444a4eb685b8bf87b'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb index d307f779226..c76f13a9873 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2018_update3.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] checksums = ['e4fd43e587886cf571225d201c9c6328841d3d61e5a36d1cd1b718da9bf94335'] diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb index f67933a3074..2c13e3a1078 100644 --- a/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2019_update2.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-inspector-xe' description = """Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['inspector_%(version)s.tar.gz'] checksums = ['cf031f38ef685d780878e334c76deb3e295509f989e393ca17d1c496135e26d7'] diff --git a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2017.1.016.eb b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2017.1.016.eb index 9e5fb6558fe..78e01abb648 100644 --- a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2017.1.016.eb +++ b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2017.1.016.eb @@ -9,7 +9,7 @@ description = """Verifies cluster components work together ― for - cost of ownership (TCO) """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_clck_p_%(version)s.tgz'] checksums = ['72fcf16e220dfc1ee1e16a633381f7957e15b0b6f322f9954d1de2a1ec3851f1'] diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb index eb9c1846954..6b6b5461486 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-2.7.15-2019.2.066.eb @@ -19,7 +19,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_pythoni%s_p_%s.tar.gz' % (pysver, relver)] checksums = ['dd0b73db5d0d79c3cdf779d10092eae32780d720b74ed8fde2a2c46e23143de1'] -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM buildininstalldir = True diff --git a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb index d63c1f055fe..3932cfdea41 100644 --- a/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb +++ b/easybuild/easyconfigs/i/IntelPython/IntelPython-3.6.8-2019.2.066.eb @@ -19,7 +19,7 @@ source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/1 sources = ['l_pythoni%s_p_%s.tar.gz' % (pysver, relver)] checksums = ['804883fc1413ee72b0ae421a8ac82ab158fc01c8b4631a44a9d2ef1a19324751'] -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM buildininstalldir = True diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb index 874cf6f7191..2c8af44aad5 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073-32bit.eb @@ -6,7 +6,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_cproc_p_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb index c8734ae2b07..9af764c1185 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.073.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.073.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_cproc_p_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-11.1.075.eb b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb index bfe3a7b793b..ab9a0190eca 100644 --- a/easybuild/easyconfigs/i/icc/icc-11.1.075.eb +++ b/easybuild/easyconfigs/i/icc/icc-11.1.075.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_cproc_p_%s_intel64.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb index 4badc609bba..64c9f7bd4eb 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.10.319.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb index b1b039262e7..1a09e20c01c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.13.367.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb index 1325123808f..7e0b7c7b94a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.3.174.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb index 8925c535520..37182c1c0c4 100644 --- a/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb +++ b/easybuild/easyconfigs/i/icc/icc-2011.6.233.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb index cc4707a957b..4dd0c8f7373 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.1.117.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb index 0cdbcc44caa..387c98328e3 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.2.146.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb index 592c9cc55cc..b42ed30cca8 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.3.163.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb index 52a1d5a100d..a0eb4608e88 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.4.183.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb index 13b5cbb4f4c..3663ca3c3b4 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192-GCC-4.8.3.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb index 2402617e196..963939ca554 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013.5.192.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb index 229dc9639f3..d6e200fc2ae 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.0.080.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb index 9752abcd0ee..0f5f5ea6d55 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.1.106.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb index ed0f198c607..084a9607bf4 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.2.144.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb index 704d527cd88..35b94395eb3 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.3.174.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb index 196bbac1d0e..1ceb2f4693e 100644 --- a/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/icc/icc-2013_sp1.4.211.eb @@ -6,7 +6,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb index 2e735a7d767..c48a5480f90 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.0.090-GCC-4.9.2.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb b/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb index 0c3779a987e..016051e25b9 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.0.090.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb index 03518844e8c..21f138798d7 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.1.133-GCC-4.9.2.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb b/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb index 93bb04fd2df..2200b6cdc3c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.1.133.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb index 6c4e26c02a8..356c6172415 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.2.164-GCC-4.9.2.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb index 77e698eb803..06f4c761ec6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb index 87a893a7b1d..fb7988f6b6c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb index 0c1d5e04128..2c53f1539fd 100644 --- a/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2015.5.223-GCC-4.9.3-2.25.eb @@ -5,7 +5,7 @@ deprecated = "icc versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_ccompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb index 3fe029f3bdb..432ab0ef562 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb index ac3b139eff6..f4053771860 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.0.109.eb @@ -6,7 +6,7 @@ version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb index acee6423cd6..ab7616ebf26 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.1.150-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.1.150' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb index ddae823dc3d..56e28dabc96 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.2.181' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb index d03f2d3cb53..aeef66368d9 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.2.181-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.2.181' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb index bbe90dab4fc..62803077963 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb index 19f9a279fc5..f9f5b20a779 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb index 9e624b5c3f5..ef917400457 100644 --- a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb index e554131ea4a..08695b1740a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.0.098-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2017.0.098' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb index 9f1524cfe8a..a9e48124f1c 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2017.1.132' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb index 1b9a91bff73..d47cc95f9ea 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.1.132-GCC-6.3.0-2.27.eb @@ -6,7 +6,7 @@ version = '2017.1.132' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb index 9f323aeae8a..24163148c11 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.2.174-GCC-6.3.0-2.27.eb @@ -6,7 +6,7 @@ version = '2017.2.174' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb index a0716886c4c..97476f1b534 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.4.196-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2017.4.196' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb index 83e7ddb2e29..6d029c01f82 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.5.239-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2017.5.239' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb index 0b9b4fd2233..e647ee44092 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.6.256-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2017.6.256' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb index 675cf2ba85e..2faa508bbd6 100644 --- a/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2017.7.259-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2017.7.259' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb index 79219828af8..5d4d3b6bbcd 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.0.128-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2018.0.128' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb index 0d91211867d..d757e160a95 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.1.163-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2018.1.163' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12382/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb index fddf3dd0097..9d394c13b70 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.2.199-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2018.2.199' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] checksums = ['ce2c8886b3ae2eaf6e1514c5255bd2ec9ee8506460ba68c7e8164c65716cde82'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb index a3900a4e92d..429625fee44 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.3.222-GCC-7.3.0-2.30.eb @@ -6,7 +6,7 @@ version = '2018.3.222' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13003/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb index 8998036ff64..e81103c9c89 100644 --- a/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/icc/icc-2018.5.274-GCC-7.3.0-2.30.eb @@ -6,7 +6,7 @@ version = '2018.5.274' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13723/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template diff --git a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb index 5c7a9fbb207..bc3feb1b43b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -6,7 +6,7 @@ version = '2019.0.117' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13582/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb index 6a08a11675d..5b36c7f1710 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -6,7 +6,7 @@ version = '2019.1.144' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14865/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb index 87b5da692d0..6aec27b4f8a 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -6,7 +6,7 @@ version = '2019.2.187' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15093/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb index 0913db092da..a149d779f0b 100644 --- a/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/icc/icc-2019.3.199-GCC-8.3.0-2.32.eb @@ -6,7 +6,7 @@ version = '2019.3.199' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel C and C++ compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15273/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_cpp.tgz'] diff --git a/easybuild/easyconfigs/i/icc/icc-system-GCC-system-2.29.eb b/easybuild/easyconfigs/i/icc/icc-system-GCC-system-2.29.eb index 0df920c0b75..4ecd38467e1 100644 --- a/easybuild/easyconfigs/i/icc/icc-system-GCC-system-2.29.eb +++ b/easybuild/easyconfigs/i/icc/icc-system-GCC-system-2.29.eb @@ -6,7 +6,7 @@ version = 'system' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "C and C++ compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM generate_standalone_module = True diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2013.2.146.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2013.2.146.eb index 9278bf20bac..c73f28c22b3 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2013.2.146.eb @@ -7,7 +7,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2013.3.163.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2013.3.163.eb index d4afc28d001..03ce3e4bbc7 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2013.3.163.eb @@ -7,7 +7,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2013.4.183.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2013.4.183.eb index fd4ff7f0e61..0189d1dcaeb 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2013.4.183.eb @@ -7,7 +7,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2013.5.192-GCC-4.8.3.eb index 0772fb1a926..3a4645911b1 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2013.5.192-GCC-4.8.3.eb @@ -8,7 +8,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2013.5.192.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2013.5.192.eb index bd96b0b3af0..960ef593b34 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2013.5.192.eb @@ -7,7 +7,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.1.106.eb index 147da335898..7f9e35cd91d 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.1.106.eb @@ -7,7 +7,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb index cec141aafba..c2beed933eb 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.2.144.eb @@ -7,7 +7,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.4.211.eb index 93f87a331b5..2fea62d7cdd 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2013_sp1.4.211.eb @@ -8,7 +8,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090-GCC-4.9.2.eb index 1e985b0280d..24f347acca5 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090-GCC-4.9.2.eb @@ -8,7 +8,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb index b52be14e00a..0999586a56d 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.0.090.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133-GCC-4.9.2.eb index 42f97119e7b..1df16f920d2 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133-GCC-4.9.2.eb @@ -8,7 +8,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb index 67fa91201cd..876e89c729b 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.1.133.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.2.164-GCC-4.9.2.eb index 58ee680c25c..97beec602b5 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.2.164-GCC-4.9.2.eb @@ -8,7 +8,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-4.9.3-2.25.eb index 7b3691c8ba3..7dfbf71c0d4 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -8,7 +8,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb index 0c90e9a4ffe..de00bc42ced 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.5.223-GCC-4.9.3-2.25.eb index 84366e04867..31299e8ff39 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -8,7 +8,7 @@ deprecated = "iccifort versions older than 2016.1.150 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C, C++ and Fortran compilers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb index f450e454cc5..3f62f21fa2b 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -10,7 +10,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb index af9894e9c4b..335e623376a 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.0.109.eb @@ -9,7 +9,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb index cc24a9ab546..1b07873af54 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -9,7 +9,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb index 297fe048543..dff09fc82a8 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -9,7 +9,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb index f2c485ee204..027fdac31ac 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -9,7 +9,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb index 3683fdab6ec..eb4e8f81f13 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -9,7 +9,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb index 0401f8025e0..3b13633ede0 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -9,7 +9,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb index fdf3a88aa50..2ec5a8c8a01 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -9,7 +9,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb index a77c406ff7f..ae921192882 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -9,7 +9,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb index 3fc87e0a0a6..93474bab9b9 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -9,7 +9,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb index d4e78567c72..95c9260412c 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -9,7 +9,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb index 577b2283008..1f960fe1c56 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -9,7 +9,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb index a34c1351e05..b974446f754 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-6.4.0-2.28' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2017.5.239-GCC-6.4.0-2.28.eb index f361d08058f..928de594be4 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2017.5.239-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-6.4.0-2.28' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2018.0.128-GCC-6.4.0-2.28.eb index 9a60a272ff1..af7e955fd04 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2018.0.128-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-6.4.0-2.28' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 5fdd2513248..353d8ce136f 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-6.4.0-2.28' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2018.2.199-GCC-6.4.0-2.28.eb index 42909b5fcea..26ac157b8bd 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2018.2.199-GCC-6.4.0-2.28.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-6.4.0-2.28' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2018.3.222-GCC-7.3.0-2.30.eb index 2a94dbc508b..3a7f708d377 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-7.3.0-2.30' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2018.5.274-GCC-7.3.0-2.30.eb index 946b25006b5..25f263b14e4 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-7.3.0-2.30' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb index 28317788a50..6c6fdbb92f6 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-8.2.0-2.31.1' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index d171ce09375..6db79ff6802 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-8.2.0-2.31.1' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb index 4df7dcbde6b..a9d10c5b108 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-8.2.0-2.31.1' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2019.3.199-GCC-8.3.0-2.32.eb index b0673da2366..3e0105b5be5 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-8.3.0-2.32' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-system-GCC-system-2.29.eb b/easybuild/easyconfigs/i/iccifort/iccifort-system-GCC-system-2.29.eb index 8df356d232d..9aa9e9d01df 100644 --- a/easybuild/easyconfigs/i/iccifort/iccifort-system-GCC-system-2.29.eb +++ b/easybuild/easyconfigs/i/iccifort/iccifort-system-GCC-system-2.29.eb @@ -7,7 +7,7 @@ versionsuffix = '-GCC-system-2.29' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = "Intel C, C++ & Fortran compilers" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb index 2e8347c1bef..edbc8dd3960 100644 --- a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2016.10.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'iccifort' comp_ver = '2016.3.210' diff --git a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb index 30afab120ee..8004e07e709 100644 --- a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2017.4.196-GCC-6.4.0-2.28.eb @@ -7,7 +7,7 @@ versionsuffix = '-GCC-6.4.0-2.28' homepage = '(none)' description = """Intel C, C++ & Fortran compilers with CUDA toolkit""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2019a.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2019a.eb index ea5817b53f9..21c01c8d909 100644 --- a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2019a.eb +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2019a.eb @@ -6,7 +6,7 @@ version = '2019a' homepage = '(none)' description = """Intel C, C++ & Fortran compilers with CUDA toolkit""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'iccifort' comp_ver = '2019.1.144' diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb index d9dd237554e..752b1df6264 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.2.0.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2013.2.146' dependencies = [ diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb index 8f48b5fcf10..37443518315 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.3.0.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compsuffix = '.3.163' compver = '2013' + compsuffix diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb index c7ded9c4409..0b7d23527ba 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.4.0.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compsuffix = '.4.183' compver = '2013' + compsuffix diff --git a/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb b/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb index 4ba7576cb8b..67e9c0e4b54 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-5.5.0.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compsuffix = '.5.192' compver = '2013' + compsuffix diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb b/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb index 9b0ec672709..e72a4e50c17 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-6.1.5.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '1.106' compver = '2013_sp1.%s' % suff diff --git a/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb index fa9ca4abaa1..61e1ef65209 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-6.2.5.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '2.144' compver = '2013_sp1.%s' % suff diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb b/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb index 4f7745b3937..b5fc7089478 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-7.1.2.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '0.090' compver = '2015.%s' % suff diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb index df90d5a56f4..692566a61eb 100644 --- a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb +++ b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '3.187' compver = '2015.%s' % suff diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb index 53a7f04d2c1..37e4e7923e5 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073-32bit.eb @@ -6,7 +6,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_cprof_p_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb index bccd5d1c732..1cbc90adfca 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.073.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_cprof_p_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb index 242fe677bf7..eeadfdd1088 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-11.1.075.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_cprof_p_%s_intel64.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb index 3297de6d533..01f72e54934 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.10.319.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb index ba54a48aaff..ec72aeae195 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.13.367.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb index 7911d9434d4..783e11ec554 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.3.174.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb index 345a2b95631..863a80d31b2 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2011.6.233.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_intel64_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb index 7718c5c0d7b..651f4287d02 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.1.117.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb index 29c81234427..8734ef81b3b 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.2.146.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb index 236234cd0e4..69864ca7806 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.3.163.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb index d66b69e7f86..c372525ab86 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.4.183.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb index 61d09ca76fd..f240b82adb9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192-GCC-4.8.3.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb index 5a7c89af1d0..a8676034d25 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013.5.192.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb index 107120381e5..21ceaf74682 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.0.080.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb index 955d65cdbd4..5b1032e8bde 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.1.106.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb index ddab13a0463..7152f93a826 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.2.144.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb index 3cab269ffbc..7eb8a9a63ab 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.3.174.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb index b2f3d59b401..844b15418c5 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2013_sp1.4.211.eb @@ -6,7 +6,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb index 4a77713ac37..2c8c51ffe40 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090-GCC-4.9.2.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb index 2db458a90d7..d073c1b55d9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.0.090.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb index 500c655757a..50972bc5bdb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133-GCC-4.9.2.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb index ffc3a60df69..29457f4cce4 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.1.133.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb index 562fa39a983..2b95cd408fa 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.2.164-GCC-4.9.2.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb index 4f840aba997..318961c3243 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb index ff658250ced..2f812ffdac9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb index f223e026368..62dee2d537a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.5.223-GCC-4.9.3-2.25.eb @@ -5,7 +5,7 @@ deprecated = "ifort versions older than 2016.0 are deprecated" homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_fcompxe_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb index aabb1cd11ec..3384142be28 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb index 7579c77a3d5..044e031df59 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.0.109.eb @@ -6,7 +6,7 @@ version = '2016.0.109' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb index 9b682724411..7fa0f61d571 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.1.150-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.1.150' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb index 3ee959b67ba..7ad0988f1c5 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.2.181' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb index f0b7f28bbb8..dfdcab55078 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.2.181-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.2.181' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb index 3b0e1e5deb1..06a28ac283d 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb index a3e1cae6fd6..845de68b573 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.3.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb index 44913634e31..424b17efcdd 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.3.210' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran_update%(version_minor)s.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb index 73541611678..bee20c3b701 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.0.098-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2017.0.098' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb index 2f49c69f893..c21ad799d11 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2017.1.132' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb index fba25174428..50d0b05add0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.1.132-GCC-6.3.0-2.27.eb @@ -6,7 +6,7 @@ version = '2017.1.132' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb index aa15e0062d6..87e504c52e0 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.2.174-GCC-6.3.0-2.27.eb @@ -6,7 +6,7 @@ version = '2017.2.174' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb index 1a8d245ef94..ad635f708aa 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.4.196-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2017.4.196' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb index 7673687015f..5c96c3caa1a 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.5.239-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2017.5.239' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb index e05e4ab7180..5167e233ab9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.6.256-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2017.6.256' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb index 8fd3c0675b7..0a00e0c7f1c 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2017.7.259-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2017.7.259' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb index 6c675f6f175..d6965f2056c 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.0.128-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2018.0.128' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb index 0392283da83..7496bbc0240 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2018.1.163' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12383/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb index 5cfedef3cef..72f9347e1d9 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.2.199-GCC-6.4.0-2.28.eb @@ -6,7 +6,7 @@ version = '2018.2.199' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] patches = ['ifort_%(version)s_no_mpi_mic_dependency.patch'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb index 6e874685593..1cf62fe37eb 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.3.222-GCC-7.3.0-2.30.eb @@ -6,7 +6,7 @@ version = '2018.3.222' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13004/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb index 825a94e3684..d072f8da932 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2018.5.274-GCC-7.3.0-2.30.eb @@ -6,7 +6,7 @@ version = '2018.5.274' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13724/'] # released as "2018 update 4" despite internal version number if 2018.5.274, so can't use %(version_minor)s template diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb index d9c0fbd27a6..99d57accd0f 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.0.117-GCC-8.2.0-2.31.1.eb @@ -6,7 +6,7 @@ version = '2019.0.117' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13583/'] sources = ['parallel_studio_xe_%(version_major)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 8e122a3d39e..418da0f2b07 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -6,7 +6,7 @@ version = '2019.1.144' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/14866/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb index ec71efeb29b..1f4546e2fc2 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.2.187-GCC-8.2.0-2.31.1.eb @@ -6,7 +6,7 @@ version = '2019.2.187' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15094/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb index d911088959e..2c970915fef 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-2019.3.199-GCC-8.3.0-2.32.eb @@ -6,7 +6,7 @@ version = '2019.3.199' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Intel Fortran compiler" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15274/'] sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition_for_fortran.tgz'] diff --git a/easybuild/easyconfigs/i/ifort/ifort-system-GCC-system-2.29.eb b/easybuild/easyconfigs/i/ifort/ifort-system-GCC-system-2.29.eb index 9ae9fe59bad..b73f1e13408 100644 --- a/easybuild/easyconfigs/i/ifort/ifort-system-GCC-system-2.29.eb +++ b/easybuild/easyconfigs/i/ifort/ifort-system-GCC-system-2.29.eb @@ -6,7 +6,7 @@ version = 'system' homepage = 'http://software.intel.com/en-us/intel-compilers/' description = "Fortran compiler from Intel" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM generate_standalone_module = True diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb index fe7f40c56ea..c5c608db1ef 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.00-GCC-4.9.3-2.25.eb @@ -9,7 +9,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.0.109' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb index 476d9acb2bc..385ca4b29ea 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.01-GCC-4.9.3-2.25.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '1.150' compver = '2016.%s' % suff diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb index 7878168e2e0..502d9e7bb50 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-4.9.3-2.25.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '2.181' compver = '2016.%s' % suff diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb index 9510f7e46a4..5fd077f736d 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.02-GCC-5.3.0-2.26.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-5.3.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '2.181' compver = '2016.%s' % suff diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb index 08b9b3f5070..1fa91cde77e 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-4.9.3-2.25.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb index a8596d5825f..bc923dab4cf 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.3.0-2.26.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-5.3.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb index 7ac8a1f5c15..c3a2eaa857c 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb index 4df51c98955..e6e2bc6606d 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb @@ -7,7 +7,7 @@ version = '2016b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210' suff = '-GCC-5.4.0-2.26' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb index 843a2fdb37b..49c9d2f1104 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.00-GCC-5.4.0-2.26.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.0.098' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb index cfdd91b0bf6..539f2249710 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.01-GCC-5.4.0-2.26.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.1.132' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb index 65c861bb3f8..bb3e3bc6295 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.02-GCC-6.3.0-2.27.eb @@ -8,7 +8,7 @@ versionsuffix = '-GCC-6.3.0-2.27' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.2.174' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017.09.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017.09.eb index 908d5ed6b8e..949e5ceb0d1 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017.09.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017.09.eb @@ -7,7 +7,7 @@ version = '2017.09' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.5.239' compsuff = '-GCC-6.4.0-2.28' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb index 14c6d0426dc..cdf516f6766 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017a.eb @@ -7,7 +7,7 @@ version = '2017a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.1.132' suff = '-GCC-6.3.0-2.27' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb index 76e9e5a6d7d..20a6c41fd5a 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2017b.eb @@ -7,7 +7,7 @@ version = '2017b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.4.196' suff = '-GCC-6.4.0-2.28' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2018.00.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2018.00.eb index 9bbf335ebad..c3acd6fa05e 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2018.00.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2018.00.eb @@ -7,7 +7,7 @@ version = '2018.00' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.0.128' suff = '-GCC-6.4.0-2.28' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2018.01.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2018.01.eb index dcf12f88020..1acddd27e20 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2018.01.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2018.01.eb @@ -7,7 +7,7 @@ version = '2018.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.1.163' suff = '-GCC-6.4.0-2.28' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2018.02.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2018.02.eb index f571851aedd..a8ac21359bc 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2018.02.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2018.02.eb @@ -7,7 +7,7 @@ version = '2018.02' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.2.199' suff = '-GCC-6.4.0-2.28' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2018.04.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2018.04.eb index 347b51faa4f..7e09c201658 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2018.04.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2018.04.eb @@ -7,7 +7,7 @@ version = '2018.04' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.5.274' suff = '-GCC-7.3.0-2.30' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2018a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2018a.eb index b7af0392875..6e1fc4e26ec 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2018a.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2018a.eb @@ -7,7 +7,7 @@ version = '2018a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.1.163' suff = '-GCC-6.4.0-2.28' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2018b.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2018b.eb index 5fa91196158..c0092cb1572 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2018b.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2018b.eb @@ -7,7 +7,7 @@ version = '2018b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.3.222' suff = '-GCC-7.3.0-2.30' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2019.00.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2019.00.eb index 063794e3261..0e0b4317831 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2019.00.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2019.00.eb @@ -7,7 +7,7 @@ version = '2019.00' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.0.117' suff = '-GCC-8.2.0-2.31.1' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2019.01.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2019.01.eb index f4374e67129..ee52a35b4fc 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2019.01.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2019.01.eb @@ -7,7 +7,7 @@ version = '2019.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.1.144' suff = '-GCC-8.2.0-2.31.1' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2019.02.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2019.02.eb index b492c9b55d4..03702c6ecc1 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2019.02.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2019.02.eb @@ -7,7 +7,7 @@ version = '2019.02' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.2.187' suff = '-GCC-8.2.0-2.31.1' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2019.03.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2019.03.eb index e526714c3d9..7d67271117b 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2019.03.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2019.03.eb @@ -7,7 +7,7 @@ version = '2019.03' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.3.199' suff = '-GCC-8.3.0-2.32' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2019a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2019a.eb index 1bcd5ce8508..6feabcd93d1 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2019a.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2019a.eb @@ -6,7 +6,7 @@ version = '2019a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.1.144' suff = '-GCC-8.2.0-2.31.1' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-5.2.0.eb b/easybuild/easyconfigs/i/iimpi/iimpi-5.2.0.eb index a1e0096afda..deae323dfb3 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-5.2.0.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-5.2.0.eb @@ -7,7 +7,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2013.2.146' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-5.3.0.eb b/easybuild/easyconfigs/i/iimpi/iimpi-5.3.0.eb index 3aea6764853..1d366f98696 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-5.3.0.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-5.3.0.eb @@ -7,7 +7,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compsuffix = '.3.163' compver = '2013' + compsuffix diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-5.4.0.eb b/easybuild/easyconfigs/i/iimpi/iimpi-5.4.0.eb index d603f0c6d2f..7b7f7a37322 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-5.4.0.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-5.4.0.eb @@ -7,7 +7,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compsuffix = '.4.183' compver = '2013' + compsuffix diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb index 1fec8e4fcb7..ccd6bb33ff1 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb @@ -8,7 +8,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '5.192' compver = '2013.%s' % suff diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0.eb b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0.eb index 869da6b41f9..2d50c6faba5 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0.eb @@ -7,7 +7,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compsuffix = '.5.192' compver = '2013' + compsuffix diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-5.5.3-GCC-4.8.3.eb b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.3-GCC-4.8.3.eb index 1176e3b7010..bf4f82b50c5 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-5.5.3-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.3-GCC-4.8.3.eb @@ -8,7 +8,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '5.192' compver = '2013.%s' % suff diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-6.1.5.eb b/easybuild/easyconfigs/i/iimpi/iimpi-6.1.5.eb index 12e0bed097d..74b26fb19bb 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-6.1.5.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-6.1.5.eb @@ -7,7 +7,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '1.106' compver = '2013_sp1.%s' % suff diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-6.2.5.eb b/easybuild/easyconfigs/i/iimpi/iimpi-6.2.5.eb index d9a0ed7135b..6bed0c83015 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-6.2.5.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-6.2.5.eb @@ -7,7 +7,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '2.144' compver = '2013_sp1.%s' % suff diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2-GCC-4.9.2.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2-GCC-4.9.2.eb index fc3fe7de4df..34f160fe399 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2-GCC-4.9.2.eb @@ -8,7 +8,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '0.090' compver = '2015.%s' % suff diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb index 4f70ed10e83..10faccadda5 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.1.2.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.0.090' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.2.3-GCC-4.9.2.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.2.3-GCC-4.9.2.eb index 6726bd2ec01..1ec3efab472 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.2.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.2.3-GCC-4.9.2.eb @@ -8,7 +8,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '1.133' compver = '2015.%s' % suff diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb index 26afdfbeb76..eb985e29f2e 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.2.5-GCC-4.9.2.eb @@ -8,7 +8,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '2.164' compver = '2015.%s' % suff diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-4.9.3-2.25.eb index 280b810a589..776f0e8a26c 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-4.9.3-2.25.eb @@ -8,7 +8,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '3.187' compver = '2015.%s' % suff diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb index f71c287e248..35001491970 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb @@ -8,7 +8,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.3.187' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.5.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.5.5-GCC-4.9.3-2.25.eb index d255dc937b4..5e9b712ef6a 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-7.5.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.5.5-GCC-4.9.3-2.25.eb @@ -8,7 +8,7 @@ deprecated = "iimpi versions older than 2016.01 are deprecated" homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.5.223' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-8.1.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-8.1.5-GCC-4.9.3-2.25.eb index 43b5e47c986..548dbd00132 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-8.1.5-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-8.1.5-GCC-4.9.3-2.25.eb @@ -7,7 +7,7 @@ versionsuffix = '-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.1.150' dependencies = [ diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-system-GCC-system-2.29.eb b/easybuild/easyconfigs/i/iimpi/iimpi-system-GCC-system-2.29.eb index 70acaf1c9f2..4149c1291e4 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-system-GCC-system-2.29.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-system-GCC-system-2.29.eb @@ -7,7 +7,7 @@ versionsuffix = '-GCC-system-2.29' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [ ('icc', version, versionsuffix), diff --git a/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb index 568c34ad3f4..6c427420fc4 100644 --- a/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb +++ b/easybuild/easyconfigs/i/iimpic/iimpic-2016.10.eb @@ -7,7 +7,7 @@ version = '2016.10' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210' suff = '-GCC-5.4.0-2.26' diff --git a/easybuild/easyconfigs/i/iimpic/iimpic-2017b.eb b/easybuild/easyconfigs/i/iimpic/iimpic-2017b.eb index 201459974ab..f1fc376bdd9 100644 --- a/easybuild/easyconfigs/i/iimpic/iimpic-2017b.eb +++ b/easybuild/easyconfigs/i/iimpic/iimpic-2017b.eb @@ -7,7 +7,7 @@ version = '2017b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.4.196' gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/iimpic/iimpic-2019a.eb b/easybuild/easyconfigs/i/iimpic/iimpic-2019a.eb index cefe5a9e722..0fc6296d689 100644 --- a/easybuild/easyconfigs/i/iimpic/iimpic-2019a.eb +++ b/easybuild/easyconfigs/i/iimpic/iimpic-2019a.eb @@ -7,7 +7,7 @@ version = '2019a' homepage = 'https://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.1.144' gccver = '8.2.0' diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb index 9674e452a7c..63d8f50e147 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038-32bit.eb @@ -9,7 +9,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_p_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb index 224df10292e..a80a0f74e9d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.2.6.038.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_p_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb index 92262ace6b4..6044b0e15e0 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.10.319.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s_intel64.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb index 0f0ad0b4688..d31f4f3af98 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.12.361.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb index 06c591fa6b3..ee65728c248 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-10.3.6.233.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s_intel64.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb index f9a326cbfe9..88b0e2f248d 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.1.117.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb index 5a878265754..6fefb4b3702 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.2.146.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb index c52e13018b0..88ce936f481 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.3.163.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb index adfdb012196..569208ab6b5 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.4.183.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb index 2d1363c0c58..41e7bec8204 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb index 95b59f73eef..ed556a71494 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.0.080.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb index ccf2955cf16..a8b981d62b4 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.1.106.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb index f4004604a3e..3bee32bcaff 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-2013.5.192-GCC-4.8.3.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb index 5f6d62acc41..c8831230202 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-GCC-4.8.3.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb index 71049b3d95d..db1fec3a5d9 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144-OpenMPI-1.6.5.eb @@ -7,7 +7,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, ext for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb index 6194e4eb597..108e906bdfc 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.2.144.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb index 38d77e753bf..ef344cdb462 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-11.1.3.174.eb @@ -8,7 +8,7 @@ description = """Intel Math Kernel Library is a library of highly optimized, applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['l_mkl_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index 9eb4b8eae61..d845600ff46 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -7,7 +7,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index 12cebf7bc33..5cd4f104035 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -8,7 +8,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_mpi_pu_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index 0b50b25a5e7..aac6f783f65 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -7,7 +7,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_mpi_pu_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index abc7cce0095..0d8622e1903 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -7,7 +7,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 625ccb1b29b..f9807bc5ab9 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -7,7 +7,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 48dec1a2063..2d507e73d39 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -7,7 +7,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index c5498f175f1..cf07a9c863a 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -7,7 +7,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index 47d0c15126c..d98ce241ba1 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -7,7 +7,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index 7f603a47816..bb0c047e177 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -7,7 +7,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index ca5580f74c2..a486e579876 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -7,7 +7,7 @@ description = """The Intel(R) MPI Library for Linux* OS is a multi-fabric messag passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2.2 (MPI-2) specification.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_mpi_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/intel/intel-2014.06.eb b/easybuild/easyconfigs/i/intel/intel-2014.06.eb index 036203558ae..93e6962e372 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.06.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.06.eb @@ -8,7 +8,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '5.192' compver = '2013.%s' % suff diff --git a/easybuild/easyconfigs/i/intel/intel-2014.10.eb b/easybuild/easyconfigs/i/intel/intel-2014.10.eb index deb4a7c763d..9f69a18cc83 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.10.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.10.eb @@ -8,7 +8,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '0.090' compver = '2015.%s' % suff diff --git a/easybuild/easyconfigs/i/intel/intel-2014.11.eb b/easybuild/easyconfigs/i/intel/intel-2014.11.eb index 84b7fac6caa..e74ad39ebbd 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014.11.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014.11.eb @@ -8,7 +8,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '1.133' compver = '2015.%s' % suff diff --git a/easybuild/easyconfigs/i/intel/intel-2014b.eb b/easybuild/easyconfigs/i/intel/intel-2014b.eb index 7a1bfb0742a..e56a8da742b 100644 --- a/easybuild/easyconfigs/i/intel/intel-2014b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2014b.eb @@ -8,7 +8,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM suff = '5.192' compver = '2013.%s' % suff diff --git a/easybuild/easyconfigs/i/intel/intel-2015.02.eb b/easybuild/easyconfigs/i/intel/intel-2015.02.eb index cdbec70f283..436cd244af1 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015.02.eb @@ -8,7 +8,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.2.164' gccsuff = '-GCC-4.9.2' diff --git a/easybuild/easyconfigs/i/intel/intel-2015.08.eb b/easybuild/easyconfigs/i/intel/intel-2015.08.eb index fdbd85c4dfc..91fbfdaad05 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015.08.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015.08.eb @@ -8,7 +8,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.5.223' diff --git a/easybuild/easyconfigs/i/intel/intel-2015a.eb b/easybuild/easyconfigs/i/intel/intel-2015a.eb index db7abe3c9f7..5c137ac3988 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015a.eb @@ -8,7 +8,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.1.133' gccsuff = '-GCC-4.9.2' diff --git a/easybuild/easyconfigs/i/intel/intel-2015b.eb b/easybuild/easyconfigs/i/intel/intel-2015b.eb index 603eb2f4a62..d0927d74cd4 100644 --- a/easybuild/easyconfigs/i/intel/intel-2015b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2015b.eb @@ -8,7 +8,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.3.187' gccsuff = '-GNU-4.9.3-2.25' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.00.eb b/easybuild/easyconfigs/i/intel/intel-2016.00.eb index 4cf74e6fd4b..a30f5b789b7 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.00.eb @@ -8,7 +8,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.0.109' gccver = '4.9.3' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.01.eb b/easybuild/easyconfigs/i/intel/intel-2016.01.eb index 07eda34eb8b..5d24191a941 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.01.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.1.150' gccver = '4.9.3' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb index 3a3e7c09937..8753f50010e 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-4.9.eb @@ -9,7 +9,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.2.181' gccver = '%s.3' % gcc_maj_min diff --git a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb index d6d21970070..6316017fe86 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.02-GCC-5.3.eb @@ -9,7 +9,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.2.181' gccver = '%s.0' % gcc_maj_min diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb index a951ec0696d..ab75a0e68e6 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-4.9.eb @@ -9,7 +9,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210' gccver = '%s.3' % gcc_maj_min diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb index b6077c2f5b9..a6f8d2b6e2d 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.3.eb @@ -9,7 +9,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210' gccver = '%s.0' % gcc_maj_min diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb index 81612d6c021..2bd861e5b2c 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb @@ -9,7 +9,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210' gccver = '%s.0' % gcc_maj_min diff --git a/easybuild/easyconfigs/i/intel/intel-2016a.eb b/easybuild/easyconfigs/i/intel/intel-2016a.eb index e68cb956d6a..b2f739d46f4 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016a.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.1.150' gccsuff = '-GCC-4.9.3-2.25' diff --git a/easybuild/easyconfigs/i/intel/intel-2016b.eb b/easybuild/easyconfigs/i/intel/intel-2016b.eb index b4945e4b515..a3da237c87e 100644 --- a/easybuild/easyconfigs/i/intel/intel-2016b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2016b.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210' gccver = '5.4.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2017.00.eb b/easybuild/easyconfigs/i/intel/intel-2017.00.eb index beafad3bfcc..8e84faee0b5 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.00.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.0.098' gccver = '5.4.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2017.01.eb b/easybuild/easyconfigs/i/intel/intel-2017.01.eb index 768269691cc..9707efae38f 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.01.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.1.132' gccver = '5.4.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2017.02.eb b/easybuild/easyconfigs/i/intel/intel-2017.02.eb index 0aeac694913..ff32523d77d 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.02.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.2.174' gccver = '6.3.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2017.09.eb b/easybuild/easyconfigs/i/intel/intel-2017.09.eb index 43b427c9bb7..c573a315f4c 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017.09.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017.09.eb @@ -6,7 +6,7 @@ version = '2017.09' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.5.239' gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2017a.eb b/easybuild/easyconfigs/i/intel/intel-2017a.eb index 23472c6be54..0e8a38b6ddb 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017a.eb @@ -7,7 +7,7 @@ homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#in description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM intelver = '2017.1.132' gccver = '6.3.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2017b.eb b/easybuild/easyconfigs/i/intel/intel-2017b.eb index f17353f796e..39d1b29662a 100644 --- a/easybuild/easyconfigs/i/intel/intel-2017b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2017b.eb @@ -6,7 +6,7 @@ version = '2017b' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.4.196' gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2018.00.eb b/easybuild/easyconfigs/i/intel/intel-2018.00.eb index f67c0fc4390..313fb728d86 100644 --- a/easybuild/easyconfigs/i/intel/intel-2018.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2018.00.eb @@ -6,7 +6,7 @@ version = '2018.00' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.0.128' gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2018.01.eb b/easybuild/easyconfigs/i/intel/intel-2018.01.eb index 63c678442d4..c775b7e1a62 100644 --- a/easybuild/easyconfigs/i/intel/intel-2018.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2018.01.eb @@ -6,7 +6,7 @@ version = '2018.01' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.1.163' gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2018.02.eb b/easybuild/easyconfigs/i/intel/intel-2018.02.eb index 8ced8f92f9d..3ce57bad815 100644 --- a/easybuild/easyconfigs/i/intel/intel-2018.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2018.02.eb @@ -6,7 +6,7 @@ version = '2018.02' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.2.199' gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2018.04.eb b/easybuild/easyconfigs/i/intel/intel-2018.04.eb index 415760652f7..e3e59c746fd 100644 --- a/easybuild/easyconfigs/i/intel/intel-2018.04.eb +++ b/easybuild/easyconfigs/i/intel/intel-2018.04.eb @@ -6,7 +6,7 @@ version = '2018.04' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.5.274' gccver = '7.3.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2018a.eb b/easybuild/easyconfigs/i/intel/intel-2018a.eb index cf11b028b88..0c518bbfae8 100644 --- a/easybuild/easyconfigs/i/intel/intel-2018a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2018a.eb @@ -6,7 +6,7 @@ version = '2018a' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.1.163' gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2018b.eb b/easybuild/easyconfigs/i/intel/intel-2018b.eb index aae8de3016c..6dcf8d1ef36 100644 --- a/easybuild/easyconfigs/i/intel/intel-2018b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2018b.eb @@ -6,7 +6,7 @@ version = '2018b' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.3.222' gccver = '7.3.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2019.00.eb b/easybuild/easyconfigs/i/intel/intel-2019.00.eb index 1621affb5f0..b89a76419f5 100644 --- a/easybuild/easyconfigs/i/intel/intel-2019.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2019.00.eb @@ -6,7 +6,7 @@ version = '2019.00' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.0.117' gccver = '8.2.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2019.01.eb b/easybuild/easyconfigs/i/intel/intel-2019.01.eb index 90479c245ed..23e8b5bde43 100644 --- a/easybuild/easyconfigs/i/intel/intel-2019.01.eb +++ b/easybuild/easyconfigs/i/intel/intel-2019.01.eb @@ -6,7 +6,7 @@ version = '2019.01' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.1.144' gccver = '8.2.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2019.02.eb b/easybuild/easyconfigs/i/intel/intel-2019.02.eb index d12e6866f2b..4b8f7464543 100644 --- a/easybuild/easyconfigs/i/intel/intel-2019.02.eb +++ b/easybuild/easyconfigs/i/intel/intel-2019.02.eb @@ -6,7 +6,7 @@ version = '2019.02' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.2.187' gccver = '8.2.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2019.03.eb b/easybuild/easyconfigs/i/intel/intel-2019.03.eb index 4d8289207a0..f3944e63581 100644 --- a/easybuild/easyconfigs/i/intel/intel-2019.03.eb +++ b/easybuild/easyconfigs/i/intel/intel-2019.03.eb @@ -6,7 +6,7 @@ version = '2019.03' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.3.199' gccver = '8.3.0' diff --git a/easybuild/easyconfigs/i/intel/intel-2019a.eb b/easybuild/easyconfigs/i/intel/intel-2019a.eb index 0b4c3860c29..2310e83aa93 100644 --- a/easybuild/easyconfigs/i/intel/intel-2019a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2019a.eb @@ -6,7 +6,7 @@ version = '2019a' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.1.144' gccver = '8.2.0' diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb index 14c19568ad7..13cc03c128c 100644 --- a/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2016.10.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM comp_name = 'iccifort' comp_ver = '2016.3.210' diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2017b.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2017b.eb index 614bb7606f8..0fbf19cbda2 100644 --- a/easybuild/easyconfigs/i/intelcuda/intelcuda-2017b.eb +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2017b.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.4.196' gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2019a.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2019a.eb index 65125927922..48e3309dc9c 100644 --- a/easybuild/easyconfigs/i/intelcuda/intelcuda-2019a.eb +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2019a.eb @@ -7,7 +7,7 @@ homepage = '(none)' description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.1.144' gccver = '8.2.0' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb index a9a545eec79..df403b4331f 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.01.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.1.133-GCC-4.9.2' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb index e17fa43dd23..7a728ef8445 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.02.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.2.164-GCC-4.9.2' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb index 93dbfc98f80..d90653a1396 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2015.03.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.3.187-GNU-4.9.3-2.25' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb index 5d1d7432421..407b4dbab0b 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210-GCC-5.4.0-2.26' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb index ced0e875851..cf47d79c7f1 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-4.9.3-2.25.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210-GCC-4.9.3-2.25' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb index f0219ff350b..6d8595e98bb 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.09-GCC-5.4.0-2.26.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210-GCC-5.4.0-2.26' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb index 9d9e8846e67..80ba7061f0c 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017.01.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.1.132' gcc_maj_min = '5.4' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb index 4d75373f4f9..181e5bd610e 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017a.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.1.132' gccsuff = '-GCC-6.3.0-2.27' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2017b.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2017b.eb index 3a41c0a1b3a..4529f4be063 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2017b.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2017b.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.4.196' gccsuff = '-GCC-6.4.0-2.28' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2018.02.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2018.02.eb index 770890281b0..dc1e434157c 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2018.02.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2018.02.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.2.199' gccver = '6.4.0' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2018a.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2018a.eb index 5c2c9dac046..5a9c3a97c04 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2018a.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2018a.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.1.163' gccsuff = '-GCC-6.4.0-2.28' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2018b.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2018b.eb index f92e039c285..c776cee3d51 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2018b.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2018b.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.3.222' gccver = '7.3.0' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2019.01.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2019.01.eb index 9bc80aad1a3..c097ad0a0d9 100644 --- a/easybuild/easyconfigs/i/iomkl/iomkl-2019.01.eb +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2019.01.eb @@ -7,7 +7,7 @@ homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.1.144' gccver = '8.2.0' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2015.01.eb b/easybuild/easyconfigs/i/iompi/iompi-2015.01.eb index 5bd039e031d..90a5c0dca97 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2015.01.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2015.01.eb @@ -6,7 +6,7 @@ version = '2015.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.1.133-GCC-4.9.2' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2015.02.eb b/easybuild/easyconfigs/i/iompi/iompi-2015.02.eb index 726413e1620..991c65b58ff 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2015.02.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2015.02.eb @@ -6,7 +6,7 @@ version = '2015.02' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.2.164-GCC-4.9.2' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2015.03.eb b/easybuild/easyconfigs/i/iompi/iompi-2015.03.eb index 83b42beffd4..1f324aabeb4 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2015.03.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2015.03.eb @@ -6,7 +6,7 @@ version = '2015.03' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2015.3.187-GNU-4.9.3-2.25' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.07.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.07.eb index 6cfe2ee8254..6a25a583813 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2016.07.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.07.eb @@ -6,7 +6,7 @@ version = '2016.07' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210-GCC-5.4.0-2.26' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb index f69ecfb47aa..5f754616aa4 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-4.9.3-2.25.eb @@ -6,7 +6,7 @@ version = '2016.09-GCC-4.9.3-2.25' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210-GCC-4.9.3-2.25' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb index 7a279c30c60..e23e17c9f97 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.09-GCC-5.4.0-2.26.eb @@ -6,7 +6,7 @@ version = '2016.09-GCC-5.4.0-2.26' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2016.3.210-GCC-5.4.0-2.26' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb b/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb index cf97e1f426a..5817eac1ba8 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2017.01.eb @@ -7,7 +7,7 @@ version = '2017.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.1.132' compversuff = '-GCC-5.4.0-2.26' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb index f5e1679c27d..0a6cfea7a54 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2017a.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2017a.eb @@ -7,7 +7,7 @@ version = '2017a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.1.132' compversuff = '-GCC-6.3.0-2.27' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2017b.eb b/easybuild/easyconfigs/i/iompi/iompi-2017b.eb index 218aa8ffd0b..6aee96a9d3d 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2017b.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2017b.eb @@ -7,7 +7,7 @@ version = '2017b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2017.4.196' compversuff = '-GCC-6.4.0-2.28' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2018.02.eb b/easybuild/easyconfigs/i/iompi/iompi-2018.02.eb index 0228bce8d4f..06823ed426f 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2018.02.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2018.02.eb @@ -7,7 +7,7 @@ version = '2018.02' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.2.199' compversuff = '-GCC-6.4.0-2.28' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2018a.eb b/easybuild/easyconfigs/i/iompi/iompi-2018a.eb index c9dab061584..c8f73a297f4 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2018a.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2018a.eb @@ -7,7 +7,7 @@ version = '2018a' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.1.163' compversuff = '-GCC-6.4.0-2.28' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2018b.eb b/easybuild/easyconfigs/i/iompi/iompi-2018b.eb index b0026681a89..a9b93572ae9 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2018b.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2018b.eb @@ -7,7 +7,7 @@ version = '2018b' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2018.3.222' gccver = '7.3.0' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2019.01.eb b/easybuild/easyconfigs/i/iompi/iompi-2019.01.eb index 31c8e8e29fb..79a5dbde6b0 100644 --- a/easybuild/easyconfigs/i/iompi/iompi-2019.01.eb +++ b/easybuild/easyconfigs/i/iompi/iompi-2019.01.eb @@ -7,7 +7,7 @@ version = '2019.01' homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '2019.1.144' gccver = '8.2.0' diff --git a/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb b/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb index 0e78bfb109f..779092d0af4 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-2017.1.132.eb @@ -7,7 +7,7 @@ description = """Intel Integrated Performance Primitives (Intel IPP) is an exten and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_ipp_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb index af01ee3cccc..7128d121088 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-7.0.5.233.eb @@ -7,7 +7,7 @@ description = """Intel Integrated Performance Primitives (Intel IPP) is an exten and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_ipp_%s_intel64.tgz' % version] diff --git a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb index 2df68edb57c..21f023aced6 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-8.1.0.144.eb @@ -7,7 +7,7 @@ description = """Intel Integrated Performance Primitives (Intel IPP) is an exten and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_ipp_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb index c7f19f61c1e..3b22735f1a5 100644 --- a/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb +++ b/easybuild/easyconfigs/i/ipp/ipp-9.0.1.150.eb @@ -7,7 +7,7 @@ description = """Intel Integrated Performance Primitives (Intel IPP) is an exten and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_ipp_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb index 82c7a63390c..c83e203d15d 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb @@ -11,7 +11,7 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high- to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['ispc-v%(version)s-linux.tar.gz'] source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb index 0e49c82636c..b266d99faac 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb @@ -11,7 +11,7 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high- to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['ispc-v%(version)s-linux.tar.gz'] source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] diff --git a/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb b/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb index f4c7fa5a53b..07b50cccf1c 100644 --- a/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb +++ b/easybuild/easyconfigs/i/itac/itac-2017.1.024.eb @@ -6,7 +6,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb b/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb index 601c8fbfdfb..da7e799b2df 100644 --- a/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb +++ b/easybuild/easyconfigs/i/itac/itac-2018.1.017.eb @@ -6,7 +6,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] checksums = ['c907d5883cfa965b8f5d625e927c24a9da2ff7bc25bb211dd5047ddffc69be01'] diff --git a/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb b/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb index 560875c3fcd..a912ed96a0f 100644 --- a/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb +++ b/easybuild/easyconfigs/i/itac/itac-2018.3.022.eb @@ -6,7 +6,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] checksums = ['837b712ae2ef458868197a04068b710d76ee3037aceb8ab09b33392b92a97fe7'] diff --git a/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb b/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb index 9249d901083..f69e8157eb7 100644 --- a/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb +++ b/easybuild/easyconfigs/i/itac/itac-2019.2.026.eb @@ -6,7 +6,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] checksums = ['c66890beaf6e81da0f2ecb9695059a6686c95f6f01f467e32a076eb84ca8e40e'] diff --git a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb index 5e7c7075829..fb681a8fe20 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.0.0.011.eb @@ -6,7 +6,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_itac_p_%s.tgz' % version] diff --git a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb index 546ec403615..9e6efed69a8 100644 --- a/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb +++ b/easybuild/easyconfigs/i/itac/itac-8.1.4.045.eb @@ -6,7 +6,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb index 89228066326..c89e47a906a 100644 --- a/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb +++ b/easybuild/easyconfigs/i/itac/itac-9.0.3.051.eb @@ -6,7 +6,7 @@ description = """The Intel Trace Collector is a low-overhead tracing library tha event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_itac_p_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/j/JAXFrontCE/JAXFrontCE-2.75.eb b/easybuild/easyconfigs/j/JAXFrontCE/JAXFrontCE-2.75.eb index f8d7de59424..e79264369f7 100644 --- a/easybuild/easyconfigs/j/JAXFrontCE/JAXFrontCE-2.75.eb +++ b/easybuild/easyconfigs/j/JAXFrontCE/JAXFrontCE-2.75.eb @@ -7,7 +7,7 @@ homepage = 'http://www.jaxfront.org/pages/free_community_edition.html' description = """JAXFront is a technology to generate graphical user interfaces on multiple channels (Java Swing, HTML, PDF) on the basis of an XML schema.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://www.jaxfront.com/download'] sources = [{ diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb index 9ff6f83aaf3..9eb4441b03b 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -7,7 +7,7 @@ homepage = "http://www.fz-juelich.de/jsc/jube" description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, run those sets on different computer systems and evaluate the results.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb index 6a73bae83a7..b8c6d9ff61a 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -7,7 +7,7 @@ homepage = "http://www.fz-juelich.de/jsc/jube" description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, run those sets on different computer systems and evaluate the results.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb index 0d36653ae0e..3ebaf78e1a5 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -7,7 +7,7 @@ homepage = "http://www.fz-juelich.de/jsc/jube" description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, run those sets on different computer systems and evaluate the results.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.10-Java-1.7.0_10.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.10-Java-1.7.0_10.eb index 165cacf2425..fdcb001d148 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.10-Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.10-Java-1.7.0_10.eb @@ -6,7 +6,7 @@ version = '4.10' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%s-%s.jar' % (name.lower(), version)] source_urls = [('http://sourceforge.net/projects/junit/files/junit/%s/' % version, 'download')] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.10-Java-1.7.0_21.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.10-Java-1.7.0_21.eb index 2dd73aa62b4..da04a25f55d 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.10-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.10-Java-1.7.0_21.eb @@ -6,7 +6,7 @@ version = '4.10' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%s-%s.jar' % (name.lower(), version)] source_urls = [('http://sourceforge.net/projects/junit/files/junit/%s/' % version, 'download')] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_15.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_15.eb index 26e0f55b427..6c9eb8773a8 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_15.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_15.eb @@ -6,7 +6,7 @@ version = '4.11' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%s-%s.jar' % (name.lower(), version)] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%s' % version] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_21.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_21.eb index f4ab22bb792..f93557a5f1c 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_21.eb @@ -6,7 +6,7 @@ version = '4.11' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%s-%s.jar' % (name.lower(), version)] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%s/' % version] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_60.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_60.eb index 64746de0537..7377b714cfb 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_60.eb @@ -6,7 +6,7 @@ version = '4.11' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.jar'] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_75.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_75.eb index 73ee3252a1a..caf57434ba6 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_75.eb @@ -6,7 +6,7 @@ version = '4.11' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.jar'] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb index 4c4751893b4..85597bf7afe 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb @@ -6,7 +6,7 @@ version = '4.11' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.jar'] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.7.0_80.eb index c0074dc071d..bbccd1fa18a 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.7.0_80.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.jar'] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_112.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_112.eb index 363163f77e6..01f8058447e 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_112.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.jar'] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb index 43aa70ed7bf..0fc1767adf5 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_121.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.jar'] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_144.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_144.eb index 4d57c600d0e..e2013d4e577 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_144.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_144.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] sources = ['%(namelower)s-%(version)s.jar'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_152.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_152.eb index 84e5ce03793..958469cd188 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_152.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] sources = ['%(namelower)s-%(version)s.jar'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_162.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_162.eb index 9fec2043b04..d17a4fa83db 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_162.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] sources = ['%(namelower)s-%(version)s.jar'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_66.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_66.eb index 5ad39de4e08..2cba499f2f5 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_66.eb @@ -6,7 +6,7 @@ version = '4.12' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.jar'] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_72.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_72.eb index e078225e6a9..1f20ba73010 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_72.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_72.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.jar'] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_77.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_77.eb index 1879fb86c09..ca69bb47e12 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_77.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_77.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.jar'] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_92.eb index f9eed98346b..4177d85e749 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_92.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.jar'] source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb index a98374886f7..d773a1008c5 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb @@ -10,7 +10,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/junit' description = """A programmer-oriented testing framework for Java.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] sources = ['%(namelower)s-%(version)s.jar'] diff --git a/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb b/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb index ec1642238fe..41c29998f9a 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.6.0_24.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_10.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_10.eb index aab1041c12c..014408d3f3e 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_10.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_10.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_15.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_15.eb index 5c86c312a90..800d5289684 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_15.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_15.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_21.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_21.eb index dbfbd849914..389979062f5 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_21.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_21.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_40.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_40.eb index cf9d4f4b74c..149fce85703 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_40.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_40.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb index 3387dbbb89f..43a881fd24b 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_45.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_60.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_60.eb index d635702f022..21295bad832 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_60.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_75.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_75.eb index 72fde0f6bc0..4f8227d8bc0 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_75.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_76.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_76.eb index 7e3b9df3d0c..328645e5ece 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_76.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_76.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb index d7b280abb23..0f23aa31d4d 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb index 9acb602fa14..ef915286cff 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb index 6b87f36815b..f5b943abf3b 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_112.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb index f95da7cf075..bfd432df42e 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_121.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb index 2bb2551e956..9e76c7655f2 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_131.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_141.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_141.eb index 5ecb4ab81cc..eda3b7b86bb 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_141.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_141.eb @@ -8,7 +8,7 @@ description = """ Java applications on desktops and servers. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from # http://www.oracle.com/technetwork/java/javase/downloads/index.html diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_144.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_144.eb index dc8a2bb0a1a..6e302a21580 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_144.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_144.eb @@ -8,7 +8,7 @@ description = """ Java applications on desktops and servers. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from # http://www.oracle.com/technetwork/java/javase/downloads/index.html diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_152.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_152.eb index 738ebc75000..cc40e2d81d7 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_152.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from # http://www.oracle.com/technetwork/java/javase/downloads/index.html diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_162.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_162.eb index ce43b1b3dc8..f84544a084e 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_162.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from # http://www.oracle.com/technetwork/java/javase/downloads/index.html diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_172.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_172.eb index 55753333859..33d081c3d52 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_172.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_172.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from # http://www.oracle.com/technetwork/java/javase/downloads/index.html diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_181.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_181.eb index eadfb3b107d..b0349e483d6 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_181.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_181.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from # http://www.oracle.com/technetwork/java/javase/downloads/index.html diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_192.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_192.eb index d15e1a9e7de..8b2fa280de1 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_192.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_192.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from # http://www.oracle.com/technetwork/java/javase/downloads/index.html diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_20.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_20.eb index 74de18d58ca..553af22fb73 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_20.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_20.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb index 0fbdf71c830..095cf2aeee3 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb @@ -8,7 +8,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from # http://www.oracle.com/technetwork/java/javase/downloads/index.html diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_25.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_25.eb index b2b319db51c..4881ccd0952 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_25.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_25.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_31.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_31.eb index 0ab768fe895..95fc5c1dbce 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_31.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_31.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_40.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_40.eb index f3234cbd872..219190f0f20 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_40.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_40.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb index 50a687a0505..0b282163732 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_60.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_60.eb index 92f4204c591..86e32728f96 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_60.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_60.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_65.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_65.eb index 2e200cf6d29..7157dadf394 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_65.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_65.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_66.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_66.eb index dc31c447d58..e1903b00f05 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_66.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb index 9d370ddcef0..b3fd71593ab 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_72.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb index c9ef30b97ee..3ef093cdf87 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_74.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb index fa48d66cd48..67d0e531403 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_77.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_92.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_92.eb index 4944428be1f..ba7f330f50d 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_92.eb @@ -5,7 +5,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html (vp, vs) = version.split('_') diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.eb b/easybuild/easyconfigs/j/Java/Java-1.8.eb index 353e55e8b14..59a289715f1 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.eb @@ -11,7 +11,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [('Java', '%(version)s.0_202')] diff --git a/easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb b/easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb index ce860f4a217..012fdc39a69 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.9.0.4.eb @@ -8,7 +8,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download the tar.gz directly from # http://www.oracle.com/technetwork/java/javase/downloads/index.html diff --git a/easybuild/easyconfigs/j/Java/Java-11.0.2.eb b/easybuild/easyconfigs/j/Java/Java-11.0.2.eb index c4210cc0d8f..63426e4b195 100644 --- a/easybuild/easyconfigs/j/Java/Java-11.0.2.eb +++ b/easybuild/easyconfigs/j/Java/Java-11.0.2.eb @@ -5,7 +5,7 @@ homepage = 'http://openjdk.java.net' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://download.java.net/java/GA/jdk%(version_major)s/9/GPL/'] sources = ['openjdk-%(version)s_linux-x64_bin.tar.gz'] diff --git a/easybuild/easyconfigs/j/Java/Java-11.eb b/easybuild/easyconfigs/j/Java/Java-11.eb index 6c4c3689409..bcb525e1e7c 100644 --- a/easybuild/easyconfigs/j/Java/Java-11.eb +++ b/easybuild/easyconfigs/j/Java/Java-11.eb @@ -11,7 +11,7 @@ homepage = 'http://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM dependencies = [('Java', '%(version)s.0.2')] diff --git a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb index e619e71cb48..357e3aaf5ec 100644 --- a/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/j/jModelTest/jModelTest-2.1.10r20160303-Java-1.8.0_92.eb @@ -12,7 +12,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/ddarriba/jmodeltest2' description = "jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution." -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/ddarriba/jmodeltest2/archive/'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb b/easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb index 32355d287f7..8cf2980c40c 100644 --- a/easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb +++ b/easybuild/easyconfigs/k/KNIME/KNIME-3.6.2.eb @@ -11,7 +11,7 @@ for creating data science applications and services. KNIME stands for KoNstanz Information MinEr. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://download.knime.org/analytics-platform/linux/'] sources = ['%(namelower)s_%(version)s.linux.gtk.x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20130806-linux.x86_64.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20130806-linux.x86_64.eb index 0decf968d53..27d6b37b423 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20130806-linux.x86_64.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20130806-linux.x86_64.eb @@ -7,7 +7,7 @@ versionsuffix = '-linux.x86_64' homepage = 'http://genome.cse.ucsc.edu/' description = """Kent tools: collection of tools used by the UCSC genome browser.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/, and pack into tarball with: # mkdir Kent_tools diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20171107-linux.x86_64.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20171107-linux.x86_64.eb index 69e526ea3fc..304ab74cf3a 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20171107-linux.x86_64.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20171107-linux.x86_64.eb @@ -7,7 +7,7 @@ versionsuffix = '-linux.x86_64' homepage = 'http://genome.cse.ucsc.edu/' description = """Kent tools: collection of tools used by the UCSC genome browser.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/, and pack into tarball with: # mkdir Kent_tools diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20180716-linux.x86_64.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20180716-linux.x86_64.eb index f01df45df47..4e0206b9411 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20180716-linux.x86_64.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20180716-linux.x86_64.eb @@ -7,7 +7,7 @@ versionsuffix = '-linux.x86_64' homepage = 'http://genome.cse.ucsc.edu/' description = """Kent tools: collection of tools used by the UCSC genome browser.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Check the last modified date at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64 # Then and pack into tarball with: diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb index 9caa766ffab..bfd090d6622 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20190326-linux.x86_64.eb @@ -7,7 +7,7 @@ versionsuffix = '-linux.x86_64' homepage = 'http://genome.cse.ucsc.edu/' description = """Kent tools: collection of tools used by the UCSC genome browser.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Check the last modified date at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64 # Then and pack into tarball with: diff --git a/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6.eb b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6.eb index ac8a96481ef..cfd3246ecfc 100644 --- a/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6.eb +++ b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos6.eb @@ -8,7 +8,7 @@ versionsuffix = '-centos6' homepage = 'http://lstc.com/products/ls-prepost' description = """LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp.lstc.com/anonymous/outgoing/lsprepost/%(version)s/linux64/'] sources = ['lsprepost-%%(version)s_mesa%s-%s.tgz' % (versionsuffix, release_date)] diff --git a/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7.eb b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7.eb index e746e93ebd9..89f18ae16b5 100644 --- a/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7.eb +++ b/easybuild/easyconfigs/l/LS-PrePost/LS-PrePost-4.6-centos7.eb @@ -8,7 +8,7 @@ versionsuffix = '-centos7' homepage = 'http://lstc.com/products/ls-prepost' description = """LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp.lstc.com/anonymous/outgoing/lsprepost/%(version)s/linux64/'] sources = ['lsprepost-%%(version)s_mesa%s-%s.tgz' % (versionsuffix, release_date)] diff --git a/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb index 42320985442..c965be041a3 100644 --- a/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb +++ b/easybuild/easyconfigs/l/LeadIT/LeadIT-2.1.9.eb @@ -10,7 +10,7 @@ version = '2.1.9' homepage = 'http://www.biosolveit.de/LeadIT/index.html' description = """Visually Informed LeadOpt""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # You need to get the software manually from http://www.biosolveit.de/LeadIT/index.html sources = ['leadit-%(version)s-Linux-x64.tar.gz'] diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-6.4.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-6.4.2.eb index 8be10c542cf..2cd101e5c85 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-6.4.2.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-6.4.2.eb @@ -9,7 +9,7 @@ description = """Lmod is a Lua based module system. Modules allow for dynamic mo for a complete description. Lmod is a new implementation that easily handles the MODULEPATH Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(version)s.tar.gz'] source_urls = [ diff --git a/easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb b/easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb index d56882eb941..2b4adfdc0c3 100644 --- a/easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb +++ b/easybuild/easyconfigs/l/Lmod/Lmod-7.3.eb @@ -9,7 +9,7 @@ description = """Lmod is a Lua based module system. Modules allow for dynamic mo for a complete description. Lmod is a new implementation that easily handles the MODULEPATH Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(version)s.tar.gz'] source_urls = [ diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb index 08d864aaf62..d078f1ec05d 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb @@ -11,7 +11,7 @@ description = """Lua is a powerful, fast, lightweight, embeddable scripting lang and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['lua-%s.tar.gz' % version.replace('-', '.')] source_urls = ['http://sourceforge.net/projects/lmod/files/'] diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb index c46350b406a..b3654d23147 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.4.eb @@ -9,7 +9,7 @@ description = """Lua is a powerful, fast, lightweight, embeddable scripting lang and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://www.lua.org/ftp/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb index 825d95f267a..095395661ec 100644 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.5.eb @@ -9,7 +9,7 @@ description = """Lua is a powerful, fast, lightweight, embeddable scripting lang and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://www.%(namelower)s.org/ftp/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb index 6aab03ee448..cc20619975f 100644 --- a/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb +++ b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/chrismattmann/lucene-geo-gazetteer' description = """A command line gazetteer built around the Geonames.org dataset, that uses the Apache Lucene library to create a searchable gazetteer.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/chrismattmann/lucene-geo-gazetteer/archive/'] sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': '6c38272.tar.gz'}] diff --git a/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb b/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb index 5a0206f9503..deb28af5fbf 100644 --- a/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb +++ b/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb @@ -6,7 +6,7 @@ version = '2.0' homepage = 'http://oss.sgi.com/projects/cpusets/' description = "libbitmask provides a convenient, powerful bitmask data type" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['ftp://oss.sgi.com/projects/cpusets/download/'] sources = [SOURCE_TAR_BZ2] diff --git a/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb b/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb index 51fb71266e5..c8baf823ca2 100644 --- a/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb +++ b/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb @@ -6,7 +6,7 @@ version = '1.0' homepage = 'http://oss.sgi.com/projects/cpusets/' description = "libcpuset provides full access to cpuset capabilities" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['ftp://oss.sgi.com/projects/cpusets/download/'] sources = [SOURCE_TAR_BZ2] diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb index 41eaa5ab15c..e4b5bb295d1 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8.eb @@ -8,7 +8,7 @@ description = """The libevent API provides a mechanism to execute a callback fun event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ 'https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/', diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1.eb index a466d743d7b..c80739d1162 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.2.1.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1.eb @@ -11,7 +11,7 @@ description = """ specified by a call interface description at run-time. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM toolchainopts = {'pic': True} source_urls = [ diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.2.58.eb b/easybuild/easyconfigs/l/libpng/libpng-1.2.58.eb index 84633253cb0..f27688fd625 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.2.58.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.2.58.eb @@ -7,7 +7,7 @@ homepage = 'http://www.libpng.org/pub/png/libpng.html' description = "libpng is the official PNG reference library" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb index 141b4c010a1..930d271fe1a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3.eb @@ -9,7 +9,7 @@ description = """The GNU Readline library provides a set of functions for use by The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['readline-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.0.eb index b95217dbd94..44e1e6d5799 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-8.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.0.eb @@ -14,7 +14,7 @@ description = """ previous commands. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM toolchainopts = {'pic': True} source_urls = ['http://ftp.gnu.org/gnu/readline'] diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb index 27ff7d8fd5b..f66e4ba2078 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/libtool' description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb index c04077ae4e0..12404621cea 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.7.eb @@ -15,7 +15,7 @@ version = '0.1.7' homepage = 'http://pyyaml.org/wiki/LibYAML' description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://pyyaml.org/download/libyaml/'] sources = ['yaml-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.1.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.1.eb index 15c25e3a718..add136c0aa4 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.1.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.1.eb @@ -15,7 +15,7 @@ version = '0.2.1' homepage = 'http://pyyaml.org/wiki/LibYAML' description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://pyyaml.org/download/libyaml/'] sources = ['yaml-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16.eb index 8481c86edda..a1969a8a6af 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.16.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16.eb @@ -10,7 +10,7 @@ It is mostly SVR4 compatible although it has some extensions GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb index 17dc7e811fb..6400fa40267 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -12,7 +12,7 @@ description = """ functions for including files, running shell commands, doing arithmetic, etc. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb index 4fe14c3a3af..79f53be742f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -12,7 +12,7 @@ description = """ functions for including files, running shell commands, doing arithmetic, etc. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/MACH/MACH-1.0.18.eb b/easybuild/easyconfigs/m/MACH/MACH-1.0.18.eb index 708d54f1462..69983d3ccd1 100644 --- a/easybuild/easyconfigs/m/MACH/MACH-1.0.18.eb +++ b/easybuild/easyconfigs/m/MACH/MACH-1.0.18.eb @@ -12,7 +12,7 @@ description = """MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://csg.sph.umich.edu/abecasis/MACH/download/'] sources = ['mach.%(version)s.Linux.tgz'] diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb index 2d79a877dec..dc347a2bb89 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2012b.eb @@ -6,7 +6,7 @@ description = """MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2013b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2013b.eb index a43a1a8b756..b5c6e2317ee 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2013b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2013b.eb @@ -6,7 +6,7 @@ description = """MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb index 068032d3106..0e158b5ef76 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb @@ -6,7 +6,7 @@ description = """MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb index 02024eedffa..8627a5ba0e7 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2016a.eb @@ -6,7 +6,7 @@ description = """MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb index 5aa71b404fc..e47c2172ecb 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2017a.eb @@ -6,7 +6,7 @@ description = """MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # be sure to copy both DVD content to the SAME directory, # including the hidden files, especially .dvd1 and .dvd2 diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb index 2f3b02aa9c1..5152f91ac7e 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2018b.eb @@ -6,7 +6,7 @@ description = """MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # be sure to copy both DVD content to the SAME directory, # including the hidden files, especially .dvd1 and .dvd2 diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb index caffaedaa31..82d21db8f85 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'http://www.mathworks.com/supportfiles/MCR_Runtime/%(version)s/', diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb index 4d025dab9a4..662c706d84e 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013b.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb index 67a1f390964..e40e471f630 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2014b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2014b.eb index 1aaf9193508..42e4879d50a 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2014b.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2014b.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb index ccbd003e89a..59faeaa3b98 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2015b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2015b.eb index 02cf05532e7..53a1d1abf9b 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2015b.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2015b.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2016a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2016a.eb index 7314d95a8c3..a543e5a853c 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2016a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2016a.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2016b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2016b.eb index 78ab492fb84..a42c9f967d6 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2016b.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2016b.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2018a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2018a.eb index d527f1b52f1..6519c5f1b59 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2018a.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2018a.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2018b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2018b.eb index c6347f89101..761bc286598 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2018b.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2018b.eb @@ -6,7 +6,7 @@ description = """The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/', diff --git a/easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb b/easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb index 4513c7f7b64..33d584848a9 100644 --- a/easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb +++ b/easybuild/easyconfigs/m/MEGA/MEGA-7.0.20-1.eb @@ -7,7 +7,7 @@ homepage = 'http://www.megasoftware.net/' description = """MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools for statistics-based comparative analysis of molecular sequence data based on evolutionary principles.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download requires agreeing with license & filling out a form, see http://www.megasoftware.net/ sources = ['megacc-%(version)s.x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/m/MEGACC/MEGACC-7.0.18-1.eb b/easybuild/easyconfigs/m/MEGACC/MEGACC-7.0.18-1.eb index 82d928f9029..683487959fb 100644 --- a/easybuild/easyconfigs/m/MEGACC/MEGACC-7.0.18-1.eb +++ b/easybuild/easyconfigs/m/MEGACC/MEGACC-7.0.18-1.eb @@ -16,7 +16,7 @@ homepage = 'http://www.megasoftware.net' description = """MEGA-Computing Core - Sophisticated and user-friendly software suite for analyzing DNA and protein sequence data from species and populations.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.x86_64.tar.gz'] source_urls = ['http://www.megasoftware.net/releases/'] diff --git a/easybuild/easyconfigs/m/MLC/MLC-3.0.eb b/easybuild/easyconfigs/m/MLC/MLC-3.0.eb index 6f9d7320eae..06c086feaba 100644 --- a/easybuild/easyconfigs/m/MLC/MLC-3.0.eb +++ b/easybuild/easyconfigs/m/MLC/MLC-3.0.eb @@ -7,7 +7,7 @@ homepage = 'https://software.intel.com/en-us/articles/intelr-memory-latency-chec description = """Intel Memory Latency Checker (Intel MLC) is a tool used to measure memory latencies and b/w, and how they change with increasing load on the system.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download requires agreeing to license # https://software.intel.com/en-us/articles/intelr-memory-latency-checker#download diff --git a/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb b/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb index c3c02301be7..35d6463aaa0 100644 --- a/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb +++ b/easybuild/easyconfigs/m/MMSEQ/MMSEQ-1.0.8-linux64-static.eb @@ -13,7 +13,7 @@ homepage = 'https://github.com/eturro/mmseq' description = """ The MMSEQ package contains a collection of statistical tools for analysing RNA-seq expression data. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://github.com/eturro/mmseq/archive/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-2.4.2.eb b/easybuild/easyconfigs/m/MPFR/MPFR-2.4.2.eb index 6de1d0207b9..2073f4ef70a 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-2.4.2.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-2.4.2.eb @@ -7,7 +7,7 @@ homepage = 'http://www.mpfr.org' description = """The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-1.0.20180614.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-1.0.20180614.eb index 8b016d2e038..573065b81cd 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-1.0.20180614.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-1.0.20180614.eb @@ -13,7 +13,7 @@ includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://github.com/neurolabusc/MRIcron/releases/download/v%(version)s/'] sources = [ diff --git a/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb b/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb index 733f6228b4e..49e96808e1e 100644 --- a/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb +++ b/easybuild/easyconfigs/m/MRIcron/MRIcron-20150601.eb @@ -13,7 +13,7 @@ includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Automatic Download doesn't work for this software as you need to accept their license, # so you can download it manually at https://www.nitrc.org/frs/download.php/7765/ diff --git a/easybuild/easyconfigs/m/MTL4/MTL4-4.0.8878.eb b/easybuild/easyconfigs/m/MTL4/MTL4-4.0.8878.eb index 0c54cfb6384..bb46bc88be5 100644 --- a/easybuild/easyconfigs/m/MTL4/MTL4-4.0.8878.eb +++ b/easybuild/easyconfigs/m/MTL4/MTL4-4.0.8878.eb @@ -7,7 +7,7 @@ description = """The Matrix Template Library 4 incorporates the most modern prog mathematical notation in MTL4 empowers all engineers and scientists to implement their algorithms and models in minimal time. All technical aspects are encapsulated in the library.""" -toolchain = {'name': "dummy", 'version': "dummy"} +toolchain = SYSTEM source_urls = ['http://www.simunova.com/downloads/mtl4'] sources = ["MTL-all-%s-Linux.tar.gz" % version] diff --git a/easybuild/easyconfigs/m/MTL4/MTL4-4.0.9555.eb b/easybuild/easyconfigs/m/MTL4/MTL4-4.0.9555.eb index 980fa06b14f..02a22b654c1 100644 --- a/easybuild/easyconfigs/m/MTL4/MTL4-4.0.9555.eb +++ b/easybuild/easyconfigs/m/MTL4/MTL4-4.0.9555.eb @@ -7,7 +7,7 @@ description = """The Matrix Template Library 4 incorporates the most modern prog mathematical notation in MTL4 empowers all engineers and scientists to implement their algorithms and models in minimal time. All technical aspects are encapsulated in the library.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://www.simunova.com/downloads/mtl4'] sources = ['MTL-all-%(version)s-Linux.tar.gz'] diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-i86linux64.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-i86linux64.eb index 839544e3dd8..c3995965e51 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-i86linux64.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-i86linux64.eb @@ -18,7 +18,7 @@ description = """MUSCLE is a program for creating multiple alignments of amino a sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://www.drive5.com/muscle/downloads%(version)s'] sources = ['%%(namelower)s%%(version)s_%s.tar.gz' % versionsuffix[1:]] diff --git a/easybuild/easyconfigs/m/Maple/Maple-15.eb b/easybuild/easyconfigs/m/Maple/Maple-15.eb index 94abb4cba4c..0d937408fdd 100644 --- a/easybuild/easyconfigs/m/Maple/Maple-15.eb +++ b/easybuild/easyconfigs/m/Maple/Maple-15.eb @@ -5,7 +5,7 @@ homepage = 'http://www.maplesoft.com/products/maple/' description = """Maple combines the world's most powerful mathematical computation engine with an intuitive, 'clickable' user interface.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%s%sLinuxX86_64Installer.bin' % (name, version)] diff --git a/easybuild/easyconfigs/m/Maple/Maple-2017.2.eb b/easybuild/easyconfigs/m/Maple/Maple-2017.2.eb index 1c83d4243cd..a7020acf020 100644 --- a/easybuild/easyconfigs/m/Maple/Maple-2017.2.eb +++ b/easybuild/easyconfigs/m/Maple/Maple-2017.2.eb @@ -5,7 +5,7 @@ homepage = 'http://www.maplesoft.com/products/maple/' description = """Maple combines the world's most powerful mathematical computation engine with an intuitive, 'clickable' user interface.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [ '%(name)s%(version_major)s.0LinuxX64Installer.run', diff --git a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb index b268eeb1639..bd8bd5efe52 100644 --- a/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb +++ b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb @@ -11,7 +11,7 @@ homepage = 'http://maq.sourceforge.net/maq-man.shtml' description = """Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://sourceforge.net/projects/maq/files/maq/%(version)s/'] sources = ['maq-%(version)s_x86_64-linux.tar.bz2'] diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb index e1bdcca9dab..bf857094218 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb @@ -5,7 +5,7 @@ homepage = 'http://www.wolfram.com/mathematica' description = """Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['Mathematica_%(version)s_LINUX.sh'] diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb index 0093f6a4c2b..75db567be46 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb @@ -5,7 +5,7 @@ homepage = 'http://www.wolfram.com/mathematica' description = """Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['Mathematica_%(version)s_LINUX.sh'] diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb index 9d13deaf533..e7037291899 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.4.1.eb @@ -5,7 +5,7 @@ homepage = 'http://www.wolfram.com/mathematica' description = """Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['Mathematica_%(version)s_LINUX.sh'] diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb index 2afcde55708..a274ff9c5d8 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.0.1.eb @@ -5,7 +5,7 @@ homepage = 'http://www.wolfram.com/mathematica' description = """Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['Mathematica_%(version)s_LINUX.sh'] diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.1.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.1.1.eb index 6bf4ec71713..6fc08df28f7 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.1.1.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.1.1.eb @@ -5,7 +5,7 @@ homepage = 'http://www.wolfram.com/mathematica' description = """Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['Mathematica_%(version)s_LINUX.sh'] checksums = ['80cb3a25337d809bf865e5405cf5975dccf1dcaa20874ee301c98d41011281ce'] diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.3.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.3.0.eb index d3cf561129c..de851117e64 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-11.3.0.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-11.3.0.eb @@ -5,7 +5,7 @@ homepage = 'http://www.wolfram.com/mathematica' description = """Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['Mathematica_%(version)s_LINUX.sh'] checksums = ['0fcfe208c1eac8448e7be3af0bdb84370b17bd9c5d066c013928c8ee95aed10e'] diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb index d78f7e39dfc..3e349754db8 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-12.0.0.eb @@ -5,7 +5,7 @@ homepage = 'http://www.wolfram.com/mathematica' description = """Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['Mathematica_%(version)s_LINUX.sh'] checksums = ['b9fb71e1afcc1d72c200196ffa434512d208fa2920e207878433f504e58ae9d7'] diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb index aafd02cf83c..8a4244b10a3 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb @@ -5,7 +5,7 @@ homepage = 'http://www.wolfram.com/mathematica' description = """Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['Mathematica_%(version)s_LINUX.sh'] diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb b/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb index 8f18c08a6eb..2c53aed0a7c 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.2.3.eb @@ -9,7 +9,7 @@ the concept of a project object model (POM), Maven can manage a project's build, central piece of information. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['apache-maven-%(version)s-bin.tar.gz'] source_urls = ['http://archive.apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb index e4b7cb5e438..409b928b28b 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb @@ -9,7 +9,7 @@ the concept of a project object model (POM), Maven can manage a project's build, central piece of information. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['apache-maven-%(version)s-bin.tar.gz'] source_urls = ['http://archive.apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb b/easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb index f38f753af8b..5f15b32b280 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.3.9.eb @@ -9,7 +9,7 @@ the concept of a project object model (POM), Maven can manage a project's build, central piece of information. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['apache-maven-%(version)s-bin.tar.gz'] source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.5.0.eb b/easybuild/easyconfigs/m/Maven/Maven-3.5.0.eb index cae59a3997c..51241851242 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.5.0.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.5.0.eb @@ -9,7 +9,7 @@ the concept of a project object model (POM), Maven can manage a project's build, central piece of information. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['apache-maven-%(version)s-bin.tar.gz'] source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.5.2.eb b/easybuild/easyconfigs/m/Maven/Maven-3.5.2.eb index 49dadfe05e7..402186a1860 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.5.2.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.5.2.eb @@ -9,7 +9,7 @@ the concept of a project object model (POM), Maven can manage a project's build, central piece of information. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['apache-maven-%(version)s-bin.tar.gz'] source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb b/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb index 384cbea2cf3..7a136218baf 100644 --- a/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb +++ b/easybuild/easyconfigs/m/Maven/Maven-3.6.0.eb @@ -12,7 +12,7 @@ the concept of a project object model (POM), Maven can manage a project's build, central piece of information. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['apache-maven-%(version)s-bin.tar.gz'] source_urls = ['http://archive.apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] diff --git a/easybuild/easyconfigs/m/MetaGeneAnnotator/MetaGeneAnnotator-20080819-x86-64.eb b/easybuild/easyconfigs/m/MetaGeneAnnotator/MetaGeneAnnotator-20080819-x86-64.eb index c2a182a4a91..a4fbbed55ca 100644 --- a/easybuild/easyconfigs/m/MetaGeneAnnotator/MetaGeneAnnotator-20080819-x86-64.eb +++ b/easybuild/easyconfigs/m/MetaGeneAnnotator/MetaGeneAnnotator-20080819-x86-64.eb @@ -7,7 +7,7 @@ versionsuffix = '-x86-64' homepage = 'http://metagene.nig.ac.jp/' description = """MetaGeneAnnotator is a gene-finding program for prokaryote and phage.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://metagene.nig.ac.jp/metagene/'] sources = ['mga_x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.8-Java-1.8.0_162.eb b/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.8-Java-1.8.0_162.eb index 905fc1b337e..5bd447930c0 100644 --- a/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.8-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.8-Java-1.8.0_162.eb @@ -13,7 +13,7 @@ homepage = 'https://milaboratory.com/software/migec/' description = """ MIGEC is a software pipeline that facilitates processing and analysis of immune repertoire sequencing data generated using molecular barcoding technique""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/mikessh/migec/releases/download/%(version)s/'] sources = ['%(namelower)s-%(version)s.zip'] diff --git a/easybuild/easyconfigs/m/MiXCR/MiXCR-2.1.9-Java-1.8.0_162.eb b/easybuild/easyconfigs/m/MiXCR/MiXCR-2.1.9-Java-1.8.0_162.eb index 715d229004c..cc848c1e83a 100644 --- a/easybuild/easyconfigs/m/MiXCR/MiXCR-2.1.9-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/m/MiXCR/MiXCR-2.1.9-Java-1.8.0_162.eb @@ -13,7 +13,7 @@ homepage = 'https://milaboratory.com/software/mixcr/' description = """ MiXCR processes big immunome data from raw sequences to quantitated clonotypes """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/milaboratory/mixcr/releases/download/v%(version)s/'] sources = ['%(namelower)s-%(version)s.zip'] diff --git a/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb index 033d561b738..864fd64611c 100644 --- a/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb +++ b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb @@ -13,7 +13,7 @@ homepage = 'https://milaboratory.com/software/mixcr/' description = """ MiXCR processes big immunome data from raw sequences to quantitated clonotypes """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/milaboratory/mixcr/releases/download/v%(version)s/'] sources = ['%(namelower)s-%(version)s.zip'] diff --git a/easybuild/easyconfigs/m/Miniconda2/Miniconda2-4.3.21.eb b/easybuild/easyconfigs/m/Miniconda2/Miniconda2-4.3.21.eb index a5ae211a5c5..af743809ef5 100644 --- a/easybuild/easyconfigs/m/Miniconda2/Miniconda2-4.3.21.eb +++ b/easybuild/easyconfigs/m/Miniconda2/Miniconda2-4.3.21.eb @@ -9,7 +9,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/miniconda/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.4.10.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.4.10.eb index d3d4eeee7ee..f683fe223e5 100644 --- a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.4.10.eb +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.4.10.eb @@ -9,7 +9,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/miniconda/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.5.12.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.5.12.eb index 0565a5cfa43..837822d9dcc 100644 --- a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.5.12.eb +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.5.12.eb @@ -9,7 +9,7 @@ the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://repo.continuum.io/miniconda/'] sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] diff --git a/easybuild/easyconfigs/m/Molcas/Molcas-8.0-15.06.18_CentOS_6.6_x86_64.eb b/easybuild/easyconfigs/m/Molcas/Molcas-8.0-15.06.18_CentOS_6.6_x86_64.eb index 2bf90d3dc11..a1890e6d645 100644 --- a/easybuild/easyconfigs/m/Molcas/Molcas-8.0-15.06.18_CentOS_6.6_x86_64.eb +++ b/easybuild/easyconfigs/m/Molcas/Molcas-8.0-15.06.18_CentOS_6.6_x86_64.eb @@ -12,7 +12,7 @@ atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download requires registration, see http://www.kvant.kemi.uu.se/molcas/ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] diff --git a/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-mkl-par.eb b/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-mkl-par.eb index 5bcbc9e8202..abf2a02008a 100644 --- a/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-mkl-par.eb +++ b/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-mkl-par.eb @@ -12,7 +12,7 @@ atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download requires registration, see http://www.molcas.org/download.html sources = ['%(namelower)s%(version_major)s%(version_minor)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-par.eb b/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-par.eb index 14ca91925d8..fa32092f796 100644 --- a/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-par.eb +++ b/easybuild/easyconfigs/m/Molcas/Molcas-8.2-centos-par.eb @@ -12,7 +12,7 @@ atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download requires registration, see http://www.molcas.org/download.html sources = ['%(namelower)s%(version_major)s%(version_minor)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb index 51f747c203e..e96428a58de 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb @@ -6,7 +6,7 @@ versionsuffix = '.Linux_x86_64' homepage = 'https://www.molpro.net' description = """Molpro is a complete system of ab initio programs for molecular electronic structure calculations.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # no source URL available, requires registration to download sources = ['%(namelower)s-%(versionprefix)s%(version)s%(versionsuffix)s.sh'] diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb index 678309eb8a1..c72b8ac8356 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb @@ -6,7 +6,7 @@ versionsuffix = '.linux_x86_64_intel' homepage = 'https://www.molpro.net' description = """Molpro is a complete system of ab initio programs for molecular electronic structure calculations.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # no source URL available, requires registration to download sources = ['%(namelower)s-%(versionprefix)s%(version)s%(versionsuffix)s.sh'] diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb index b2738fff577..798e86b8e78 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb @@ -6,7 +6,7 @@ versionsuffix = '.linux_x86_64_openmp' homepage = 'https://www.molpro.net' description = """Molpro is a complete system of ab initio programs for molecular electronic structure calculations.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # no source URL available, requires registration to download sources = ['%(namelower)s-%(versionprefix)s%(version)s%(versionsuffix)s.sh'] diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb index 3639fc72f42..cd73432ef79 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb @@ -6,7 +6,7 @@ versionsuffix = '.linux_x86_64_openmp' homepage = 'https://www.molpro.net' description = """Molpro is a complete system of ab initio programs for molecular electronic structure calculations.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # no source URL available, requires registration to download sources = ['%(namelower)s-%(versionprefix)s%(version)s%(versionsuffix)s.sh'] diff --git a/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb index 5d4a7d1a7d7..179790d7f2d 100644 --- a/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb +++ b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb @@ -5,7 +5,7 @@ homepage = 'http://mono-framework.com' description = """An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://download.mono-project.com/sources/mono/'] sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb index 025271c90bc..fbede353227 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb @@ -13,7 +13,7 @@ description = """ MuTect is a method developed at the Broad Institute for the re and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] sources = ['muTect-%(version)s-bin.zip'] diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb index 46a5db5d00f..358c06031ef 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb @@ -17,7 +17,7 @@ description = """ MuTect is a method developed at the Broad Institute for the re and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # Need to be logged in to download, at this URL # http://www.broadinstitute.org/cancer/cga/mutect_download diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb index e09b7d71286..c1a535e7ba1 100644 --- a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.7-Java-1.7.0_80.eb @@ -17,7 +17,7 @@ description = """ MuTect is a method developed at the Broad Institute for the re and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # Need to be logged in to download, at this URL # and to click the checkbox to agree to the licence diff --git a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb index 0d549f79770..41a93ccc2f1 100644 --- a/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb +++ b/easybuild/easyconfigs/m/meRanTK/meRanTK-1.1.1b.eb @@ -17,7 +17,7 @@ version = '1.1.1b' homepage = 'http://www.icbi.at/index.html' description = """meRanTK is a versatile high performance toolkit for complete analysis of methylated RNA data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://www.icbi.at/software/meRanTK/downloads/%(version)s/'] sources = ['meRanTK-%(version)s.zip'] diff --git a/easybuild/easyconfigs/n/NAGfor/NAGfor-6.2.14.eb b/easybuild/easyconfigs/n/NAGfor/NAGfor-6.2.14.eb index 16ca74a12a6..5f50ca59af2 100644 --- a/easybuild/easyconfigs/n/NAGfor/NAGfor-6.2.14.eb +++ b/easybuild/easyconfigs/n/NAGfor/NAGfor-6.2.14.eb @@ -6,7 +6,7 @@ version = '6.2.14' homepage = 'http://www.nag.co.uk' description = """The checking compiler for improved code portability and detailed error reporting.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [{ 'source_urls': ['https://www.nag.co.uk/downloads/impl'], diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.1.4-CUDA-9.0.176.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.1.4-CUDA-9.0.176.eb index c4faf8f3182..ff0334fa07f 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.1.4-CUDA-9.0.176.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.1.4-CUDA-9.0.176.eb @@ -9,7 +9,7 @@ homepage = 'https://developer.nvidia.com/nccl' description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # Sources can be downloaded from https://developer.nvidia.com/nccl/nccl-download but need membership sources = ['%%(namelower)s_%%(version)s-1+cuda%s_x86_64.txz' % '.'.join(cuda_version.split('.')[0:2])] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.2.13-CUDA-9.2.148.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.2.13-CUDA-9.2.148.1.eb index 20b8b40445b..333c75b2cb3 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.2.13-CUDA-9.2.148.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.2.13-CUDA-9.2.148.1.eb @@ -9,7 +9,7 @@ homepage = 'https://developer.nvidia.com/nccl' description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # Download from https://developer.nvidia.com/nccl/nccl-download (after log in) sources = ['%%(namelower)s_%%(version)s-1+cuda%s_x86_64.txz' % '.'.join(cuda_version.split('.')[0:2])] diff --git a/easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb b/easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb index e439135d325..88ab85475a3 100644 --- a/easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb +++ b/easybuild/easyconfigs/n/Net-core/Net-core-2.1.8.eb @@ -12,7 +12,7 @@ homepage = 'https://dotnet.microsoft.com/' description = """.NET Core is a free and open-source managed computer software framework for the Windows, Linux, and macOS operating systems .NET Core fully supports C# and F# and partially supports Visual Basic""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [ 'https://download.visualstudio.microsoft.com/download/pr/' + diff --git a/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb index bd778d69d8b..c8e0d8d9e26 100644 --- a/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb +++ b/easybuild/easyconfigs/n/NetLogo/NetLogo-5.3.1-64.eb @@ -12,7 +12,7 @@ and developed at the CCL.""" # NetLogo is precompiled and needs no particular toolchain. # It even comes with its own Java. -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ccl.northwestern.edu/netlogo/%(version)s/'] sources = ['%(name)s-%(version)s%(versionsuffix)s.tgz'] diff --git a/easybuild/easyconfigs/n/NetLogo/NetLogo-6.0.4-64.eb b/easybuild/easyconfigs/n/NetLogo/NetLogo-6.0.4-64.eb index 7b0edcdf28c..e2a67f9be95 100644 --- a/easybuild/easyconfigs/n/NetLogo/NetLogo-6.0.4-64.eb +++ b/easybuild/easyconfigs/n/NetLogo/NetLogo-6.0.4-64.eb @@ -12,7 +12,7 @@ and developed at the CCL.""" # NetLogo is precompiled and needs no particular toolchain. # It even comes with its own Java. -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ccl.northwestern.edu/netlogo/%(version)s/'] sources = ['%(name)s-%(version)s%(versionsuffix)s.tgz'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb index 5ff49255844..4c737da9890 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb @@ -10,7 +10,7 @@ homepage = 'https://www.nextflow.io/' description = """Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/'] sources = ['%(namelower)s-%(version)s-all'] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 297893f8db0..896822a9f66 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -8,7 +8,7 @@ description = """The Ncurses (new curses) library is a free software emulation o and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 8b68569a0e3..f620dae390a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -8,7 +8,7 @@ description = """The Ncurses (new curses) library is a free software emulation o and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb index 8e9c00a9c69..f48fba6d8b3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb @@ -8,7 +8,7 @@ description = """The Ncurses (new curses) library is a free software emulation o and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb b/easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb index 6de3a9692db..5cf8e1384e9 100644 --- a/easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb +++ b/easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC' description = """ NetMHC 4.0 software predicts binding of peptides to a number of different HLA alleles using artificial neural networks (ANN). """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # netMHC is proprietary software, but free for academcs # see: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC diff --git a/easybuild/easyconfigs/n/netMHCpan/netMHCpan-4.0a.eb b/easybuild/easyconfigs/n/netMHCpan/netMHCpan-4.0a.eb index 2ddc841c500..7cda16cb513 100644 --- a/easybuild/easyconfigs/n/netMHCpan/netMHCpan-4.0a.eb +++ b/easybuild/easyconfigs/n/netMHCpan/netMHCpan-4.0a.eb @@ -7,7 +7,7 @@ homepage = 'http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan' description = """ The NetMHCpan software predicts binding of peptides to any known MHC molecule using artificial neural networks (ANNs). """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # netMHCpan is proprietary software, but free for academcs # see: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan diff --git a/easybuild/easyconfigs/n/novoalign/novoalign-3.09.00.eb b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.00.eb index 5657ffa81e6..8ce342800e2 100644 --- a/easybuild/easyconfigs/n/novoalign/novoalign-3.09.00.eb +++ b/easybuild/easyconfigs/n/novoalign/novoalign-3.09.00.eb @@ -14,7 +14,7 @@ homepage = 'http://www.novocraft.com/products/novoalign/' description = """Map short reads onto a reference genome from Illumina, Ion Torrent, and 454 next generation sequencing platforms""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Download manually from http://www.novocraft.com/support/download/ # source_urls = ['http://www.novocraft.com/support/download/download.php?filename=V(%version)s/'] diff --git a/easybuild/easyconfigs/o/OMA/OMA-2.1.1.eb b/easybuild/easyconfigs/o/OMA/OMA-2.1.1.eb index 927df51cf86..e5e78e70317 100644 --- a/easybuild/easyconfigs/o/OMA/OMA-2.1.1.eb +++ b/easybuild/easyconfigs/o/OMA/OMA-2.1.1.eb @@ -12,7 +12,7 @@ homepage = 'https://omabrowser.org/standalone/' description = """The OMA ('Orthologous MAtrix') project is a method and database for the inference of orthologs among complete genomes""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://omabrowser.org/standalone/'] sources = ['%(name)s.%(version)s.tgz'] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb index 95182fb7f63..ac435adab22 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-2_9_1-linux_x86-64.eb @@ -10,7 +10,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb index a2fb635e480..7e93129deb3 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_0-linux_x86-64_openmpi_165.eb @@ -11,7 +11,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb index b51b51028cf..81eb3c551e1 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64-OpenMPI-1.8.1.eb @@ -13,7 +13,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb index 9cd49048acd..f7583301a32 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_2-linux_x86-64.eb @@ -10,7 +10,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb index 82c2d0b54b3..7e441f102d4 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-3_0_3-linux_x86-64.eb @@ -10,7 +10,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%%(namelower)s_%s_%s.tbz' % (version.split('-')[0], '-'.join(version.split('-')[1:]))] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb index 20a5faa3973..b6231dd084f 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb @@ -13,7 +13,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # Download from https://cec.mpg.de/orcadownload/index.php sources = ['%%(namelower)s_%s_linux_x86-64_openmpi%s.tbz' % (version.replace('.', '_'), ompi_ver.replace('.', ''))] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb index b28cb7f1c00..5a7b7ac9313 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb @@ -13,7 +13,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # Download from https://cec.mpg.de/orcadownload/index.php sources = ['%%(namelower)s_%s_linux_x86-64_openmpi%s.tar.xz' % (version.replace('.', '_'), ompi_ver.replace('.', ''))] diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.1.0-OpenMPI-3.1.3.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.1.0-OpenMPI-3.1.3.eb index 63707b48c63..6a3371c51e0 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.1.0-OpenMPI-3.1.3.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.1.0-OpenMPI-3.1.3.eb @@ -13,7 +13,7 @@ description = """ORCA is a flexible, efficient and easy-to-use general purpose t and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # Download from https://orcaforum.kofo.mpg.de sources = ['%%(namelower)s_%s_linux_x86-64_openmpi%s.tar.xz' % (version.replace('.', '_'), ompi_ver.replace('.', ''))] diff --git a/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb b/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb index 19f1ce98bb1..cf4351f1b79 100644 --- a/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb +++ b/easybuild/easyconfigs/o/OpenNLP/OpenNLP-1.8.1.eb @@ -7,7 +7,7 @@ homepage = 'https://opennlp.apache.org/' description = """The Apache OpenNLP library is a machine learning based toolkit for the processing of natural language text.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [APACHE_SOURCE + '/%(namelower)s-%(version)s'] sources = ['apache-opennlp-%(version)s-src.tar.gz'] diff --git a/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb index 43fc8d1f704..ff54cc30a4b 100644 --- a/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb +++ b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb @@ -8,7 +8,7 @@ homepage = 'https://github.com/OpenRefine/OpenRefine' description = """OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, and augment it with data coming from the web.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/OpenRefine/OpenRefine/archive/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/p/PCC/PCC-20131024.eb b/easybuild/easyconfigs/p/PCC/PCC-20131024.eb index ed87db57299..b684e54273a 100644 --- a/easybuild/easyconfigs/p/PCC/PCC-20131024.eb +++ b/easybuild/easyconfigs/p/PCC/PCC-20131024.eb @@ -16,7 +16,7 @@ homepage = 'http://pcc.ludd.ltu.se/' description = """The compiler is based on the original Portable C Compiler by S. C. Johnson, written in the late 70's. About 50% of the frontend code and 80% of the backend code has been modified.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # eg. http://pcc.ludd.ltu.se/ftp/pub/pcc/2013/pcc-20131024.tgz sources = ['pcc-%(version)s.tgz'] diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb index 6c18c7665d9..53475269537 100644 --- a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb @@ -12,7 +12,7 @@ versionsuffix = "-Java-%(javaver)s" homepage = 'http://cmpg.unibe.ch/software/PGDSpider/' description = """An automated data conversion tool for connecting population genetics and genomics programs""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://cmpg.unibe.ch/software/PGDSpider/'] sources = ['%(name)s_%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb index 9c72ac2b2d3..5a3a7a62645 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.10-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '15.10' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb index 13e9f7b5d75..ebf15495778 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.2-2.25.eb @@ -4,7 +4,7 @@ version = '15.7' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb index 7e8ea9120da..d480b5992ac 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-15.7-GNU-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '15.7' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.1-CDK-GCC-4.9.2-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.1-CDK-GCC-4.9.2-2.25.eb index 1d1a323c11a..0273916834b 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.1-CDK-GCC-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.1-CDK-GCC-4.9.2-2.25.eb @@ -4,7 +4,7 @@ version = '16.1' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgicdk-%(version_major)s%(version_minor)s.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.10-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/PGI/PGI-16.10-GCC-5.4.0-2.26.eb index 29aaf5fc97c..14dc1868242 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.10-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.10-GCC-5.4.0-2.26.eb @@ -4,7 +4,7 @@ version = '16.10' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb index 5f199caad47..75deffb03bb 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.3-GCC-4.9.3-2.25.eb @@ -4,7 +4,7 @@ version = '16.3' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb b/easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb index 500d36d203f..9d1a77e6ae4 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.4-GCC-5.3.0-2.26.eb @@ -4,7 +4,7 @@ version = '16.4' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/PGI/PGI-16.7-GCC-5.4.0-2.26.eb index bbb7bebfc8c..3281fbf2cd9 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-16.7-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-16.7-GCC-5.4.0-2.26.eb @@ -4,7 +4,7 @@ version = '16.7' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb b/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb index 6c0267bb0a0..221c03ce47e 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-17.1-GCC-6.3.0-2.27.eb @@ -4,7 +4,7 @@ version = '17.1' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-17.10-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PGI/PGI-17.10-GCC-6.4.0-2.28.eb index 944ddd82ba5..6bae462053a 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-17.10-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-17.10-GCC-6.4.0-2.28.eb @@ -4,7 +4,7 @@ version = '17.10' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb b/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb index b676f02d53d..335b3213260 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-17.3-GCC-6.3.0-2.28.eb @@ -4,7 +4,7 @@ version = '17.3' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-17.4-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PGI/PGI-17.4-GCC-6.4.0-2.28.eb index 2ad5bad5428..88c804e4c9a 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-17.4-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-17.4-GCC-6.4.0-2.28.eb @@ -4,7 +4,7 @@ version = '17.4' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86_64.tar.gz'] checksums = ['115c212d526695fc116fe44f1e722793e60b6f7d1b341cd7e77a95da8e7f6c34'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-18.1-GCC-7.2.0-2.29.eb b/easybuild/easyconfigs/p/PGI/PGI-18.1-GCC-7.2.0-2.29.eb index ab4492f013d..6e65db72657 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-18.1-GCC-7.2.0-2.29.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-18.1-GCC-7.2.0-2.29.eb @@ -4,7 +4,7 @@ version = '18.1' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # needs to be downloaded manually, see http://www.pgroup.com/support/release_archive.php sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86-64.tar.gz'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-18.10-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PGI/PGI-18.10-GCC-6.4.0-2.28.eb index 0e5d5162924..bfad036209e 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-18.10-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-18.10-GCC-6.4.0-2.28.eb @@ -4,7 +4,7 @@ version = '18.10' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86-64.tar.gz'] checksums = ['4b3ff83d2a13de6001bed599246eff8e63ef711b8952d4a9ee12efd666b3e326'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-18.4-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/p/PGI/PGI-18.4-GCC-6.4.0-2.28.eb index 7dbed209fb7..b7a92ad3773 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-18.4-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-18.4-GCC-6.4.0-2.28.eb @@ -4,7 +4,7 @@ version = '18.4' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86-64.tar.gz'] checksums = ['81e0dcf6000b026093ece180d42d77854c23269fb8409cedcf51c674ca580a0f'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-18.7-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/p/PGI/PGI-18.7-GCC-7.3.0-2.30.eb index 90367654d0e..1beaea9ae39 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-18.7-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-18.7-GCC-7.3.0-2.30.eb @@ -4,7 +4,7 @@ version = '18.7' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86-64.tar.gz'] checksums = ['d97225585127b841075576859fc7782c9dbe3f7e1569bbce5f465046d4679d8d'] diff --git a/easybuild/easyconfigs/p/PGI/PGI-19.1-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/p/PGI/PGI-19.1-GCC-8.2.0-2.31.1.eb index 72262bb10c0..b04f45d5614 100644 --- a/easybuild/easyconfigs/p/PGI/PGI-19.1-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/p/PGI/PGI-19.1-GCC-8.2.0-2.31.1.eb @@ -4,7 +4,7 @@ version = '19.1' homepage = 'http://www.pgroup.com/' description = "C, C++ and Fortran compilers from The Portland Group - PGI" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['pgilinux-20%(version_major)s-%(version_major)s%(version_minor)s-x86-64.tar.gz'] checksums = ['3e05a6db2bf80b5d15f6ff83188f20cb89dc23e233417921e5c0822e7e57d34f'] diff --git a/easybuild/easyconfigs/p/PHASE/PHASE-2.1.1.eb b/easybuild/easyconfigs/p/PHASE/PHASE-2.1.1.eb index d018f814f23..632096ced4b 100644 --- a/easybuild/easyconfigs/p/PHASE/PHASE-2.1.1.eb +++ b/easybuild/easyconfigs/p/PHASE/PHASE-2.1.1.eb @@ -12,7 +12,7 @@ description = """ The program PHASE implements a Bayesian statistical method for reconstructing haplotypes from population genotype data. Documentation: http://stephenslab.uchicago.edu/assets/software/phase/instruct2.1.pdf""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://stephenslab.uchicago.edu/assets/software/phase/phasecode/'] sources = ['phase.%(version)s.linux.tar.gz'] diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb index f2b5d4628b9..f63d4b314c0 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb @@ -6,7 +6,7 @@ version = '1.07-x86_64' homepage = 'http://zzz.bwh.harvard.edu/plink/dist' description = 'plink-1.07-src: Whole-genome association analysis toolset' -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s.zip'] source_urls = ['http://zzz.bwh.harvard.edu/plink/dist'] diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb index 1454e1f4986..2da38ad650e 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b_4.1-x86_64.eb @@ -6,7 +6,7 @@ version = '1.9b_4.1-x86_64' homepage = 'https://www.cog-genomics.org/plink/1.9/' description = 'plink-1.9-x86_64: Whole-genome association analysis toolset' -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['plink_linux_x86_64.zip'] source_urls = ['https://www.cog-genomics.org/static/bin/plink170330/'] diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00-alpha1-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00-alpha1-x86_64.eb index e2f3d3f5340..23677955bfb 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-2.00-alpha1-x86_64.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00-alpha1-x86_64.eb @@ -6,7 +6,7 @@ version = '2.00-alpha1-x86_64' homepage = 'https://www.cog-genomics.org/plink/1.9/' description = 'Whole-genome association analysis toolset' -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://s3.amazonaws.com/plink2-assets/alpha1/'] sources = ['plink2_linux_x86_64.zip'] diff --git a/easybuild/easyconfigs/p/PPfold/PPfold-3.1.1-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/PPfold/PPfold-3.1.1-Java-1.8.0_66.eb index 952aab37b92..43fdd202985 100644 --- a/easybuild/easyconfigs/p/PPfold/PPfold-3.1.1-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/p/PPfold/PPfold-3.1.1-Java-1.8.0_66.eb @@ -9,7 +9,7 @@ description = """PPfold is a new implementation of pfold, written in Java 6.0. I It can also use data from chemical probing experiments to predict RNA secondary structure. PPfold is multithreaded, and can solve the structure of much longer alignments than pfold.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.daimi.au.dk/~compbio/pfold/PPfold/'] sources = ['PPfold%(version)s.jar'] diff --git a/easybuild/easyconfigs/p/Pandoc/Pandoc-2.1.3.eb b/easybuild/easyconfigs/p/Pandoc/Pandoc-2.1.3.eb index 5806fbc2abf..1b67251149a 100644 --- a/easybuild/easyconfigs/p/Pandoc/Pandoc-2.1.3.eb +++ b/easybuild/easyconfigs/p/Pandoc/Pandoc-2.1.3.eb @@ -11,7 +11,7 @@ version = '2.1.3' homepage = 'http://pandoc.org' description = "If you need to convert files from one markup format into another, pandoc is your swiss-army knife" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/jgm/pandoc/releases/download/%(version)s/'] sources = ['%(name)s-%(version)s-linux.tar.gz'] diff --git a/easybuild/easyconfigs/p/Pandoc/Pandoc-2.5.eb b/easybuild/easyconfigs/p/Pandoc/Pandoc-2.5.eb index ae750904ec6..48402ff7bdf 100644 --- a/easybuild/easyconfigs/p/Pandoc/Pandoc-2.5.eb +++ b/easybuild/easyconfigs/p/Pandoc/Pandoc-2.5.eb @@ -11,7 +11,7 @@ version = '2.5' homepage = 'http://pandoc.org' description = "If you need to convert files from one markup format into another, pandoc is your swiss-army knife" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/jgm/pandoc/releases/download/%(version)s/'] sources = ['%(name)s-%(version)s-linux.tar.gz'] diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_162.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_162.eb index ded1fcad458..551e41de9b2 100644 --- a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.0_162.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/broadinstitute/pilon' description = " Pilon is an automated genome assembly improvement and variant detection tool" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(version)s/'] sources = ['%(namelower)s-%(version)s.jar'] diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.eb index 5469cd44e5b..940bf88bcdb 100644 --- a/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.eb +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.22-Java-1.8.eb @@ -12,7 +12,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/broadinstitute/pilon' description = "Pilon is an automated genome assembly improvement and variant detection tool" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(version)s/'] sources = ['%(namelower)s-%(version)s.jar'] diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb index 30ce452926f..3cf1555fe1d 100644 --- a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-1.8.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/broadinstitute/pilon' description = " Pilon is an automated genome assembly improvement and variant detection tool" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(version)s/'] sources = ['%(namelower)s-%(version)s.jar'] diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb index 2fa31617c3e..dec8e3e2d34 100644 --- a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb @@ -7,7 +7,7 @@ versionsuffix = '-linux-x86_64' homepage = 'http://platanus.bio.titech.ac.jp/' description = """PLATform for Assembling NUcleotide Sequences""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201'] sources = ['platanus'] diff --git a/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb b/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb index 4c23222ada7..67496a580d5 100644 --- a/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb +++ b/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb @@ -7,7 +7,7 @@ homepage = "http://www.genabel.org/packages/ProbABEL" description = """Tool for genome-wide association analysis of imputed genetic data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://www.genabel.org/sites/default/files/software/'] sources = ['probabel-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb index 5b238210ee0..e146802ebe4 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.12.eb @@ -6,7 +6,7 @@ version = '3.12' homepage = "https://pypi.python.org/pypi/PyYAML/" description = """PyYAML is a YAML parser and emitter for the Python programming language.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13.eb index f2eb2df97c4..7cf219e6596 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.13.eb @@ -6,7 +6,7 @@ version = '3.13' homepage = "https://pypi.python.org/pypi/PyYAML/" description = """PyYAML is a YAML parser and emitter for the Python programming language.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb index 082cc254b85..81224726d5c 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb @@ -7,7 +7,7 @@ homepage = 'http://p7zip.sourceforge.net/' description = """p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = ['p7zip_%(version)s_src_all.tar.bz2'] diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0.eb index e0b6cd1a17e..df5ad3717f0 100644 --- a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0.eb +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0.eb @@ -9,7 +9,7 @@ description = """The pbs_python package is a wrapper class for the Torque C libr an ascii version named pbsmon. PBSQuery is also included in this package. This is a python module build on top of the pbs python module to simplify querying the batch server, eg: how many jobs, how many nodes, ...""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://ftp.sara.nl/pub/outgoing/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb b/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb index 2b1fc2a612a..73fc68b6fb7 100644 --- a/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb +++ b/easybuild/easyconfigs/p/perl-app-cpanminus/perl-app-cpanminus-1.7039.eb @@ -19,7 +19,7 @@ variant = "Linux-x86_64" homepage = 'https://github.com/miyagawa/cpanminus' description = """ cpanm - get, unpack build and install modules from CPAN """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM requirements = "%(name)s=%(version)s" channels = ['bioconda', 'conda-forge'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.100.eb b/easybuild/easyconfigs/p/picard/picard-1.100.eb index aa4b9cb85c3..a621e220290 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.100.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.100.eb @@ -4,7 +4,7 @@ version = '1.100' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.109.eb b/easybuild/easyconfigs/p/picard/picard-1.109.eb index 054ac53148a..22432c8cdec 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.109.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.109.eb @@ -4,7 +4,7 @@ version = '1.109' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb index 0d8e511c3f7..2206600ac42 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb @@ -4,7 +4,7 @@ version = '1.119' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.119.eb b/easybuild/easyconfigs/p/picard/picard-1.119.eb index b8822ebb221..e89e995b8af 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.119.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.119.eb @@ -4,7 +4,7 @@ version = '1.119' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb index 6e8d731733d..2fcab9293b1 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.120-Java-1.8.0_66.eb @@ -5,7 +5,7 @@ homepage = 'http://broadinstitute.github.io/picard/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb index a7d48bf6b0b..86c019c9a9a 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.141-Java-1.8.0_74.eb @@ -5,7 +5,7 @@ homepage = 'http://broadinstitute.github.io/picard/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-1.39.eb b/easybuild/easyconfigs/p/picard/picard-1.39.eb index 3f179ac9b7e..73e0a6e2dfb 100644 --- a/easybuild/easyconfigs/p/picard/picard-1.39.eb +++ b/easybuild/easyconfigs/p/picard/picard-1.39.eb @@ -4,7 +4,7 @@ version = '1.39' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb index 1d6200df1a1..2f8e9f2db97 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.0.1-Java-1.8.0_66.eb @@ -5,7 +5,7 @@ homepage = 'http://broadinstitute.github.io/picard/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb index 80d1371c6d9..19ea7960c7f 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.0-Java-1.8.0_74.eb @@ -5,7 +5,7 @@ homepage = 'http://broadinstitute.github.io/picard/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.0.eb b/easybuild/easyconfigs/p/picard/picard-2.1.0.eb index 9cc6b0c56aa..d24095f14a7 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.0.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.0.eb @@ -10,7 +10,7 @@ description = """ A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/%(name)s/releases/download/%(version)s'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb index c0f8364e0a9..3540e80ef09 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb @@ -6,7 +6,7 @@ homepage = 'http://broadinstitute.github.io/picard/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb index 0e3b3995917..2a0c6309cea 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_74.eb @@ -6,7 +6,7 @@ homepage = 'http://broadinstitute.github.io/picard/' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s/'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb b/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb index c43fee9ce0f..f2e0de142f3 100755 --- a/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.10.1-Java-1.8.0_131.eb @@ -21,7 +21,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] sources = [{ diff --git a/easybuild/easyconfigs/p/picard/picard-2.18.11-Java-1.8.0_162.eb b/easybuild/easyconfigs/p/picard/picard-2.18.11-Java-1.8.0_162.eb index e4b1253826e..88a351534de 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.18.11-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.18.11-Java-1.8.0_162.eb @@ -25,7 +25,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] sources = [{ diff --git a/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb b/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb index 14037c83061..ad1bce59ad9 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb @@ -25,7 +25,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] sources = [{ diff --git a/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb b/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb index 8653a96e9f1..570181a5407 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb @@ -25,7 +25,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] sources = [{ diff --git a/easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb b/easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb index 7db9240a7af..c4498a6ed35 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.18.27-Java-1.8.eb @@ -25,7 +25,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] sources = [{ diff --git a/easybuild/easyconfigs/p/picard/picard-2.18.5-Java-1.8.0_162.eb b/easybuild/easyconfigs/p/picard/picard-2.18.5-Java-1.8.0_162.eb index 77151757310..c87f02fae65 100755 --- a/easybuild/easyconfigs/p/picard/picard-2.18.5-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.18.5-Java-1.8.0_162.eb @@ -21,7 +21,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] sources = [{ diff --git a/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_92.eb index 291785d9354..fd8f5e41d00 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.2.4-Java-1.8.0_92.eb @@ -14,7 +14,7 @@ version = '2.2.4' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] sources = ['%(name)s-tools-%(version)s.zip'] diff --git a/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb b/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb index 69a4a7e6bb2..d159a4a40bb 100755 --- a/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.6.0-Java-1.8.0_131.eb @@ -20,7 +20,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://sourceforge.net/projects/picard' description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] sources = ['%(name)s.jar'] diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb index 2bc0b18247f..46d7ee378a4 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb @@ -13,7 +13,7 @@ description = """ libraries). """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://pkg-config.freedesktop.org/releases/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb b/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb index 6b7d80bf525..aeedcc6493a 100644 --- a/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb +++ b/easybuild/easyconfigs/p/pomkl/pomkl-2016.03.eb @@ -6,7 +6,7 @@ version = '2016.03' homepage = 'http://www.pgroup.com/index.htm' description = """Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '16.3' gccsuff = '-GCC-4.9.3-2.25' diff --git a/easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb b/easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb index 1c27eb79621..1badefc01ff 100644 --- a/easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb +++ b/easybuild/easyconfigs/p/pomkl/pomkl-2016.04.eb @@ -6,7 +6,7 @@ version = '2016.04' homepage = 'http://www.pgroup.com/index.htm' description = """Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '16.4' gccsuff = '-GCC-5.3.0-2.26' diff --git a/easybuild/easyconfigs/p/pomkl/pomkl-2016.09.eb b/easybuild/easyconfigs/p/pomkl/pomkl-2016.09.eb index 74076e42f0e..25f5575492f 100644 --- a/easybuild/easyconfigs/p/pomkl/pomkl-2016.09.eb +++ b/easybuild/easyconfigs/p/pomkl/pomkl-2016.09.eb @@ -6,7 +6,7 @@ version = '2016.09' homepage = 'http://www.pgroup.com/index.htm' description = """Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '16.7' gccsuff = '-GCC-5.4.0-2.26' diff --git a/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb b/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb index 0bf9bb7552e..b1eac5951eb 100644 --- a/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb +++ b/easybuild/easyconfigs/p/pompi/pompi-2016.03.eb @@ -7,7 +7,7 @@ pgisuffix = '-GCC-4.9.3-2.25' homepage = 'http://www.pgroup.com/index.htm' description = """Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '16.3' diff --git a/easybuild/easyconfigs/p/pompi/pompi-2016.04.eb b/easybuild/easyconfigs/p/pompi/pompi-2016.04.eb index b7e500bb5f6..fb055d8fa0b 100644 --- a/easybuild/easyconfigs/p/pompi/pompi-2016.04.eb +++ b/easybuild/easyconfigs/p/pompi/pompi-2016.04.eb @@ -7,7 +7,7 @@ pgisuffix = '-GCC-5.3.0-2.26' homepage = 'http://www.pgroup.com/index.htm' description = """Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '16.4' diff --git a/easybuild/easyconfigs/p/pompi/pompi-2016.09.eb b/easybuild/easyconfigs/p/pompi/pompi-2016.09.eb index b83ba47007d..a9f77edae05 100644 --- a/easybuild/easyconfigs/p/pompi/pompi-2016.09.eb +++ b/easybuild/easyconfigs/p/pompi/pompi-2016.09.eb @@ -7,7 +7,7 @@ pgisuffix = '-GCC-5.4.0-2.26' homepage = 'http://www.pgroup.com/index.htm' description = """Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM compver = '16.7' diff --git a/easybuild/easyconfigs/p/popt/popt-1.16.eb b/easybuild/easyconfigs/p/popt/popt-1.16.eb index 4b05ae3e4e8..f7fab754028 100644 --- a/easybuild/easyconfigs/p/popt/popt-1.16.eb +++ b/easybuild/easyconfigs/p/popt/popt-1.16.eb @@ -5,7 +5,7 @@ version = "1.16" homepage = "http://freecode.com/projects/popt" description = """Popt is a C library for parsing command line parameters.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://rpm5.org/files/popt/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb index add3919aeec..efe823ae1c7 100644 --- a/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb +++ b/easybuild/easyconfigs/p/pplacer/pplacer-1.1.alpha19.eb @@ -8,7 +8,7 @@ description = """Pplacer places query sequences on a fixed reference phylogeneti likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # compiling pplacer from source requires an ancient OCaml version, # which is a huge PITA with recent compilers diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb index 73f50dd0e5a..d157dede011 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0.eb @@ -6,7 +6,7 @@ version = '2.5.0' homepage = 'https://code.google.com/p/protobuf/' description = """Google Protocol Buffers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://github.com/google/%(namelower)s/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.6.1.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.6.1.eb index cf874829a55..a5b3f44d1fa 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-2.6.1.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.6.1.eb @@ -6,7 +6,7 @@ version = '2.6.1' homepage = 'https://github.com/google/protobuf/' description = """Google Protocol Buffers""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://github.com/google/protobuf/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb index ec72cdf71da..4ef952e6268 100644 --- a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-5.0.0.eb @@ -6,7 +6,7 @@ version = '5.0.0' homepage = 'https://github.com/workhorsy/py-cpuinfo' description = "py-cpuinfo gets CPU info with pure Python." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb index b1a1d1feb4d..64f0484db25 100644 --- a/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb +++ b/easybuild/easyconfigs/q/QIIME/QIIME-1.9.1.eb @@ -12,7 +12,7 @@ homepage = 'http://qiime.org/' description = """QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM requirements = "%(namelower)s=%(version)s matplotlib=1.4.3 mock nose" channels = ['bioconda', 'conda-forge'] diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2017.10.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2017.10.eb index 866e3661c00..2c0c0f8edb8 100644 --- a/easybuild/easyconfigs/q/QIIME2/QIIME2-2017.10.eb +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2017.10.eb @@ -11,7 +11,7 @@ homepage = 'http://qiime2.org/' description = """QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM requirements = "%(namelower)s-%(version)s " requirements += "--file https://data.qiime2.org/distro/core/%(namelower)s-%(version)s-conda-linux-64.txt" diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2018.2.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2018.2.eb index 52bff2876a7..19409b7d922 100644 --- a/easybuild/easyconfigs/q/QIIME2/QIIME2-2018.2.eb +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2018.2.eb @@ -15,7 +15,7 @@ source_urls = ['https://data.qiime2.org/distro/core/'] sources = ['qiime2-%(version)s-py35-linux-conda.yml'] checksums = ['f90cbd04e123ba62a735b16af556442ff06dc7b2c124681ba89b245c1121a93f'] -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM builddependencies = [('Miniconda3', '4.4.10')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb index 48881e75e80..ef7007590d8 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6.eb @@ -4,7 +4,7 @@ version = '4.8.6' homepage = 'http://qt-project.org/' description = "Qt is a comprehensive cross-platform C++ application framework." -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://download.qt.io/official_releases/qt/4.8/%(version)s'] sources = ['qt-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/qtop/qtop-53-1.eb b/easybuild/easyconfigs/q/qtop/qtop-53-1.eb index 5c02ce39e59..0f98c2591a1 100644 --- a/easybuild/easyconfigs/q/qtop/qtop-53-1.eb +++ b/easybuild/easyconfigs/q/qtop/qtop-53-1.eb @@ -20,7 +20,7 @@ description = """qtop is a nifty command-line tool for monitoring queueing syste It is possible to write wrappers for other platforms -people have done so for SGE, OAR etc- or, even examine traces offline and present the sampled information.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # eg. https://cern.ch/fotis/QTOP/qtop-53.tar.gz sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb index 24380b2e17f..ca307411c78 100644 --- a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb +++ b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.12-Java-1.8.eb @@ -8,7 +8,7 @@ homepage = 'http://sourceforge.net/projects/rdp-classifier' description = """The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = ['rdp_classifier_%(version)s.zip'] diff --git a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.7-Java-1.7.0_60.eb b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.7-Java-1.7.0_60.eb index 4e45b17fd87..8e2933fb504 100644 --- a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.7-Java-1.7.0_60.eb +++ b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.7-Java-1.7.0_60.eb @@ -7,7 +7,7 @@ homepage = 'http://sourceforge.net/projects/rdp-classifier' description = """The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = ['rdp_classifier_%(version)s.zip'] diff --git a/easybuild/easyconfigs/r/RTG-Tools/RTG-Tools-3.9.1-Java-1.8.eb b/easybuild/easyconfigs/r/RTG-Tools/RTG-Tools-3.9.1-Java-1.8.eb index 1619d0d050f..e6cf85a051c 100644 --- a/easybuild/easyconfigs/r/RTG-Tools/RTG-Tools-3.9.1-Java-1.8.eb +++ b/easybuild/easyconfigs/r/RTG-Tools/RTG-Tools-3.9.1-Java-1.8.eb @@ -8,7 +8,7 @@ homepage = 'https://www.realtimegenomics.com/products/rtg-tools' description = """ RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files, as well as utilities for processing other common NGS data formats. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/RealTimeGenomics/rtg-tools/archive'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb index 99b121a0e8d..47db9c8504e 100644 --- a/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb +++ b/easybuild/easyconfigs/r/Reads2snp/Reads2snp-2.0.eb @@ -14,7 +14,7 @@ description = """reads2snp is a SNP and genotype caller: it predicts the genotyp Its typical output is a vcf file. It is written in C++, based on the bio++ libraries, multi-threaded with openMP, available under Linux and MacOS""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://kimura.univ-montp2.fr/PopPhyl/resources/tools/'] sources = ['%(namelower)s_%(version)s.zip'] diff --git a/easybuild/easyconfigs/r/Roary/Roary-3.12.0.eb b/easybuild/easyconfigs/r/Roary/Roary-3.12.0.eb index 44b0a58514e..fc344c7e0c9 100644 --- a/easybuild/easyconfigs/r/Roary/Roary-3.12.0.eb +++ b/easybuild/easyconfigs/r/Roary/Roary-3.12.0.eb @@ -12,7 +12,7 @@ variant = "Linux-x86_64" homepage = 'https://github.com/sanger-pathogens/Roary' description = "Rapid large-scale prokaryote pan genome analysis" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM requirements = "%(name)s=%(version)s" channels = ['bioconda', 'conda-forge', 'r', 'defaults'] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb index 8c87deb6f61..221e9115d0e 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb @@ -15,7 +15,7 @@ description = """Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb index 873541fd421..48954c68027 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.1.eb @@ -15,7 +15,7 @@ description = """Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.3.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.3.eb index 6c9287f577d..f9e02858f73 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.3.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.3.eb @@ -15,7 +15,7 @@ description = """Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.4.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.4.eb index 3149eef3ad1..9d1578f74d0 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.3.4.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.4.eb @@ -6,7 +6,7 @@ description = """Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb index e6e619d7aea..1a86edc2918 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.3.eb @@ -12,7 +12,7 @@ description = """ S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software package containing programs for use in the genetic analysis of family, pedigree and individual data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://github.com/elstonsage/sageCore/releases/download/v%(version)s'] sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb index 44c08dffd3a..5bcbdec4dbb 100644 --- a/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb +++ b/easybuild/easyconfigs/s/SAGE/SAGE-6.4.eb @@ -12,7 +12,7 @@ description = """ S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software package containing programs for use in the genetic analysis of family, pedigree and individual data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://darwin.cwru.edu/sage/files/'] sources = ['S.A.G.E.v%(version)s_Linux_x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/s/SAS/SAS-9.4.eb b/easybuild/easyconfigs/s/SAS/SAS-9.4.eb index fbdaafe6e66..5f3ce71cc1c 100644 --- a/easybuild/easyconfigs/s/SAS/SAS-9.4.eb +++ b/easybuild/easyconfigs/s/SAS/SAS-9.4.eb @@ -5,7 +5,7 @@ homepage = 'https://www.sas.com' description = """SAS is a software suite for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # tarball needs to be created manually, by packing up the 'Linux64' directory sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb b/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb index 1d6583cd4c2..3bdbd11da1d 100644 --- a/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb +++ b/easybuild/easyconfigs/s/SDCC/SDCC-3.3.0.eb @@ -19,7 +19,7 @@ description = """SDCC is a retargettable, optimizing ANSI - C compiler suite tha MCUs (z80, z180, gbz80, Rabbit 2000/3000, Rabbit 3000A). Work is in progress on supporting the Microchip PIC16 and PIC18 targets. It can be retargeted for other microprocessors.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # eg. http://sourceforge.net/projects/sdcc/files/sdcc/3.3.0/sdcc-src-3.3.0.tar.bz2/download sources = ['sdcc-src-%(version)s.tar.bz2'] diff --git a/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb b/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb index 8b988dc0fd6..d52899194d0 100644 --- a/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb +++ b/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r837.GLIBCv2.12.eb @@ -12,7 +12,7 @@ homepage = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.htm description = """SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] sources = ['shapeit.v%(version)s%(versionsuffix)s.Linux.static.tgz'] diff --git a/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r904.glibcv2.17.eb b/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r904.glibcv2.17.eb index 9c8e01c0566..12dc7cfc755 100644 --- a/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r904.glibcv2.17.eb +++ b/easybuild/easyconfigs/s/SHAPEIT/SHAPEIT-2.r904.glibcv2.17.eb @@ -12,7 +12,7 @@ homepage = 'https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.htm description = """SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/'] sources = ['shapeit.v%(version)s%(versionsuffix)s.linux.tar.gz'] diff --git a/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-5.1.0.26412-cli-tools-only.eb b/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-5.1.0.26412-cli-tools-only.eb index 572448c7a5b..31ee46ea3af 100644 --- a/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-5.1.0.26412-cli-tools-only.eb +++ b/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-5.1.0.26412-cli-tools-only.eb @@ -15,7 +15,7 @@ description = """PacBio’s open-source SMRT Analysis software suite is designed or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # The download is a password protected zip file # Download it from https://www.pacb.com/support/software-downloads/ and uncompress diff --git a/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-6.0.0.47841-cli-tools-only.eb b/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-6.0.0.47841-cli-tools-only.eb index 2447b2c72ce..ac28bf1d4f0 100644 --- a/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-6.0.0.47841-cli-tools-only.eb +++ b/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-6.0.0.47841-cli-tools-only.eb @@ -15,7 +15,7 @@ description = """PacBio’s open-source SMRT Analysis software suite is designed or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # The download is a password protected zip file # Download it from https://www.pacb.com/support/software-downloads/ and uncompress diff --git a/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb b/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb index 8734a7daed7..6100356c0dd 100644 --- a/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb +++ b/easybuild/easyconfigs/s/SOAPaligner/SOAPaligner-2.21_Linux-x86_64.eb @@ -14,7 +14,7 @@ description = """ SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleoti Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://soap.genomics.org.cn/down/'] sources = ['soap%(version)srelease.tar.gz'] diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.3.5-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.3.5-centos_linux64.eb index cfbdcb45e7b..59f2ea3e09b 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.3.5-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.3.5-centos_linux64.eb @@ -13,7 +13,7 @@ homepage = 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std' description = """ The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.4-1-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.4-1-centos_linux64.eb index 263ce2d19fc..91eb10f4259 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.4-1-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.4-1-centos_linux64.eb @@ -13,7 +13,7 @@ homepage = 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std' description = """ The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb index 4a6fa7558ef..89822def84f 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.5.7-centos_linux64.eb @@ -16,7 +16,7 @@ description = """The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb index 07eca4b9678..edf6e2df382 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.8.2-1-centos_linux64.eb @@ -16,7 +16,7 @@ description = """The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.0-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.0-centos_linux64.eb index 930a9678c98..4838c0e3a22 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.0-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.0-centos_linux64.eb @@ -16,7 +16,7 @@ description = """The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.2-ubuntu64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.2-ubuntu64.eb index 175583c21a3..a4eacd547f8 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.2-ubuntu64.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.2-ubuntu64.eb @@ -16,7 +16,7 @@ description = """The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.4-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.4-centos_linux64.eb index febc37cc437..3142c6c71c8 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.4-centos_linux64.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-2.9.4-centos_linux64.eb @@ -18,7 +18,7 @@ description = """The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb index c7d58c5217d..3bd0d8bfc43 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb @@ -17,7 +17,7 @@ description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/'] sources = ['%%(namelower)s_v%%(version)s_%s.tgz' % versionsuffix[1:]] diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb index 24b10cedf9d..7ecaf07efb1 100644 --- a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb @@ -17,7 +17,7 @@ description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/'] sources = ['%%(namelower)s_v%%(version)s_%s.tgz' % versionsuffix[1:]] diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2.eb b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2.eb index fad5b22e02d..ba0f1153e2c 100644 --- a/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2.eb +++ b/easybuild/easyconfigs/s/Salmon/Salmon-0.8.2.eb @@ -9,7 +9,7 @@ homepage = 'https://github.com/COMBINE-lab/%(namelower)s' description = """Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://github.com/COMBINE-lab/%(namelower)s/releases/download/v%(version)s/'] sources = ['%(name)s-%(version)s_linux_x86_64.tar.gz'] diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb index aaa111b447d..7a6e9e1df52 100644 --- a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.6.6.eb @@ -13,7 +13,7 @@ description = """Sambamba is a high performance modern robust and fast tool (and written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/lomereiter/sambamba/releases/download/v%(version)s/'] sources = ['%(namelower)s_v%(version)s_linux.tar.bz2'] diff --git a/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb b/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb index 7464a3d289d..4b487981923 100644 --- a/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb +++ b/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb @@ -5,7 +5,7 @@ homepage = 'http://www.plm.automation.siemens.com/en_us/products/lms/samtech/sam description = """FEM solver solution suite for basic linear structures to advanced, flexible nonlinear mechanisms and thermal applications.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # licensed software, no source URls for automatic download # note: unpacking requires that 7z (p7zip) is available diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.21-Java-1.8.0_162.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.21-Java-1.8.0_162.eb index f4c7b514f4d..40ae01f3382 100644 --- a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.21-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.21-Java-1.8.0_162.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://saxon.sourceforge.net' description = """Open Source SAXON XSLT processor developed by Saxonica Limited.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s', 'download'] sources = ['SaxonHE%sJ.zip' % version.replace('.', '-')] diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb index 2de8d75b118..1469abcb5bc 100644 --- a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-9.7.0.4-Java-1.7.0_79.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://saxon.sourceforge.net' description = """Open Source SAXON XSLT processor developed by Saxonica Limited.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['SaxonHE%sJ.zip' % version.replace('.', '-')] source_urls = ['https://sourceforge.net/projects/saxon/files/Saxon-HE/%(version_major_minor)s', 'download'] diff --git a/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb b/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb index a58f9d8e5f6..e1c4c526c15 100644 --- a/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/s/SearchGUI/SearchGUI-3.3.3-Java-1.8.0_152.eb @@ -10,7 +10,7 @@ description = """SearchGUI is a user-friendly open-source graphical user interfa currently supporting X! Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda, OMSSA, Novor and DirecTag.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://genesis.ugent.be/maven2/eu/isas/searchgui/SearchGUI/%(version)s/'] sources = ['SearchGUI-%(version)s-mac_and_linux.tar.gz'] diff --git a/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb b/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb index a54e53ac82d..5c988cfa468 100644 --- a/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb +++ b/easybuild/easyconfigs/s/SelEstim/SelEstim-1.1.4-Linux-64bits.eb @@ -14,7 +14,7 @@ description = """SelEstim is aimed at distinguishing neutral from selected polym the intensity of selection at the latter. The SelEstim model accounts explicitly for positive selection, and it is assumed that all marker loci in the dataset are responding to selection, to some extent""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www1.montpellier.inra.fr/CBGP/software/selestim/files/'] sources = ['%(name)s_%(version)s.zip'] diff --git a/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb b/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb index 3a97b911b1c..0c36c0693ec 100644 --- a/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb +++ b/easybuild/easyconfigs/s/Spack/Spack-0.10.0.eb @@ -8,7 +8,7 @@ description = """Spack is a package manager for supercomputers, Linux, and macOS software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://github.com/LLNL/spack/archive/'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/s/Spack/Spack-0.11.2.eb b/easybuild/easyconfigs/s/Spack/Spack-0.11.2.eb index 1baa04699e7..1bb1f5dda9e 100644 --- a/easybuild/easyconfigs/s/Spack/Spack-0.11.2.eb +++ b/easybuild/easyconfigs/s/Spack/Spack-0.11.2.eb @@ -8,7 +8,7 @@ description = """Spack is a package manager for supercomputers, Linux, and macOS software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['https://github.com/LLNL/spack/archive/'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb index 41b36d91f6b..14c89a3596b 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -6,7 +6,7 @@ version = '1.3.0' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin-hadoop2.3.tgz'] source_urls = ['http://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/'] diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb b/easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb index fa568cc1446..7a9568fe691 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb @@ -6,7 +6,7 @@ version = '1.4.1' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] source_urls = [ diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb index 081d6d615b8..95093098fc0 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb @@ -6,7 +6,7 @@ version = '1.5.0' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] source_urls = [ diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.6.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.6.0.eb index 276eb5f0cf8..ef0b8e4460f 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.6.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.6.0.eb @@ -6,7 +6,7 @@ version = '1.6.0' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] source_urls = [ diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb b/easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb index e06636922a5..c1ff20cf674 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-1.6.1.eb @@ -6,7 +6,7 @@ version = '1.6.1' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] source_urls = [ diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.0.0.eb b/easybuild/easyconfigs/s/Spark/Spark-2.0.0.eb index 6ca9cd502bc..d2968c4b8b7 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.0.0.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.0.0.eb @@ -6,7 +6,7 @@ version = '2.0.0' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] source_urls = [ diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.0.2.eb b/easybuild/easyconfigs/s/Spark/Spark-2.0.2.eb index 8f5ba911816..da19c2c1bbc 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.0.2.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.0.2.eb @@ -6,7 +6,7 @@ version = '2.0.2' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] source_urls = [ diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_144.eb b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_144.eb index 8b3d26f8e74..08a011f44b3 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_144.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_144.eb @@ -7,7 +7,7 @@ versionsuffix = '-Hadoop-2.6-Java-%(javaver)s' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] source_urls = [ diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_152.eb b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_152.eb index 2d7e4dde361..3be84ba38d5 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-Hadoop-2.6-Java-1.8.0_152.eb @@ -7,7 +7,7 @@ versionsuffix = '-Hadoop-2.6-Java-%(javaver)s' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] source_urls = [ diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.3.0-Hadoop-2.7-Java-1.8.0_162.eb b/easybuild/easyconfigs/s/Spark/Spark-2.3.0-Hadoop-2.7-Java-1.8.0_162.eb index 070131a3aac..5b4293b5d16 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.3.0-Hadoop-2.7-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.3.0-Hadoop-2.7-Java-1.8.0_162.eb @@ -7,7 +7,7 @@ versionsuffix = '-Hadoop-2.7-Java-%(javaver)s' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] source_urls = [ diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb index d1ca55ff8a7..36c78ba683b 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb @@ -7,7 +7,7 @@ versionsuffix = '-Hadoop-2.7-Java-%(javaver)s' homepage = 'http://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] source_urls = [ diff --git a/easybuild/easyconfigs/s/Stata/Stata-15.eb b/easybuild/easyconfigs/s/Stata/Stata-15.eb index e05579b09ab..4ed7b0c3293 100644 --- a/easybuild/easyconfigs/s/Stata/Stata-15.eb +++ b/easybuild/easyconfigs/s/Stata/Stata-15.eb @@ -5,7 +5,7 @@ homepage = 'https://www.stata.com/' description = """Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # requires license to access source files sources = ['Stata%(version)sLinux64.tar.gz'] diff --git a/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb b/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb index a3ffead066b..09e6c9dafd7 100644 --- a/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb @@ -7,7 +7,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://www.scala-sbt.org/' description = "sbt is a build tool for Scala, Java, and more." -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/sbt/sbt/releases/download/v%(version)s'] sources = [SOURCE_TGZ] diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb index f08e79381b7..d6752459e10 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb @@ -6,7 +6,7 @@ version = "1.4.2" homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.6.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.6.eb index 7a976b306d6..d72731c25e2 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.6.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.6.eb @@ -8,7 +8,7 @@ description = """Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/google/snappy/archive/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb index 429f565ab3a..0824a0cd821 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb @@ -7,7 +7,7 @@ homepage = 'http://sourceforge.net/projects/snpeff/' description = """SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM java = 'Java' javaver = '1.7.0_80' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb index ba982d8d09c..7fc176ebda9 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb @@ -7,7 +7,7 @@ homepage = 'http://sourceforge.net/projects/snpeff/' description = """SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM java = 'Java' javaver = '1.7.0_80' diff --git a/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb index 306703a33f1..7b2db1a0982 100644 --- a/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb +++ b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb @@ -12,7 +12,7 @@ homepage = 'http://www.sph.umich.edu/csg/yli/splitRef/index.html' description = """ splitRef splits a reference haplotype file into smaller files with subsets of markers. The current version is a pre-release. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://csg.sph.umich.edu/yli/splitRef/download/'] sources = ['%s.V%s.tgz' % (name, version.replace(".", ""))] diff --git a/easybuild/easyconfigs/s/supernova/supernova-2.0.1.eb b/easybuild/easyconfigs/s/supernova/supernova-2.0.1.eb index c93bde274e0..53d3ec5cbf6 100644 --- a/easybuild/easyconfigs/s/supernova/supernova-2.0.1.eb +++ b/easybuild/easyconfigs/s/supernova/supernova-2.0.1.eb @@ -12,7 +12,7 @@ homepage = 'https://support.10xgenomics.com/de-novo-assembly/software/overview/l description = """Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # no direct download # https://support.10xgenomics.com/de-novo-assembly/software/downloads/latest diff --git a/easybuild/easyconfigs/s/supernova/supernova-2.1.1.eb b/easybuild/easyconfigs/s/supernova/supernova-2.1.1.eb index a02f70ab01a..374c178e64b 100644 --- a/easybuild/easyconfigs/s/supernova/supernova-2.1.1.eb +++ b/easybuild/easyconfigs/s/supernova/supernova-2.1.1.eb @@ -12,7 +12,7 @@ homepage = 'https://support.10xgenomics.com/de-novo-assembly/software/overview/l description = """Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # no direct download # https://support.10xgenomics.com/de-novo-assembly/software/downloads/latest diff --git a/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb b/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb index e97300a69cd..c34bf7b3d86 100644 --- a/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb +++ b/easybuild/easyconfigs/t/TCC/TCC-0.9.26.eb @@ -19,7 +19,7 @@ description = """The Tiny C Compiler (aka TCC, tCc, or TinyCC) is an x86 and x86 implement all of ANSI C (C89/C90),[1] much of the new ISO C99 standard, and many GNU C extensions including inline assembly.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # eg. http://download.savannah.nongnu.org/releases/tinycc/tcc-0.9.26.tar.bz2 sources = [SOURCELOWER_TAR_BZ2] diff --git a/easybuild/easyconfigs/t/TRF/TRF-4.09-linux64.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09-linux64.eb index 4496ef3e9c6..33b0f98aed9 100644 --- a/easybuild/easyconfigs/t/TRF/TRF-4.09-linux64.eb +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09-linux64.eb @@ -7,7 +7,7 @@ versionsuffix = '-linux64' homepage = 'https://tandem.bu.edu/trf/trf.html' description = """Tandem repeats finder: a program to analyze DNA sequences. Legacy version.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://tandem.bu.edu/trf/downloads'] sources = ['trf%(version_major)s%(version_minor)s.legacylinux64'] diff --git a/easybuild/easyconfigs/t/Tika/Tika-1.16.eb b/easybuild/easyconfigs/t/Tika/Tika-1.16.eb index d0d03178699..c4f6a84a9b3 100644 --- a/easybuild/easyconfigs/t/Tika/Tika-1.16.eb +++ b/easybuild/easyconfigs/t/Tika/Tika-1.16.eb @@ -7,7 +7,7 @@ homepage = 'https://tika.apache.org/' description = """The Apache Tika toolkit detects and extracts metadata and text from over a thousand different file types (such as PPT, XLS, and PDF).""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [APACHE_SOURCE] sources = ['tika-%(version)s-src.zip'] diff --git a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb index 2994b547740..d12ce09558a 100644 --- a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb +++ b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb @@ -23,7 +23,7 @@ description = """TotalView is a GUI-based source code defect analysis tool that You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [ '%(namelower)s.%(version)s%(versionsuffix)s.tar', diff --git a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb index b17b02345e7..2358bf2a518 100644 --- a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb +++ b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb @@ -23,7 +23,7 @@ description = """TotalView is a GUI-based source code defect analysis tool that You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [ '%(namelower)s.%(version)s%(versionsuffix)s.tar', diff --git a/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb b/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb index 2a37a8ab132..c1a6705620b 100644 --- a/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb +++ b/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb @@ -23,7 +23,7 @@ description = """TotalView is a GUI-based source code defect analysis tool that You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [ '%(namelower)s.%(version)s%(versionsuffix)s.tar', diff --git a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3.eb b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3.eb index b7ea66d83eb..394a693f69d 100644 --- a/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3.eb +++ b/easybuild/easyconfigs/t/Transrate/Transrate-1.0.3.eb @@ -12,7 +12,7 @@ description = """Transrate is software for de-novo transcriptome assembly qualit filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['transrate-%(version)s-linux-x86_64.tar.gz'] source_urls = ['https://bintray.com/artifact/download/blahah/generic'] diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb index bcb8cdfed46..db5201f57fb 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb @@ -13,7 +13,7 @@ description = """Trimmomatic performs a variety of useful trimming tasks for ill paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/'] sources = [SOURCE_ZIP] diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb index 6d0f2cee34a..420db639a96 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.36-Java-1.8.0_92.eb @@ -13,7 +13,7 @@ description = """Trimmomatic performs a variety of useful trimming tasks for ill paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/'] sources = [SOURCE_ZIP] diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.0_162.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.0_162.eb index dfe897da98b..edb5cea7819 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.0_162.eb @@ -14,7 +14,7 @@ description = """Trimmomatic performs a variety of useful trimming tasks for ill paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/'] sources = [SOURCE_ZIP] diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb index ac135acc68e..da61b4d7b33 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb @@ -14,7 +14,7 @@ description = """Trimmomatic performs a variety of useful trimming tasks for ill paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/'] sources = [SOURCE_ZIP] diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb index c472a129640..3fe9999b5e1 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.2.132.eb @@ -11,7 +11,7 @@ description = """Intel Threading Building Blocks (Intel TBB) Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb index 3644e3125eb..af3bdaf2a08 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.4.174.eb @@ -12,7 +12,7 @@ description = """Intel Threading Building Blocks (Intel TBB) that tap into the power and performance of multicore and manycore hardware platforms. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_tbb_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb b/easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb index 8156aab23b4..c7cee375355 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2017.6.196.eb @@ -14,7 +14,7 @@ description = """ and manycore hardware platforms. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_tbb_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb index fe58ba8f6dc..797a1f2402c 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb @@ -11,7 +11,7 @@ description = """Intel Threading Building Blocks (Intel TBB) Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb index db524b24077..9d44b942cbb 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb @@ -11,7 +11,7 @@ description = """Intel Threading Building Blocks (Intel TBB) Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb index 8f93bdda020..1edec2fba65 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb @@ -11,7 +11,7 @@ description = """Intel Threading Building Blocks (Intel TBB) Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb index 11fd6f658a3..50156d7348c 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb @@ -11,7 +11,7 @@ description = """Intel Threading Building Blocks (Intel TBB) Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['l_%(name)s_%(version)s.tgz'] diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20180227-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20180227-linux64.eb index ae102d27f07..f92cb787753 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20180227-linux64.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20180227-linux64.eb @@ -13,7 +13,7 @@ homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' description = """Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/'] sources = [{'download_filename': 'linux64.tbl2asn.gz', 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}] diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb index da50b02fdfb..428413c52d6 100644 --- a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb @@ -7,7 +7,7 @@ homepage = 'http://www.tecplot.com/products/tecplot-360/' description = """Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, and communicate your results with professional images and animations.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # fi. http://www.tecplot.com/my/product-releases/ installername = '%(name)s_%(version)s.sh' diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb b/easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb index 02d5fea5dec..ffb9c84c768 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-4.13a.eb @@ -9,7 +9,7 @@ description = """Texinfo is the official documentation format of the GNU project source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM osdependencies = ['texlive'] diff --git a/easybuild/easyconfigs/t/time/time-1.7.eb b/easybuild/easyconfigs/t/time/time-1.7.eb index 1c4c9402350..28e7019ceed 100644 --- a/easybuild/easyconfigs/t/time/time-1.7.eb +++ b/easybuild/easyconfigs/t/time/time-1.7.eb @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/time/' description = """The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb index 0423702965f..c9bb6cc0e85 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.3.eb @@ -8,7 +8,7 @@ description = """tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb b/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb index ebac3ec2d3f..83530eda979 100644 --- a/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb +++ b/easybuild/easyconfigs/t/travis/travis-1.8.2-Ruby-2.3.1.eb @@ -9,7 +9,7 @@ versionsuffix = '-Ruby-%s' % rubyver homepage = 'https://github.com/travis-ci/travis.rb' description = """Travis CI Client (CLI and Ruby library)""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://rubygems.org/downloads/'] sources = ['%(namelower)s-%(version)s.gem'] diff --git a/easybuild/easyconfigs/t/travis/travis-1.8.4-Ruby-2.3.3.eb b/easybuild/easyconfigs/t/travis/travis-1.8.4-Ruby-2.3.3.eb index 6327f1f42ef..45e0da20088 100644 --- a/easybuild/easyconfigs/t/travis/travis-1.8.4-Ruby-2.3.3.eb +++ b/easybuild/easyconfigs/t/travis/travis-1.8.4-Ruby-2.3.3.eb @@ -9,7 +9,7 @@ versionsuffix = '-Ruby-%s' % rubyver homepage = 'https://github.com/travis-ci/travis.rb' description = """Travis CI Client (CLI and Ruby library)""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://rubygems.org/downloads/'] sources = ['%(namelower)s-%(version)s.gem'] diff --git a/easybuild/easyconfigs/u/UCLUST/UCLUST-1.2.22q-i86linux64.eb b/easybuild/easyconfigs/u/UCLUST/UCLUST-1.2.22q-i86linux64.eb index 67741e15d9f..8e0fe954365 100644 --- a/easybuild/easyconfigs/u/UCLUST/UCLUST-1.2.22q-i86linux64.eb +++ b/easybuild/easyconfigs/u/UCLUST/UCLUST-1.2.22q-i86linux64.eb @@ -9,7 +9,7 @@ versionsuffix = '-i86linux64' homepage = 'http://www.drive5.com/usearch/index.html' description = """UCLUST: Extreme high-speed sequence clustering, alignment and database search.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # licensed for use with PyNAST and QIIME, see http://www.drive5.com/uclust/downloads1_2_22q.html source_urls = ['http://www.drive5.com/%(namelower)s/'] diff --git a/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb index cc2a64b9ff3..e5e0371c9bd 100644 --- a/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb +++ b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb @@ -10,7 +10,7 @@ homepage = 'http://www.drive5.com/usearch/index.html' description = """USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download via http://www.drive5.com/usearch/download.html usearch5_bin = 'usearch%s_%s' % (ver1, versionsuffix[1:]) diff --git a/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb index d2a22ed8a6a..4370f24a14c 100644 --- a/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb +++ b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-i86linux32.eb @@ -8,7 +8,7 @@ homepage = 'http://www.drive5.com/usearch/index.html' description = """USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download via http://www.drive5.com/usearch/download.html usearch_bin = 'usearch%s_%s' % (version, versionsuffix[1:]) diff --git a/easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb b/easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb index c09d3e96a20..4590f9093c0 100644 --- a/easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb +++ b/easybuild/easyconfigs/u/USEARCH/USEARCH-6.1.544-i86linux32.eb @@ -8,7 +8,7 @@ homepage = 'http://www.drive5.com/usearch/index.html' description = """USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # download via http://www.drive5.com/usearch/download.html usearch_bin = 'usearch%s_%s' % (version, versionsuffix[1:]) diff --git a/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb b/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb index ecaa08a9807..2b15c696263 100644 --- a/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb +++ b/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb @@ -12,7 +12,7 @@ description = """ VEGAS (Versatile Gene-based Association Study) is a free program for performing gene-based tests for association using the results from genetic association studies """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://gump.qimr.edu.au/VEGAS/'] sources = ['vegas-%(version)s-hapmapCEU.tar.gz'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2013_update10.eb b/easybuild/easyconfigs/v/VTune/VTune-2013_update10.eb index 2c12506de30..e8504525b02 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2013_update10.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2013_update10.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2013_update11.eb b/easybuild/easyconfigs/v/VTune/VTune-2013_update11.eb index de5d90713e7..adacbfc7658 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2013_update11.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2013_update11.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2013_update12.eb b/easybuild/easyconfigs/v/VTune/VTune-2013_update12.eb index de203548a6f..69fc6bbf28b 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2013_update12.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2013_update12.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2013_update6.eb b/easybuild/easyconfigs/v/VTune/VTune-2013_update6.eb index 3a689d53475..72ed679b1c4 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2013_update6.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2013_update6.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2013_update8.eb b/easybuild/easyconfigs/v/VTune/VTune-2013_update8.eb index 210397b41a5..165d64e06ba 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2013_update8.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2013_update8.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2013_update9.eb b/easybuild/easyconfigs/v/VTune/VTune-2013_update9.eb index c56eb223252..3fac4e4efa6 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2013_update9.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2013_update9.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2016_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2016_update3.eb index 50be4c3b4ab..8fb085cbf11 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2016_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2016_update3.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2017.eb b/easybuild/easyconfigs/v/VTune/VTune-2017.eb index 13d248cd6c4..21c659ba3b6 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2017.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2017.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2017_update1.eb b/easybuild/easyconfigs/v/VTune/VTune-2017_update1.eb index 7c95b0c1d73..d9186b4497f 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2017_update1.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2017_update1.eb @@ -7,7 +7,7 @@ description = """Intel VTune Amplifier XE is the premier performance profiler fo checksums = ['c3524d972072780023c3839b1188baaa'] -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb b/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb index 5db4d180bab..385b08a8d2b 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2017_update2.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] checksums = ['1ef91898e107a1da015305def80091e4'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2017_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2017_update3.eb index e35eec89968..fd9bf8d7768 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2017_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2017_update3.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_xe_%(version)s.tar.gz'] checksums = ['1e32ce4a591439d42b23ad2960350f3354fe5f805f96c98f21ce315b66789025'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2018_update1.eb b/easybuild/easyconfigs/v/VTune/VTune-2018_update1.eb index 34be4538644..878828eeca7 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2018_update1.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2018_update1.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['bf9a95c09c570b9b6b4f335f8b2bf6dbf5145c0b2603b8d96ff2820721c6abcb'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2018_update2.eb b/easybuild/easyconfigs/v/VTune/VTune-2018_update2.eb index 6121c0cc647..f6a4bb8367d 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2018_update2.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2018_update2.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['5b21dd0c598e7e8a80be7095e13869a746c5074fa030211ca698ae2cfc65da93'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb index eaf62006e25..0938ca5f98f 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2018_update3.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13079/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update2.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update2.eb index ec66a000137..2e1d0821903 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2019_update2.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update2.eb @@ -5,7 +5,7 @@ homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vtune_amplifier_%(version)s.tar.gz'] checksums = ['25a3d9af6cc630c6aabcd724b8faef2703b16e96e4731970ebed37cf6a2e9b16'] diff --git a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb index e1d77dcfea1..bd9fed83da9 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2019_update3.eb @@ -5,7 +5,7 @@ homepage = 'https://software.intel.com/en-us/vtune' description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15214/'] sources = ['vtune_amplifier_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb index 920b6b2d143..5897b45b1bb 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb @@ -23,7 +23,7 @@ description = """The Vampir software tool provides an easy-to-use framework that The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb index d365513d883..df8fde3ba7d 100644 --- a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb @@ -22,7 +22,7 @@ description = """The Vampir software tool provides an easy-to-use framework that The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = ['vampir-%s-%s-setup.bin' % (version, variant)] diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb index afd19800453..b28480a155c 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.3.6-Java-1.7.0_80.eb @@ -11,7 +11,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'http://varscan.sourceforge.net/' description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(name)s.v%(version)s.jar'] source_urls = ['https://sourceforge.net/projects/varscan/files/'] diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb index b1573bf27c3..53cdfeb8738 100644 --- a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.1-Java-1.7.0_80.eb @@ -11,7 +11,7 @@ versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/dkoboldt/varscan' description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['%(name)s.v%(version)s.jar'] source_urls = ['https://github.com/dkoboldt/varscan/releases/download/v%(version)s'] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb index 23ef4a12e71..4e148838bc0 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.6.9.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-mympirun/' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-base/archive/'] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb index a9424b79986..706fb861f1c 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-1.7.3.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-mympirun/' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-base/archive/'] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb index 24862f25191..99daff74daa 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-mympirun/' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb index b0db50051eb..c450bd072a4 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-mympirun/' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.2.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.2.eb index 2f7a0833584..5b08a0ca0fa 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.2.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.4.2.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-mympirun/' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1.eb index 92979d49417..28449d7882e 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-base/' description = """Basic Python libraries used by UGent's HPC group""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb index f961cb0b1d6..ba8206cf5cf 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.8.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-base/' description = """Basic Python libraries used by UGent's HPC group""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.0.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.0.eb index cf6a57c3b1e..55bc8fa4005 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.0.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.0.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-base/' description = """Basic Python libraries used by UGent's HPC group""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.1.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.1.eb index bd8306b4dfe..646932ec773 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.1.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.1.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-base/' description = """Basic Python libraries used by UGent's HPC group""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.3.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.3.eb index d9c6a04e266..6e91090b49b 100644 --- a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.3.eb +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.8.3.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-base/' description = """Basic Python libraries used by UGent's HPC group""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb index c821c18048e..e003f908870 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.25.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-install/' description = """Shared setuptools functions and classes for python libraries developed by UGent's HPC group""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb index 66693d8845b..8658f415c3d 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.26.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-install/' description = """Shared setuptools functions and classes for python libraries developed by UGent's HPC group""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6.eb index a143ba12d52..e750674da38 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.6.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-install/' description = """Shared setuptools functions and classes for python libraries developed by UGent's HPC group""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [PYPI_SOURCE] diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.1.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.1.eb index bda0955addc..33cfcb92ae7 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.1.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.1.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-install/' description = """Shared setuptools functions and classes for python libraries developed by UGent's HPC group""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.2.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.2.eb index ebb99f52423..f5ec8686953 100644 --- a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.2.eb +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.11.2.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-install/' description = """Shared setuptools functions and classes for python libraries developed by UGent's HPC group""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb index 1243b5ec82a..750d4bed761 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.2.1.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/hpcugent/vsc-mympirun/' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb index 5617b0766fe..63dd6ca2d84 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.3.0.eb @@ -7,7 +7,7 @@ homepage = 'http://hpcugent.github.com/vsc-mympirun/' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-vsc-base-2.4.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-vsc-base-2.4.2.eb index 900f4b0d3dd..a8819776777 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-vsc-base-2.4.2.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2-vsc-base-2.4.2.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # purposely built with system compilers & Python -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb index e24521bcf5d..b1e49e0f492 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb index 2a97ab5dabc..037eb855a22 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb index b31dee5a6e3..e41b414d6d0 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.0b0.eb @@ -6,7 +6,7 @@ version = '4.0.0b0' homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = ['vsc-mympirun-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb index 5e6aaec33a5..b16e61489ec 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.1.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb index 09d422daec6..264a1ac2031 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.0.2.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.4.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.4.eb index 1cb498eba4a..cc3c8cdba11 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.4.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.4.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.5.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.5.eb index 1cdf96c7466..3ccb5528c4e 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.5.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.5.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.6.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.6.eb index 4bb83eb4e1f..c321ad7e94a 100755 --- a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.6.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-4.1.6.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/hpcugent/vsc-mympirun' description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0-vsc-base-2.1.2.eb b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0-vsc-base-2.1.2.eb index 761d760aa28..f5064d67161 100644 --- a/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0-vsc-base-2.1.2.eb +++ b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0-vsc-base-2.1.2.eb @@ -8,7 +8,7 @@ description = """vsc-processcontrol is a module to abstract process control like from actual implementations like vsc.affinity and psutil.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-processcontrol/archive/'] diff --git a/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb index e6b6aa4d747..e54ec03cc74 100644 --- a/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb +++ b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb @@ -8,7 +8,7 @@ description = """vsc-processcontrol is a module to abstract process control like from actual implementations like vsc.affinity and psutil.""" # we build this to work with every python version -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-processcontrol/archive/'] diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb index 94ae40e0cdc..ae1e2eba52a 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb @@ -15,7 +15,7 @@ description = """ Weka is a collection of machine learning algorithms for data m association rules, and visualization. It is also well-suited for developing new machine learning schemes.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://prdownloads.sourceforge.net/weka/'] sources = ['%s-%s.zip' % (name.lower(), version.replace('.', '-'))] diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb index a06d973254a..cfaea4ce2ed 100644 --- a/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.7.0-Java-1.7.0_80.eb @@ -15,7 +15,7 @@ description = """ Weka is a collection of machine learning algorithms for data m association rules, and visualization. It is also well-suited for developing new machine learning schemes.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['http://prdownloads.sourceforge.net/weka/'] sources = ['%s-%s.zip' % (name.lower(), version.replace('.', '-'))] diff --git a/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb b/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb index e5405f953c0..e19241bbef6 100644 --- a/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb +++ b/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb @@ -14,7 +14,7 @@ description = """wkhtmltopdf and wkhtmltoimage are open source (LGPLv3) command HTML into PDF and various image formats using the Qt WebKit rendering engine. These run entirely headless and do not require a display or display service.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/wkhtmltopdf/wkhtmltopdf/releases/download/%(version)s/'] sources = ['wkhtmltox-%(version)s_linux-generic-amd64.tar.xz'] diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb index 043cc16faa0..31b1cb52d13 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb @@ -8,7 +8,7 @@ description = """The Worker framework has been developed to help deal with param that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb index 0d863808956..c91e837a413 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb @@ -8,7 +8,7 @@ description = """The Worker framework has been developed to help deal with param that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb index 59a378bf10b..bde1a04a13b 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb @@ -8,7 +8,7 @@ description = """The Worker framework has been developed to help deal with param that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb index ec4c6b9e75e..0e1b561a407 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb @@ -8,7 +8,7 @@ description = """The Worker framework has been developed to help deal with param that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb index 1b2bcb3758e..5d2f57c5768 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb @@ -8,7 +8,7 @@ description = """The Worker framework has been developed to help deal with param that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb index b56ca14110a..64413328716 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1.eb @@ -6,7 +6,7 @@ version = '1.1.1' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """provides bitmaps for x""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM sources = [SOURCE_TAR_GZ] source_urls = [XORG_DATA_SOURCE] diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.2.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.2.eb index 8901d061902..9f0ddecae50 100644 --- a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.2.eb +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.2.eb @@ -6,7 +6,7 @@ version = '1.1.2' homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """provides bitmaps for x""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [XORG_DATA_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb index 6a306d862ec..5cd6a8ade3e 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e # even though xcb-proto is installed with configure-make-make install, nothing is actually built; # only .py files are installed using Python, and some .xlm flies copied, so OK to use dummy toolchain -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb index df836d072b7..9f593c6511c 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.10.eb @@ -8,7 +8,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM toolchainopts = {'pic': True} source_urls = ['http://zlib.net/fossils/'] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb index d8f38e9cade..5ebc3bc8df5 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb @@ -11,7 +11,7 @@ description = """ on virtually any computer hardware and operating system. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM toolchainopts = {'pic': True} source_urls = ['http://zlib.net/fossils/'] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb index 0c29b70864d..0e9868a8b63 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8.eb @@ -8,7 +8,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM toolchainopts = {'pic': True} source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9a501880674..2a935b8c3bc 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -559,6 +559,10 @@ def template_easyconfig_test(self, spec): self.assertTrue(name, app.name) self.assertTrue(ec['version'], app.version) + # make sure that deprecated 'dummy' toolchain is no longer used, should use 'system' toolchain instead + error_msg_tmpl = "%s should use 'system' toolchain rather than deprecated 'dummy' toolchain" + self.assertFalse(ec['toolchain']['name'] == 'dummy', error_msg_tmpl % os.path.basename(spec)) + # make sure that $root is not used, since it is not compatible with module files in Lua syntax res = re.findall('.*\$root.*', ec.rawtxt, re.M) error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" From 2ef4f35e6aa2450338ffabab0f2bee5769351892 Mon Sep 17 00:00:00 2001 From: Ward Poelmans Date: Wed, 22 May 2019 20:17:46 +0200 Subject: [PATCH 1705/5331] Fix hardcoded python version --- .../easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch | 4 ++-- .../o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch index c5fe6c35eae..c274acd2a6d 100644 --- a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-fix-makefiles.patch @@ -12,8 +12,8 @@ index 2b548e0..b7f72ae 100755 .PHONY: install_python # Install Python OR-Tools on the host system install_python: pypi_archive - cd "$(PYPI_ARCHIVE_TEMP_DIR)$Sortools" && "$(PYTHON_EXECUTABLE)" setup.py install --user -+ mkdir -p $(DESTDIR)/lib/python3.7/site-packages -+ cd "$(PYPI_ARCHIVE_TEMP_DIR)$Sortools" && PYTHONPATH=$(DESTDIR)/lib/python3.7/site-packages:$(PYTHONPATH) "$(PYTHON_EXECUTABLE)" setup.py install --prefix $(DESTDIR) ++ mkdir -p $(DESTDIR)/lib/python$(UNIX_PYTHON_VER)/site-packages ++ cd "$(PYPI_ARCHIVE_TEMP_DIR)$Sortools" && PYTHONPATH=$(DESTDIR)/lib/python$(UNIX_PYTHON_VER)/site-packages:$(PYTHONPATH) "$(PYTHON_EXECUTABLE)" setup.py install --prefix $(DESTDIR) .PHONY: uninstall_python # Uninstall Python OR-Tools from the host system uninstall_python: diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb index 043f805b0f1..bcba52d63ce 100644 --- a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb @@ -16,7 +16,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s-fix-makefiles.patch'] checksums = [ '6118a931ffcf172c7e2371c3392f82380e9d2a29840daba7caff239ad70d4b44', # v7.1.tar.gz - 'ca5040a5031a3ef42f5ce6634d27f4550e8eb435a066ad44231f7ef1c20723c7', # OR-Tools-7.1-fix-makefiles.patch + '33872137acd45dba13e6ebd9cd9d2671cfdff73774937e8e82baae3ca3c83b95', # OR-Tools-7.1-fix-makefiles.patch ] builddependencies = [ From 987c0f91960bff36d75de6a79c6d6759308416bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 May 2019 21:37:48 +0200 Subject: [PATCH 1706/5331] also replace use of 'dummy' toolchain with SYSTEM in case name/version are not in order --- easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb | 2 +- easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb | 2 +- easybuild/easyconfigs/m/Molekel/Molekel-5.4.0-Linux_x86_64.eb | 2 +- easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb | 2 +- easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb | 2 +- easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb | 2 +- .../easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb | 2 +- .../easyconfigs/r/rCUDA/rCUDA-5.0_linux_64_scientificLinux6.eb | 2 +- easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb | 2 +- .../t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb index 7bbeac455b9..6b48f27b2fe 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.20.eb @@ -12,7 +12,7 @@ description = """BEDOPS is an open-source command-line toolkit that performs hig and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.""" -toolchain = {'version': 'dummy', 'name': 'dummy'} +toolchain = SYSTEM sources = ['%(namelower)s_linux_x86_64-v%(version)s.v2.tar.bz2'] source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb index 8a52cdc7285..38808243c7e 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.26.eb @@ -11,7 +11,7 @@ description = """BEDOPS is an open-source command-line toolkit that performs hig and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.""" -toolchain = {'version': 'dummy', 'name': 'dummy'} +toolchain = SYSTEM sources = ['%(namelower)s_linux_x86_64-v%(version)s.tar.bz2'] source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] diff --git a/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0-Linux_x86_64.eb b/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0-Linux_x86_64.eb index d68a450d82d..f69c22f76b8 100644 --- a/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0-Linux_x86_64.eb +++ b/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0-Linux_x86_64.eb @@ -7,7 +7,7 @@ versionsuffix = "-Linux_x86_64" homepage = "http://molekel.cscs.ch/" description = """Molekel is an open-source multi-platform molecular visualization program.""" -toolchain = {'version': 'dummy', 'name': 'dummy'} +toolchain = SYSTEM sources = ['molekel_%s_%s.tar.gz' % (version.replace('.', '_'), versionsuffix.lower()[1:])] source_urls = ['ftp://ftp.cscs.ch/out/molekel/molekel_%(version_major_minor)s'] diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb index 3c181896245..c8e4ffb7bcc 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02.eb @@ -6,7 +6,7 @@ version = '2.12.02' homepage = 'http://www.nasm.us/' description = """NASM: General-purpose x86 assembler""" -toolchain = {'version': 'dummy', 'name': 'dummy'} +toolchain = SYSTEM sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] diff --git a/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb b/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb index 48049683384..68665277b5b 100644 --- a/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb +++ b/easybuild/easyconfigs/n/NEdit/NEdit-5.5-Linux-x86.eb @@ -9,7 +9,7 @@ description = """NEdit is a multi-purpose text editor for the X Window System, which combines a standard, easy to use, graphical user interface with the thorough functionality and stability required by users who edit text eight hours a day.""" -toolchain = {'version': 'dummy', 'name': 'dummy'} +toolchain = SYSTEM subdir = '_'.join(version.split('-')[0].split('.')) source_urls = ['http://ftp.vim.org/editors/NEdit/v%s/executables' % subdir] diff --git a/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb b/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb index fc283ffce3f..dbb2dabffc2 100644 --- a/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb +++ b/easybuild/easyconfigs/p/pscom/pscom-5.0.48-1.eb @@ -7,7 +7,7 @@ homepage = 'http://www.par-tec.com' description = """ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer.""" -toolchain = {'version': '', 'name': 'dummy'} +toolchain = SYSTEM sources = ['%(version)s.zip'] source_urls = ['https://github.com/ParaStation/%(name)s/archive/'] diff --git a/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb b/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb index a2dd96fcb99..64f556061a4 100644 --- a/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb +++ b/easybuild/easyconfigs/r/rCUDA/rCUDA-4.0.1_linux_64_Ubuntu10.04.eb @@ -19,7 +19,7 @@ versionsuffix = "_linux_64_Ubuntu10.04" homepage = 'http://www.rcuda.net/' description = """The rCUDA Framework enables the concurrent usage of CUDA-compatible devices remotely.""" -toolchain = {'version': 'dummy', 'name': 'dummy'} +toolchain = SYSTEM # Obtain source via http://www.rcuda.net/index.php/software-request-form.html sources = ['rCUDA_%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/r/rCUDA/rCUDA-5.0_linux_64_scientificLinux6.eb b/easybuild/easyconfigs/r/rCUDA/rCUDA-5.0_linux_64_scientificLinux6.eb index 0e88376e1b0..27b34743a09 100644 --- a/easybuild/easyconfigs/r/rCUDA/rCUDA-5.0_linux_64_scientificLinux6.eb +++ b/easybuild/easyconfigs/r/rCUDA/rCUDA-5.0_linux_64_scientificLinux6.eb @@ -19,7 +19,7 @@ versionsuffix = "_linux_64_scientificLinux6" homepage = 'http://www.rcuda.net/' description = """The rCUDA Framework enables the concurrent usage of CUDA-compatible devices remotely.""" -toolchain = {'version': 'dummy', 'name': 'dummy'} +toolchain = SYSTEM sources = ['rCUDA_%(version)s%(versionsuffix)s.tar.gz'] diff --git a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb index 7752f26f31e..fb6c7a61893 100644 --- a/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb +++ b/easybuild/easyconfigs/r/rpmrebuild/rpmrebuild-2.11.eb @@ -16,7 +16,7 @@ homepage = 'http://rpmrebuild.sourceforge.net/' description = """rpmrebuild is a tool to build an RPM file from a package that has already been installed in a basic use""" -toolchain = {'version': 'dummy', 'name': 'dummy'} +toolchain = SYSTEM source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb index 4ec1dc753b5..262f633d3f3 100644 --- a/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb +++ b/easybuild/easyconfigs/t/Tesla-Deployment-Kit/Tesla-Deployment-Kit-5.319.43.eb @@ -19,7 +19,7 @@ description = """The Tesla Deployment Kit is a set of tools provided primarily f * NVIDIA Management Library (NVML), * Tesla Deployment Kit - Linux Edition (Aug 1st, 2013)""" -toolchain = {'version': 'dummy', 'name': 'dummy'} +toolchain = SYSTEM sources = ['tdk_%(version)s.tar.gz'] source_urls = ['http://developer.download.nvidia.com/compute/cuda/5_5/rel/nvml'] From 6163ad6c9ae8ecf2c961c2749453d77089e0b343 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 May 2019 09:27:16 +0200 Subject: [PATCH 1707/5331] adding easyconfigs: DendroPy-4.4.0-intel-2019a.eb --- .../d/DendroPy/DendroPy-4.4.0-intel-2019a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2019a.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2019a.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2019a.eb new file mode 100644 index 00000000000..bd01f3948ae --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-intel-2019a.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.4.0' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 60780d25129ec88fdb86e76c725dcd0ad0691c65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 May 2019 09:56:04 +0200 Subject: [PATCH 1708/5331] adding easyconfigs: msprime-0.7.0-intel-2019a-Python-3.7.2.eb --- .../msprime-0.7.0-intel-2019a-Python-3.7.2.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..29cf51c5d4f --- /dev/null +++ b/easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'msprime' +version = '0.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://msprime.readthedocs.io' +description = "msprime is a coalescent simulator and library for processing tree-based genetic data." + +toolchain = {'name': 'intel', 'version': '2019a'} + +dependencies = [ + ('GSL', '2.5'), + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), # for numpy + ('h5py', '2.9.0'), +] + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +download_dep_fail = True +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('pyrsistent', '0.15.2', { + 'checksums': ['16692ee739d42cf5e39cef8d27649a8c1fdb7aa99887098f1460057c5eb75c3a'], + }), + ('jsonschema', '3.0.1', { + 'checksums': ['0c0a81564f181de3212efa2d17de1910f8732fa1b71c42266d983cd74304e20d'], + }), + ('svgwrite', '1.2.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['72ef66c9fe367989823cb237ab7f012ac809dd3ba76c1b5ebd9aa61580e2e75e'], + }), + ('tskit', '0.1.5', { + 'checksums': ['fe30797923a23c590190cb0de84bbe215fed4ceea1f083da9757765f37678348'], + }), + (name, version, { + 'checksums': ['38d6849c164cd0ba23dad8fb2e18b84f177030b8658716df9bbaeb4d26981206'], + }), +] + +sanity_check_paths = { + 'files': ['bin/msp', 'bin/mspms'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From acd4f38a4c3f406a724d23e5388db7507f5d46fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 May 2019 21:45:26 +0200 Subject: [PATCH 1709/5331] temporarily disable checks for easyconfig files touched in PRs --- test/easyconfigs/easyconfigs.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2a935b8c3bc..dd45139b76b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -501,9 +501,9 @@ def test_changed_files_pull_request(self): self.assertTrue(False, error_msg) # run checks on changed easyconfigs - self.check_sha256_checksums(changed_ecs) - self.check_python_packages(changed_ecs) - self.check_sanity_check_paths(changed_ecs) + #self.check_sha256_checksums(changed_ecs) + #self.check_python_packages(changed_ecs) + #self.check_sanity_check_paths(changed_ecs) def test_zzz_cleanup(self): """Dummy test to clean up global temporary directory.""" From d260d7bd871d0bcd4a6109cc8aac7ea7a9c25ecb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 May 2019 11:42:11 +0200 Subject: [PATCH 1710/5331] drop download_dep_fail, already enabled by default in PythonBundle --- .../m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb index 29cf51c5d4f..d3d580bc0a1 100644 --- a/easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/m/msprime/msprime-0.7.0-intel-2019a-Python-3.7.2.eb @@ -19,7 +19,6 @@ dependencies = [ # required because we're building a Python package using Intel compilers on top of Python built with GCC check_ldshared = True -download_dep_fail = True use_pip = True exts_default_options = {'source_urls': [PYPI_SOURCE]} From a8f498472cb83354bfcf1c03f6b9541969ae19ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 May 2019 12:17:35 +0200 Subject: [PATCH 1711/5331] adding easyconfigs: OpenFOAM-v1612+-foss-2018b.eb and patches: OpenFOAM-v1612+-cleanup.patch --- .../o/OpenFOAM/OpenFOAM-v1612+-cleanup.patch | 739 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-v1612+-foss-2018b.eb | 38 + 2 files changed, 777 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-foss-2018b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-cleanup.patch new file mode 100644 index 00000000000..3edcb7cdff7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-cleanup.patch @@ -0,0 +1,739 @@ +# - Replace the OpenFOAM third-party libraries with EASYBUILD variables. +# - Set install dir, compiler, etc using EASYBUILD +# +# authors: Ward Poelmans , Kenneth Hoste (HPC-UGent), Mark Olesen +diff -ru OpenFOAM-v1612+.orig/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-v1612+/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-v1612+.orig/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/applications/utilities/mesh/manipulation/setSet/Allwmake 2019-05-22 18:08:47.152405000 +0200 +@@ -9,11 +9,13 @@ + # + # use readline if available + # +-if [ -f /usr/include/readline/readline.h ] ++#system# if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo " found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" + export LINK_FLAGS="-lreadline" ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake $targetType +diff -ru OpenFOAM-v1612+.orig/etc/bashrc OpenFOAM-v1612+/etc/bashrc +--- OpenFOAM-v1612+.orig/etc/bashrc 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/etc/bashrc 2019-05-22 18:12:57.665211000 +0200 +@@ -42,8 +42,9 @@ + # + # Please set to the appropriate path if the default is not correct. + # +-[ $BASH_SOURCE ] && FOAM_INST_DIR=$(\cd ${BASH_SOURCE%/*/*/*} && \pwd -P) || \ +-FOAM_INST_DIR=$HOME/$WM_PROJECT ++# Easybuild module sets FOAM_INST_DIR ++# [ $BASH_SOURCE ] && FOAM_INST_DIR=$(\cd ${BASH_SOURCE%/*/*/*} && \pwd -P) || \ ++# FOAM_INST_DIR=$HOME/$WM_PROJECT + # FOAM_INST_DIR=~$WM_PROJECT + # FOAM_INST_DIR=/opt/$WM_PROJECT + # FOAM_INST_DIR=/usr/local/$WM_PROJECT +@@ -86,7 +87,7 @@ + #- MPI implementation: + # WM_MPLIB = SYSTEMOPENMPI | OPENMPI | SYSTEMMPI | MPICH | MPICH-GM | HPMPI + # | MPI | FJMPI | QSMPI | SGIMPI | INTELMPI +-export WM_MPLIB=SYSTEMOPENMPI ++export WM_MPLIB=EASYBUILDMPI + + #- Operating System: + # WM_OSTYPE = POSIX | ??? +@@ -115,7 +116,8 @@ + + # Location of third-party software + # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +-export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION ++# Easybuild handles all third-party ++export WM_THIRD_PARTY_DIR=$WM_PROJECT_DIR/ThirdParty + + # Location of site-specific templates etc + # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +diff -ru OpenFOAM-v1612+.orig/etc/config.sh/CGAL OpenFOAM-v1612+/etc/config.sh/CGAL +--- OpenFOAM-v1612+.orig/etc/config.sh/CGAL 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/etc/config.sh/CGAL 2019-05-22 18:16:53.958395000 +0200 +@@ -1,88 +1,3 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2014-2016 OpenFOAM Foundation +-# \\/ M anipulation | Copyright (C) 2016 OpenCFD Ltd. +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/CGAL +-# +-# Description +-# Setup file for CGAL (& boost) include/libraries. +-# Sourced from OpenFOAM-/etc/bashrc +-# +-# If using system-wide installations, use the following settings: +-# +-# boost_version=boost-system +-# cgal_version=cgal-system +-# +-# If the system boost/cgal is unusable (eg, too old) and you don't +-# have or want a ThirdParty installation: +-# +-# boost_version=boost-none +-# cgal_version=cgal-none +-# +-# If using a central installation, but not located under ThirdParty: +-# - specify boost-system / cgal-system +-# - provide full paths for BOOST_ARCH_PATH / CGAL_ARCH_PATH +-# +-# Note +-# When _foamAddLib is unset (eg, called from makeCGAL): +-# - boost_version / cgal_version variables are retained. +-# - the LD_LIBRARY_PATH is not adjusted. +-#------------------------------------------------------------------------------ +- +-boost_version=boost_1_62_0 +-cgal_version=CGAL-4.9 +- +-export BOOST_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$boost_version +-export CGAL_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cgal_version +- +-#------------------------------------------------------------------------------ +-if [ "$FOAM_VERBOSE" -a "$PS1" ] +-then +- echo "Using boost ($boost_version) -> $BOOST_ARCH_PATH" 1>&2 +- echo "Using CGAL ($cgal_version) -> $CGAL_ARCH_PATH" 1>&2 +-fi +- +-if type _foamAddLib > /dev/null 2>&1 # normal sourcing +-then +- +- # If BOOST_ARCH_PATH, CGAL_ARCH_PATH do not end with '-system' or '-none', +- # they are either located within ThirdParty, or a central installation +- # outside of ThirdParty and must be added to the lib-path. +- +- ending="${BOOST_ARCH_PATH##*-}" +- if [ "$ending" != none -a "$ending" != system ] +- then +- _foamAddLib $BOOST_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH +- fi +- +- ending="${CGAL_ARCH_PATH##*-}" +- if [ "$ending" != none -a "$ending" != system ] +- then +- _foamAddLib $CGAL_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH +- fi +- +- unset boost_version cgal_version ending +- +-fi +- +-#------------------------------------------------------------------------------ ++# EasyBuild settings ++export BOOST_ARCH_PATH=$EBROOTBOOST ++export CGAL_ARCH_PATH=$EBROOTCGAL +diff -ru OpenFOAM-v1612+.orig/etc/config.sh/ensight OpenFOAM-v1612+/etc/config.sh/ensight +--- OpenFOAM-v1612+.orig/etc/config.sh/ensight 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/etc/config.sh/ensight 2019-05-22 18:16:20.727801000 +0200 +@@ -1,60 +1,2 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation +-# \\/ M anipulation | +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/ensight +-# +-# Description +-# Setup file for Ensight +-# Sourced from OpenFOAM-*/etc/bashrc +-# +-#------------------------------------------------------------------------------ +- +-# Fallback value +-if [ ! -d "$CEI_HOME" ] +-then +- export CEI_HOME=/usr/local/ensight/CEI +-fi +- +-if [ -r $CEI_HOME ] +-then +- +- # Special treatment for 32bit OpenFOAM and 64bit Ensight +- if [ "$WM_ARCH" = linux -a `uname -m` = x86_64 ] +- then +- export CEI_ARCH=linux_2.6_32 +- fi +- +- # Add to path if required +- if [ "$CEI_HOME/bin/ensight" != "`which ensight 2>/dev/null`" ] +- then +- export PATH=$CEI_HOME/bin:$PATH +- fi +- +- export ENSIGHT9_INPUT=dummy +- export ENSIGHT9_READER=$FOAM_LIBBIN +-else +- unset CEI_HOME +-fi +- +-#------------------------------------------------------------------------------ ++# Easybuild settings ++# ununsed +diff -ru OpenFOAM-v1612+.orig/etc/config.sh/FFTW OpenFOAM-v1612+/etc/config.sh/FFTW +--- OpenFOAM-v1612+.orig/etc/config.sh/FFTW 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/etc/config.sh/FFTW 2019-05-22 18:15:15.893684000 +0200 +@@ -1,77 +1,2 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2016 OpenCFD Ltd. +-# \\/ M anipulation | +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/FFTW +-# +-# Description +-# Setup file for FFTW include/libraries. +-# Sourced from OpenFOAM-/etc/bashrc +-# +-# If using system-wide installations, use the following settings: +-# +-# fftw_version=fftw-system +-# +-# If the system fftw is unusable (eg, too old) and you don't +-# have or want a ThirdParty installation: +-# +-# fftw_version=fftw-none +-# +-# If using a central installation, but not located under ThirdParty: +-# - specify fftw-system +-# - provide full paths for FFTW_ARCH_PATH +-# +-# Note +-# When _foamAddLib is unset (eg, called from makeFFTW): +-# - fftw_version variable is retained. +-# - the LD_LIBRARY_PATH is not adjusted. +-#------------------------------------------------------------------------------ +- +-fftw_version=fftw-3.3.5 +- +-export FFTW_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$fftw_version +- +-#------------------------------------------------------------------------------ +-if [ "$FOAM_VERBOSE" -a "$PS1" ] +-then +- echo "Using fftw ($fftw_version) -> $FFTW_ARCH_PATH" 1>&2 +-fi +- +-if type _foamAddLib > /dev/null 2>&1 # normal sourcing +-then +- +- # If FFTW_ARCH_PATH does not end with '-system' or '-none', +- # it is either located within ThirdParty, or a central installation +- # outside of ThirdParty and must be added to the lib-path. +- +- ending="${FFTW_ARCH_PATH##*-}" +- if [ "$ending" != none -a "$ending" != system ] +- then +- _foamAddLib $FFTW_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH +- fi +- +- unset fftw_version ending +- +-fi +- +-#------------------------------------------------------------------------------ ++# EasyBuild settings ++export FFTW_ARCH_PATH=$EBROOTFFTW +diff -ru OpenFOAM-v1612+.orig/etc/config.sh/gperftools OpenFOAM-v1612+/etc/config.sh/gperftools +--- OpenFOAM-v1612+.orig/etc/config.sh/gperftools 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/etc/config.sh/gperftools 2019-05-22 18:14:14.368290000 +0200 +@@ -1,78 +1,3 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2012-2016 OpenFOAM Foundation +-# \\/ M anipulation | Copyright (C) 2016 OpenCFD Ltd. +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/gperftools +-# +-# Description +-# Setup file for gperftools binaries and libraries. +-# Sourced from OpenFOAM-/etc/bashrc +-# +-# If using system-wide installations, use the following settings: +-# +-# gperftools_version=gperftools-system +-# +-# If the system gperftools is unusable (eg, too old) and you don't +-# have or want a ThirdParty installation: +-# +-# gperftools_version=gperftools-none +-# +-# If using a central installation, but not located under ThirdParty: +-# - specify gperftools-system +-# - provide full paths for GPERFTOOLS_ARCH_PATH +-# +-# Note +-# When _foamAddLib is unset (eg, called from makeGperftools): +-# - gperftools_version variable are retained. +-# - the LD_LIBRARY_PATH and PATH are not adjusted. +-#------------------------------------------------------------------------------ +- +-gperftools_version=gperftools-2.5 +- +-GPERFTOOLS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$gperftools_version +- +-#------------------------------------------------------------------------------ +-if [ "$FOAM_VERBOSE" -a "$PS1" ] +-then +- echo "Using gperftools ($gperftools_version) -> $GPERFTOOLS_ARCH_PATH" 1>&2 +-fi +- +-if type _foamAddLib > /dev/null 2>&1 # normal sourcing +-then +- +- # If GPERFTOOLS_ARCH_PATH does not end with '-system' or '-none', +- # it is located within ThirdParty, or a central installation +- # outside of ThirdParty and must be added to the lib-path. +- +- ending="${GPERFTOOLS_ARCH_PATH##*-}" +- if [ "$ending" != none -a "$ending" != system ] +- then +- _foamAddLib $GPERFTOOLS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH +- _foamAddPath $GPERFTOOLS_ARCH_PATH/bin +- fi +- +- unset gperftools_version ending +- +-fi +- +-#------------------------------------------------------------------------------ ++# EasyBuild settings ++gperftools_version=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS +diff -ru OpenFOAM-v1612+.orig/etc/config.sh/metis OpenFOAM-v1612+/etc/config.sh/metis +--- OpenFOAM-v1612+.orig/etc/config.sh/metis 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/etc/config.sh/metis 2019-05-22 18:15:46.717223000 +0200 +@@ -1,60 +1,4 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2013-2016 OpenFOAM Foundation +-# \\/ M anipulation | +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/metis +-# +-# Description +-# Setup file for metis include/libraries. +-# Sourced during wmake process only. +-# +-# Normally used to specify the metis version and location for a +-# ThirdParty installation. +-# +-# If using system-wide installations, use the following setting: +-# +-# METIS_VERSION=metis-system +-# +-# If the system metis is unusable (eg, too old) and you don't +-# have or want a ThirdParty installation: +-# +-# METIS_VERSION=metis-none +-# +-# If using a central installation, but not located under ThirdParty: +-# - specify metis-system +-# - provide full paths for METIS_ARCH_PATH +-# +-# Note +-# A csh version is not needed, since the values here are only sourced +-# during the wmake process. +-# +-# Metis can also be entirely disabled, by either renaming this file or +-# by creating an empty one with the same name at a user or site location. +-# +-#------------------------------------------------------------------------------ +- +-METIS_VERSION=metis-5.1.0 +- +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION +- +-#------------------------------------------------------------------------------ ++# Easybuild settings ++METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS ++[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH=$METIS_ROOT +diff -ru OpenFOAM-v1612+.orig/etc/config.sh/mpi OpenFOAM-v1612+/etc/config.sh/mpi +--- OpenFOAM-v1612+.orig/etc/config.sh/mpi 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/etc/config.sh/mpi 2019-05-22 18:08:47.171242079 +0200 +@@ -75,6 +75,10 @@ + _foamAddMan $MPI_ARCH_PATH/share/man + ;; + ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; ++ + SYSTEMMPI) + export FOAM_MPI=mpi-system + +diff -ru OpenFOAM-v1612+.orig/etc/config.sh/paraview OpenFOAM-v1612+/etc/config.sh/paraview +--- OpenFOAM-v1612+.orig/etc/config.sh/paraview 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/etc/config.sh/paraview 2019-05-22 18:19:26.377168000 +0200 +@@ -54,7 +54,7 @@ + # - the ParaView_VERSION variable is retained. + #------------------------------------------------------------------------------ + +-ParaView_VERSION=5.0.1 ++ParaView_VERSION=$EBVERSIONPARAVIEW + ParaView_MAJOR=detect # Automatically determine major version + + cmake_version=cmake-system +@@ -69,14 +69,6 @@ + ) \ + && PATH="$cleaned" + +-# ThirdParty cmake +-cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake_version +-if [ -r $cmake/bin/cmake ] +-then +- # _foamAddPath not available when foamPV function is used +- PATH=$cmake/bin:$PATH +-fi +- + # Evaluate command-line parameters for ParaView + _foamParaviewEval() + { +@@ -117,7 +109,7 @@ + pvName=ParaView-$ParaView_VERSION + pvMajor=paraview-$ParaView_MAJOR + +- export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$pvName ++ export ParaView_DIR=$EBROOTPARAVIEW + + # Set paths if binaries are present + if [ -r $ParaView_DIR ] +@@ -130,17 +122,6 @@ + export PV_PLUGIN_PATH=$FOAM_LIBBIN/$pvMajor + export LD_LIBRARY_PATH=$pvLibDir:$LD_LIBRARY_PATH + +- # Add in python libraries if required +- if [ -r $pvPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$pvPython:$pvLibDir +- else +- export PYTHONPATH=$pvPython:$pvLibDir +- fi +- fi +- + if [ "$FOAM_VERBOSE" -a "$PS1" ] + then + echo "Using paraview" +diff -ru OpenFOAM-v1612+.orig/etc/config.sh/scotch OpenFOAM-v1612+/etc/config.sh/scotch +--- OpenFOAM-v1612+.orig/etc/config.sh/scotch 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/etc/config.sh/scotch 2019-05-22 18:14:44.931863000 +0200 +@@ -1,60 +1,4 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation +-# \\/ M anipulation | +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/scotch +-# +-# Description +-# Setup file for scotch include/libraries. +-# Sourced during wmake process only. +-# +-# Normally used to specify the scotch version and location for a +-# ThirdParty installation. +-# +-# If using system-wide installations, use the following setting: +-# +-# SCOTCH_VERSION=scotch-system +-# +-# If the system scotch is unusable (eg, too old) and you don't +-# have or want a ThirdParty installation: +-# +-# SCOTCH_VERSION=scotch-none +-# +-# If using a central installation, but not located under ThirdParty: +-# - specify scotch-system +-# - provide full path for SCOTCH_ARCH_PATH +-# +-# Note +-# A csh version is not needed, since the values here are only sourced +-# during the wmake process. +-# +-# Scotch can also be entirely disabled, by either renaming this file or +-# by creating an empty one with the same name at a user or site location. +-# +-#------------------------------------------------------------------------------ +- +-SCOTCH_VERSION=scotch_6.0.3 +- +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION +- +-#------------------------------------------------------------------------------ ++# Easybuild settings ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH ++[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH=$SCOTCH_ROOT +diff -ru OpenFOAM-v1612+.orig/etc/config.sh/settings OpenFOAM-v1612+/etc/config.sh/settings +--- OpenFOAM-v1612+.orig/etc/config.sh/settings 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/etc/config.sh/settings 2019-05-22 18:08:47.175698736 +0200 +@@ -138,6 +138,15 @@ + esac + + ++##Easybuild## compiler settings ++CXXFLAGS="$CXXFLAGS -std=c++11" # C++11 is essential ++export WM_CC=$CC ++export WM_CXX=$CXX ++export WM_CFLAGS=$CFLAGS ++export WM_CXXFLAGS=$CXXFLAGS ++export WM_LDFLAGS=$LDFLAGS ++ ++ + #------------------------------------------------------------------------------ + + # Location of the jobControl directory +diff -ru OpenFOAM-v1612+.orig/etc/config.sh/vtk OpenFOAM-v1612+/etc/config.sh/vtk +--- OpenFOAM-v1612+.orig/etc/config.sh/vtk 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/etc/config.sh/vtk 2019-05-22 18:13:44.870020000 +0200 +@@ -1,80 +1,3 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2016 OpenCFD Ltd. +-# \\/ M anipulation | +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/vtk +-# +-# Description +-# Setup file for VTK (and MESA) +-# Sourced from OpenFOAM-/etc/bashrc +-# +-# The library path is only adjusted when the paths specified here +-# actually exist at the time of sourcing. +-# +-# Note +-# When _foamAddLib is unset +-# - the vtk_version, mesa_version variables are retained. +-# (for future integration into ThirdParty build) +-# +-# It is recommended to use the VTK sources from ParaView 5.0.1. +-# +-# See the BuildIssues.txt about problems that can be encountered when using +-# the 'plain' VTK sources. +-#------------------------------------------------------------------------------ +- +-vtk_version=VTK-7.1.0 +-mesa_version=mesa-13.0.1 +- +-export VTK_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$vtk_version +-export MESA_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$mesa_version +- +-#------------------------------------------------------------------------------ +-if [ "$FOAM_VERBOSE" -a "$PS1" ] +-then +- echo "Using vtk ($vtk_version) -> $VTK_DIR" 1>&2 +- echo "Using mesa ($mesa_version) -> $MESA_ARCH_PATH" 1>&2 +-fi +- +-if type _foamAddLib > /dev/null 2>&1 # normal sourcing +-then +- +- # Set paths if binaries are present +- if [ -r $VTK_DIR ] +- then +- # Uses lib/ and not lib64/ +- _foamAddLib $VTK_DIR/lib +- else +- unset VTK_DIR +- fi +- +- if [ -r $MESA_ARCH_PATH ] +- then +- _foamAddLib $MESA_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH +- else +- unset MESA_ARCH_PATH +- fi +- +- unset vtk_version mesa_version +-fi +- +-#------------------------------------------------------------------------------ ++# Easybuild settings ++export VTK_DIR=$EBROOTVTK ++export MESA_ARCH_PATH=$EBROOTMESA +diff -ru OpenFOAM-v1612+.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-v1612+/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-v1612+.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/src/parallel/decompose/ptscotchDecomp/Make/options 2019-05-22 18:08:47.155602000 +0200 +@@ -5,7 +5,6 @@ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + /* +diff -ru OpenFOAM-v1612+.orig/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-v1612+/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-v1612+.orig/src/parallel/decompose/scotchDecomp/Make/options 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/src/parallel/decompose/scotchDecomp/Make/options 2019-05-22 18:08:47.157613000 +0200 +@@ -8,7 +8,6 @@ + EXE_INC = \ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + /* +--- OpenFOAM-v1612+.orig/src/parallel/decompose/Allwmake 2016-12-23 15:22:59.000000000 +0100 ++++ OpenFOAM-v1612+/src/parallel/decompose/Allwmake 2019-05-23 10:46:14.499279861 +0200 +@@ -36,7 +36,9 @@ + + # Library + [ -r $FOAM_EXT_LIBBIN/libmetis.so ] || \ ++ [ -r $METIS_ARCH_PATH/lib/libmetis.a ] || \ + [ -r $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libmetis.so ] || \ ++ [ -r $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libmetis.a ] || \ + [ "${METIS_ARCH_PATH##*-}" = system ] || { + echo "$warning (missing library)" + return 2 +@@ -90,7 +92,9 @@ + + # Library + [ -r $FOAM_EXT_LIBBIN/libscotch.so ] || \ ++ [ -r $SCOTCH_ARCH_PATH/lib/libscotch.a ] || \ + [ -r $SCOTCH_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libscotch.so ] || \ ++ [ -r $SCOTCH_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libscotch.a ] || \ + [ "${SCOTCH_ARCH_PATH##*-}" = system ] || { + echo "$warning (missing library)" + return 2 diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-foss-2018b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-foss-2018b.eb new file mode 100644 index 00000000000..d69a4378353 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-foss-2018b.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = 'v1612+' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2018b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/openfoamplus/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = ['OpenFOAM-%(version)s-cleanup.patch'] +checksums = [ + '2909c43506a68e1f23efd0ca6186a6948ae0fc8fe1e39c78cc23ef0d69f3569d', # OpenFOAM-v1612+.tgz + '80b3beceebb49151bc8b021e0cceeed27740bbaf3f5945eb51a1830d086aec30', # OpenFOAM-v1612+-cleanup.patch +] + +#patches = ['OpenFOAM-%(version)s-cleanup.patch'] +dependencies = [ + ('libreadline', '7.0'), + ('ncurses', '6.1'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.6'), + ('CGAL', '4.11.1', '-Python-2.7.15'), + ('ParaView', '5.4.1', '-mpi'), +] + +builddependencies = [ + ('Bison', '3.0.5'), + ('CMake', '3.11.4'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' From f903ca31ec2c877a14fefaa134618169e51dc093 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 May 2019 14:52:10 +0200 Subject: [PATCH 1712/5331] drop commented out patches line in OpenFOAM v1612+ easyconfig --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-foss-2018b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-foss-2018b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-foss-2018b.eb index d69a4378353..bee169f3c2d 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-foss-2018b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1612+-foss-2018b.eb @@ -18,7 +18,6 @@ checksums = [ '80b3beceebb49151bc8b021e0cceeed27740bbaf3f5945eb51a1830d086aec30', # OpenFOAM-v1612+-cleanup.patch ] -#patches = ['OpenFOAM-%(version)s-cleanup.patch'] dependencies = [ ('libreadline', '7.0'), ('ncurses', '6.1'), From f0a253430e0ce038e950ee389d5c56905f914927 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 23 May 2019 08:00:52 -0700 Subject: [PATCH 1713/5331] libgeotiff --with-jpeg --- .../easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb index 0ff322b64b1..3946fe78878 100644 --- a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.5.1-GCCcore-8.2.0.eb @@ -24,6 +24,7 @@ dependencies = [ ] configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' sanity_check_paths = { 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], From a953fa5dd1a291e35e50d58b17b11139faed4ecb Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Thu, 23 May 2019 17:30:19 +0200 Subject: [PATCH 1714/5331] adding easyconfigs: google-java-format-1.7-Java-1.8.eb --- .../google-java-format-1.7-Java-1.8.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/g/google-java-format/google-java-format-1.7-Java-1.8.eb diff --git a/easybuild/easyconfigs/g/google-java-format/google-java-format-1.7-Java-1.8.eb b/easybuild/easyconfigs/g/google-java-format/google-java-format-1.7-Java-1.8.eb new file mode 100644 index 00000000000..4df63027d42 --- /dev/null +++ b/easybuild/easyconfigs/g/google-java-format/google-java-format-1.7-Java-1.8.eb @@ -0,0 +1,22 @@ +easyblock = 'JAR' + +name = 'google-java-format' +version = '1.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/google/google-java-format' +description = """Reformats Java source code to comply with Google Java Style.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(name)s-%(version)s-all-deps.jar'] +source_urls = ['https://github.com/google/%(name)s/releases/download/%(name)s-%(version)s/'] + +dependencies = [('Java', '1.8')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [] +} + +moduleclass = 'devel' From 5efc306e2d4fa749cb1a47ade96df4ca391a7c55 Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Thu, 23 May 2019 17:55:57 +0200 Subject: [PATCH 1715/5331] add checksums in google-java-format-1.7-Java-1.8.eb --- .../g/google-java-format/google-java-format-1.7-Java-1.8.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/google-java-format/google-java-format-1.7-Java-1.8.eb b/easybuild/easyconfigs/g/google-java-format/google-java-format-1.7-Java-1.8.eb index 4df63027d42..d27507f68e6 100644 --- a/easybuild/easyconfigs/g/google-java-format/google-java-format-1.7-Java-1.8.eb +++ b/easybuild/easyconfigs/g/google-java-format/google-java-format-1.7-Java-1.8.eb @@ -9,8 +9,9 @@ description = """Reformats Java source code to comply with Google Java Style.""" toolchain = {'name': 'dummy', 'version': ''} -sources = ['%(name)s-%(version)s-all-deps.jar'] source_urls = ['https://github.com/google/%(name)s/releases/download/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s-all-deps.jar'] +checksums = ['0894ee02019ee8b4acd6df09fb50bac472e7199e1a5f041f8da58d08730694aa'] dependencies = [('Java', '1.8')] From a77fe292737f57f373e1a1965e07e7e11ad433b3 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 23 May 2019 09:18:18 -0700 Subject: [PATCH 1716/5331] update ImageMagick 7.0.8-46 --- .../ImageMagick-7.0.8-46-GCCcore-8.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.8-46-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.8-46-GCCcore-8.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.8-46-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..34ae28f6fc0 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.8-46-GCCcore-8.2.0.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.8-46' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/ImageMagick/ImageMagick/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e6f49b5883d26c7f85207779397bdb083e629acec8de423e6b1d32038e23ded8'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('X11', '20190311'), + ('Ghostscript', '9.27'), + ('JasPer', '2.0.14'), + ('libjpeg-turbo', '2.0.2'), + ('LibTIFF', '4.0.10'), + ('LittleCMS', '2.9'), +] + +builddependencies = [ + ('binutils', '2.31.1'), + ('pkg-config', '0.29.2'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', + 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' From 8bd208aa76ea7d2db4f6a6c3f3ce096df2f4bf53 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 23 May 2019 22:27:45 +0200 Subject: [PATCH 1717/5331] adding easyconfigs: BLAST+-2.9.0-foss-2019a.eb, Boost-1.67.0-gompi-2019a.eb --- .../b/BLAST+/BLAST+-2.9.0-foss-2019a.eb | 51 +++++++++++++++++++ .../b/Boost/Boost-1.67.0-gompi-2019a.eb | 25 +++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-foss-2019a.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.67.0-gompi-2019a.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-foss-2019a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-foss-2019a.eb new file mode 100644 index 00000000000..d53823c8b59 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-foss-2019a.eb @@ -0,0 +1,51 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.9.0' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('PCRE', '8.43'), + ('Boost', '1.67.0'), # build fails with Boost-1.70.0 + ('GMP', '6.1.2'), + ('libpng', '1.6.36'), + ('libjpeg-turbo', '2.0.2'), + ('LMDB', '0.9.23'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.67.0-gompi-2019a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.67.0-gompi-2019a.eb new file mode 100644 index 00000000000..2d27aa3c609 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.67.0-gompi-2019a.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.67.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8aa4e330c870ef50a896634c931adf468b21f8a69b77007e45c444151229f665'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('XZ', '5.2.4'), +] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' From f60e2c85146a49aa9c2814dd4676b5762aad7a75 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 23 May 2019 22:29:54 +0200 Subject: [PATCH 1718/5331] adding easyconfigs: Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb, Bowtie2-2.3.5.1-GCCcore-8.2.0.eb, SAMtools-1.9-GCCcore-8.2.0.eb, SPAdes-3.13.1-GCCcore-8.2.0.eb --- .../Bowtie2/Bowtie2-2.3.5.1-GCCcore-8.2.0.eb | 38 ++++++++++++++ .../s/SAMtools/SAMtools-1.9-GCCcore-8.2.0.eb | 34 +++++++++++++ .../s/SPAdes/SPAdes-3.13.1-GCCcore-8.2.0.eb | 49 +++++++++++++++++++ ...Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb | 37 ++++++++++++++ 4 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.5.1-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.1-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.5.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.5.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..a0a33a28275 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.3.5.1-GCCcore-8.2.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp + +name = 'Bowtie2' +version = '2.3.5.1' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('tbb', '2019_U4'), + ('zlib', '1.2.11'), +] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..8237a2d0176 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.9-GCCcore-8.2.0.eb @@ -0,0 +1,34 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +## + +name = 'SAMtools' +version = '1.9' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['083f688d7070082411c72c27372104ed472ed7a620591d06f928e653ebc23482'] + +builddependencies = [('binutils', '2.31.1')] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.1'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.4'), + ('cURL', '7.63.0'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.1-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..72ae53a7480 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.1-GCCcore-8.2.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = "CMakeMake" + +name = 'SPAdes' +version = '3.13.1' + +homepage = 'http://cab.spbu.ru/software/spades/' +description = """Genome assembler for single-cell and isolates data sets""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['8da29b72fb56170dd39e3a8ea5074071a8fa63b29346874010b8d293c2f72a3e'] + +builddependencies = [ + ('CMake', '3.13.3'), + ('binutils', '2.31.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('libreadline', '8.0'), +] + +start_dir = 'src' + +separate_build_dir = True + +configopts = ' -DBoost_NO_BOOST_CMAKE=ON' + +sanity_check_commands = [('spades.py', '--test')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', + 'spades-ionhammer', 'spades-kmercount', 'spades.py']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..763f7216106 --- /dev/null +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'Unicycler' +version = '0.4.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = '' +description = """ Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets + where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) + where it runs a miniasm+Racon pipeline. """ + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/rrwick/Unicycler/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a8cf65e46dc2694b0fbd4e9190c73a1f300921457aadfab27a1792b785620d63'] + +dependencies = [ + ('Python', '3.7.2'), + ('Java', '11', '', True), + ('Bowtie2', '2.3.5.1'), + ('SAMtools', '1.9'), + ('SPAdes', '3.13.1'), + ('Racon', '1.3.2'), + ('Pilon', '1.23', '-Java-%(javaver)s', True), + ('BLAST+', '2.9.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 6de88157a017abcb73778991fdba549764e43f81 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 23 May 2019 22:32:24 +0200 Subject: [PATCH 1719/5331] adding easyconfigs: canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb --- .../canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb diff --git a/easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb b/easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb new file mode 100644 index 00000000000..0289abea26c --- /dev/null +++ b/easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'canu' +version = '1.8' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://canu.readthedocs.io' +description = "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/marbl/canu/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4'] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [ + ('Java', '11', '', True), + ('Perl', '5.28.1'), + ('gnuplot', '5.2.6'), +] + +start_dir = 'src' + +files_to_copy = ['Linux-amd64/bin', 'Linux-amd64/lib', 'Linux-amd64/share', 'README*'] + +sanity_check_paths = { + 'files': ['bin/canu', 'lib/libcanu.a'], + 'dirs': ['lib/site_perl', 'share'], +} +sanity_check_commands = [ + "canu -version", + "canu -options", +] + +moduleclass = 'bio' From 2a3033db88988d3e1c382d618eb7cedebd5eddd6 Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 24 May 2019 09:48:04 +0800 Subject: [PATCH 1720/5331] set openmp toolchainopt to True --- easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb index a76d437222d..b45d89c3cfc 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb @@ -14,7 +14,7 @@ homepage = 'http://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2018b'} -toolchainopts = {'usempi': True} +toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb index c627fe2d009..62d6495164f 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb @@ -14,7 +14,7 @@ homepage = 'http://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2018b'} -toolchainopts = {'usempi': True} +toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb index c04ef1b2663..f890787f0a1 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb @@ -14,7 +14,7 @@ homepage = 'http://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2018b'} -toolchainopts = {'usempi': True} +toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb index 026c6c45625..eba337ae739 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb @@ -14,7 +14,7 @@ homepage = 'http://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2018b'} -toolchainopts = {'usempi': True} +toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] From ecbf4ead65a8ad648315ba09bbf35ef3239870be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 May 2019 11:25:45 +0200 Subject: [PATCH 1721/5331] adding easyconfigs: CRF++-0.58-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb --- ...58-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/CRF++/CRF++-0.58-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/c/CRF++/CRF++-0.58-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/c/CRF++/CRF++-0.58-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..ccbc66d427a --- /dev/null +++ b/easybuild/easyconfigs/c/CRF++/CRF++-0.58-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'CRF++' +version = '0.58' + +homepage = 'https://taku910.github.io/crfpp/' +description = """CRF++ is a simple, customizable, and open source implementation of + Conditional Random Fields (CRFs) for segmenting/labeling sequential data. CRF++ is + designed for generic purpose and will be applied to a variety of NLP tasks, such as + Named Entity Recognition, Information Extraction and Text Chunking. """ + +toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} +toolchainopts = {'pic': True} + +# manual download from https://taku910.github.io/crfpp/#download (via Google Drive) +sources = [SOURCE_TAR_GZ] +checksums = ['9d1c0a994f25a5025cede5e1d3a687ec98cd4949bfb2aae13f2a873a13259cb2'] + +configopts = '--with-pic' +buildopts = 'CXXFLAGS="$CXXFLAGS -Wall -finline"' + +sanity_check_paths = { + 'files': ["bin/crf_learn", "bin/crf_test"], + 'dirs': [] +} + +moduleclass = 'data' From 6f931b28d3695980d670c47a3176fe0018c192e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 May 2019 11:27:31 +0200 Subject: [PATCH 1722/5331] adding easyconfigs: TiMBL-6.4.13-iimpi-2019a.eb, TiCCutils-0.21-iimpi-2019a.eb, libtar-1.2.20-GCCcore-8.2.0.eb --- .../l/libtar/libtar-1.2.20-GCCcore-8.2.0.eb | 31 ++++++++++++++++ .../t/TiCCutils/TiCCutils-0.21-iimpi-2019a.eb | 36 +++++++++++++++++++ .../t/TiMBL/TiMBL-6.4.13-iimpi-2019a.eb | 33 +++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtar/libtar-1.2.20-GCCcore-8.2.0.eb create mode 100644 easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.21-iimpi-2019a.eb create mode 100644 easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.13-iimpi-2019a.eb diff --git a/easybuild/easyconfigs/l/libtar/libtar-1.2.20-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libtar/libtar-1.2.20-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..ec05311e883 --- /dev/null +++ b/easybuild/easyconfigs/l/libtar/libtar-1.2.20-GCCcore-8.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libtar' +version = '1.2.20' + +homepage = 'https://repo.or.cz/libtar.git' +description = "C library for manipulating POSIX tar files" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://repo.or.cz/libtar.git/snapshot/'] +sources = [{ + 'download_filename': '0907a9034eaf2a57e8e4a9439f793f3f05d446cd.tar.gz', + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['4847207d878e79a4acbe32f096e57cd72c9507171953849e4d7eafe312418d95'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.31.1'), +] + +preconfigopts = "autoreconf --force --install && " + +sanity_check_paths = { + 'files': ['bin/libtar', 'include/libtar.h', 'include/libtar_listhash.h', + 'lib/libtar.a', 'lib/libtar.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.21-iimpi-2019a.eb b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.21-iimpi-2019a.eb new file mode 100644 index 00000000000..41e60d540af --- /dev/null +++ b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.21-iimpi-2019a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'TiCCutils' +version = '0.21' + +homepage = 'https://github.com/LanguageMachines/ticcutils' +description = """TiCC utils is a collection of generic C++ software which is used in a lot of programs produced at + Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and + Centre for Dutch Language and Speech at University of Antwerp.""" + +toolchain = {'name': 'iimpi', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LanguageMachines/ticcutils/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['73a6b0327d1c14b59ec9e790ef5d5e60dd40b0fb740bf131ee4228565721bd11'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('libtar', '1.2.20'), + ('Boost', '1.70.0'), + ('ICU', '64.2'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.8'), +] + +configopts = "--with-pic --with-boost=$EBROOTBOOST --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libticcutils.%s' % SHLIB_EXT, 'lib/libticcutils.a'], + 'dirs': ['include/ticcutils'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.13-iimpi-2019a.eb b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.13-iimpi-2019a.eb new file mode 100644 index 00000000000..552d4fc75b4 --- /dev/null +++ b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.13-iimpi-2019a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'TiMBL' +version = '6.4.13' + +homepage = 'https://languagemachines.github.io/timbl' +description = """TiMBL (Tilburg Memory Based Learner) + is an open source software package implementing several memory-based learning algorithms, + among which IB1-IG, an implementation of k-nearest neighbor classification with feature weighting suitable for + symbolic feature spaces, and IGTree, a decision-tree approximation of IB1-IG. All implemented algorithms have in + common that they store some representation of the training set explicitly in memory. During testing, new cases are + classified by extrapolation from the most similar stored cases.""" + +toolchain = {'name': 'iimpi', 'version': '2019a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LanguageMachines/timbl/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e1a136e0f58486e1e2855b6ca528877d40d8b1e5de3c599a314ed6951d7c9e4b'] + +dependencies = [ + ('TiCCutils', '0.21'), + ('libxml2', '2.9.8'), +] + +configopts = '--with-ticcutils=$EBROOTTICCUTILS' + +sanity_check_paths = { + 'files': ['bin/timbl', 'lib/libtimbl.%s' % SHLIB_EXT, 'lib/libtimbl.a'], + 'dirs': ['include/timbl'] +} + +moduleclass = 'data' From f333455353c5789e05ecf5b820eb3b1ac20d557e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 May 2019 13:42:40 +0200 Subject: [PATCH 1723/5331] adding easyconfigs: cowsay-3.04.eb --- easybuild/easyconfigs/c/cowsay/cowsay-3.04.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/c/cowsay/cowsay-3.04.eb diff --git a/easybuild/easyconfigs/c/cowsay/cowsay-3.04.eb b/easybuild/easyconfigs/c/cowsay/cowsay-3.04.eb new file mode 100644 index 00000000000..6f557d61935 --- /dev/null +++ b/easybuild/easyconfigs/c/cowsay/cowsay-3.04.eb @@ -0,0 +1,23 @@ +easyblock = 'Binary' + +name = 'cowsay' +version = '3.04' + +homepage = 'https://github.com/tnalpgge/rank-amateur-cowsay' +description = "Configurable talking characters in ASCII art" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/tnalpgge/rank-amateur-cowsay/archive/'] +sources = [SOURCE_TAR_GZ] + +extract_sources = True + +install_cmd = "./install.sh %(installdir)s" + +sanity_check_paths = { + 'files': ['bin/cowsay'], + 'dirs': [], +} + +moduleclass = 'tools' From 05def0452e13dd295a289a6d22e37d9ab5aa4358 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 May 2019 14:10:31 +0200 Subject: [PATCH 1724/5331] add missing checksum to cowsay easyconfig file --- easybuild/easyconfigs/c/cowsay/cowsay-3.04.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cowsay/cowsay-3.04.eb b/easybuild/easyconfigs/c/cowsay/cowsay-3.04.eb index 6f557d61935..bdaac403f50 100644 --- a/easybuild/easyconfigs/c/cowsay/cowsay-3.04.eb +++ b/easybuild/easyconfigs/c/cowsay/cowsay-3.04.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['https://github.com/tnalpgge/rank-amateur-cowsay/archive/'] sources = [SOURCE_TAR_GZ] +checksums = ['d8b871332cfc1f0b6c16832ecca413ca0ac14d58626491a6733829e3d655878b'] extract_sources = True From daf7d54a20d40bd7ef55bac08b52fbb609a9bc8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 May 2019 14:23:56 +0200 Subject: [PATCH 1725/5331] adding easyconfigs: CRF++-0.58-intel-2018b.eb --- .../c/CRF++/CRF++-0.58-intel-2018b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/CRF++/CRF++-0.58-intel-2018b.eb diff --git a/easybuild/easyconfigs/c/CRF++/CRF++-0.58-intel-2018b.eb b/easybuild/easyconfigs/c/CRF++/CRF++-0.58-intel-2018b.eb new file mode 100644 index 00000000000..06fc981a725 --- /dev/null +++ b/easybuild/easyconfigs/c/CRF++/CRF++-0.58-intel-2018b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'CRF++' +version = '0.58' + +homepage = 'https://taku910.github.io/crfpp/' +description = """CRF++ is a simple, customizable, and open source implementation of + Conditional Random Fields (CRFs) for segmenting/labeling sequential data. CRF++ is + designed for generic purpose and will be applied to a variety of NLP tasks, such as + Named Entity Recognition, Information Extraction and Text Chunking. """ + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +# manual download from https://taku910.github.io/crfpp/#download (via Google Drive) +sources = [SOURCE_TAR_GZ] +checksums = ['9d1c0a994f25a5025cede5e1d3a687ec98cd4949bfb2aae13f2a873a13259cb2'] + +configopts = '--with-pic' +buildopts = 'CXXFLAGS="$CXXFLAGS -Wall -finline"' + +sanity_check_paths = { + 'files': ["bin/crf_learn", "bin/crf_test"], + 'dirs': [] +} + +moduleclass = 'data' From 789f1b3cff9305062c09bed0c7f1aa27298f813a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 May 2019 14:41:39 +0200 Subject: [PATCH 1726/5331] adding easyconfigs: TiMBL-6.4.13-intel-2018b.eb, TiCCutils-0.21-intel-2018b.eb, libtar-1.2.20-GCCcore-7.3.0.eb --- .../l/libtar/libtar-1.2.20-GCCcore-7.3.0.eb | 31 ++++++++++++++++ .../t/TiCCutils/TiCCutils-0.21-intel-2018b.eb | 36 +++++++++++++++++++ .../t/TiMBL/TiMBL-6.4.13-intel-2018b.eb | 33 +++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtar/libtar-1.2.20-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.21-intel-2018b.eb create mode 100644 easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.13-intel-2018b.eb diff --git a/easybuild/easyconfigs/l/libtar/libtar-1.2.20-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libtar/libtar-1.2.20-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..d42ed2c4bfa --- /dev/null +++ b/easybuild/easyconfigs/l/libtar/libtar-1.2.20-GCCcore-7.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libtar' +version = '1.2.20' + +homepage = 'https://repo.or.cz/libtar.git' +description = "C library for manipulating POSIX tar files" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://repo.or.cz/libtar.git/snapshot/'] +sources = [{ + 'download_filename': '0907a9034eaf2a57e8e4a9439f793f3f05d446cd.tar.gz', + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['4847207d878e79a4acbe32f096e57cd72c9507171953849e4d7eafe312418d95'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.30'), +] + +preconfigopts = "autoreconf --force --install && " + +sanity_check_paths = { + 'files': ['bin/libtar', 'include/libtar.h', 'include/libtar_listhash.h', + 'lib/libtar.a', 'lib/libtar.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.21-intel-2018b.eb b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.21-intel-2018b.eb new file mode 100644 index 00000000000..5bde34552ba --- /dev/null +++ b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.21-intel-2018b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'TiCCutils' +version = '0.21' + +homepage = 'https://github.com/LanguageMachines/ticcutils' +description = """TiCC utils is a collection of generic C++ software which is used in a lot of programs produced at + Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and + Centre for Dutch Language and Speech at University of Antwerp.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LanguageMachines/ticcutils/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['73a6b0327d1c14b59ec9e790ef5d5e60dd40b0fb740bf131ee4228565721bd11'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('libtar', '1.2.20'), + ('Boost', '1.67.0'), + ('ICU', '61.1'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.8'), +] + +configopts = "--with-pic --with-boost=$EBROOTBOOST --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libticcutils.%s' % SHLIB_EXT, 'lib/libticcutils.a'], + 'dirs': ['include/ticcutils'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.13-intel-2018b.eb b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.13-intel-2018b.eb new file mode 100644 index 00000000000..23a7621cef1 --- /dev/null +++ b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.13-intel-2018b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'TiMBL' +version = '6.4.13' + +homepage = 'https://languagemachines.github.io/timbl' +description = """TiMBL (Tilburg Memory Based Learner) + is an open source software package implementing several memory-based learning algorithms, + among which IB1-IG, an implementation of k-nearest neighbor classification with feature weighting suitable for + symbolic feature spaces, and IGTree, a decision-tree approximation of IB1-IG. All implemented algorithms have in + common that they store some representation of the training set explicitly in memory. During testing, new cases are + classified by extrapolation from the most similar stored cases.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LanguageMachines/timbl/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e1a136e0f58486e1e2855b6ca528877d40d8b1e5de3c599a314ed6951d7c9e4b'] + +dependencies = [ + ('TiCCutils', '0.21'), + ('libxml2', '2.9.8'), +] + +configopts = '--with-ticcutils=$EBROOTTICCUTILS' + +sanity_check_paths = { + 'files': ['bin/timbl', 'lib/libtimbl.%s' % SHLIB_EXT, 'lib/libtimbl.a'], + 'dirs': ['include/timbl'] +} + +moduleclass = 'data' From 0d34445308a6e6e4442d3ed3d579b3ef5f3ca35c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 24 May 2019 20:42:13 +0200 Subject: [PATCH 1727/5331] use Boost-1.70.0 --- .../b/BLAST+/BLAST+-2.9.0-foss-2019a.eb | 8 +- .../b/BLAST+/BLAST+-2.9.0_fix_boost.patch | 96 +++++++++++++++++++ .../b/Boost/Boost-1.67.0-gompi-2019a.eb | 25 ----- 3 files changed, 102 insertions(+), 27 deletions(-) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0_fix_boost.patch delete mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.67.0-gompi-2019a.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-foss-2019a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-foss-2019a.eb index d53823c8b59..fcae3deb12f 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-foss-2019a.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-foss-2019a.eb @@ -25,13 +25,17 @@ toolchainopts = {'usempi': True} source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] sources = ['ncbi-blast-%(version)s+-src.tar.gz'] -checksums = ['a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257'] +patches = ['BLAST+-2.9.0_fix_boost.patch'] +checksums = [ + 'a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257', # ncbi-blast-2.9.0+-src.tar.gz + '44dc4a931896953d78c13097433ea6fc8d7990bd759c4e4e5bbb9b2574fb4154', # BLAST+-2.9.0_fix_boost.patch +] dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.6'), ('PCRE', '8.43'), - ('Boost', '1.67.0'), # build fails with Boost-1.70.0 + ('Boost', '1.70.0'), ('GMP', '6.1.2'), ('libpng', '1.6.36'), ('libjpeg-turbo', '2.0.2'), diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0_fix_boost.patch b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0_fix_boost.patch new file mode 100644 index 00000000000..8a41b1d193a --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0_fix_boost.patch @@ -0,0 +1,96 @@ +Make changes necessary to work with Boost-1.70.0 +Without this patch it still works with Boost-1.67.0 +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ur ncbi-blast-2.9.0+-src.orig/c++/include/corelib/test_boost.hpp ncbi-blast-2.9.0+-src/c++/include/corelib/test_boost.hpp +--- ncbi-blast-2.9.0+-src.orig/c++/include/corelib/test_boost.hpp 2018-09-17 16:00:14.000000000 +0200 ++++ ncbi-blast-2.9.0+-src/c++/include/corelib/test_boost.hpp 2019-05-24 19:54:52.702503781 +0200 +@@ -106,7 +106,7 @@ + " expected but not raised", \ + TL, CHECK_MSG, _ ); \ + } catch( E const& ex ) { \ +- ::boost::unit_test::ut_detail::ignore_unused_variable_warning( ex ); \ ++ ::boost::ignore_unused( ex ); \ + BOOST_TEST_TOOL_IMPL( 2, P, \ + "exception \"" BOOST_STRINGIZE( E ) \ + "\" raised as expected" postfix, \ +@@ -129,7 +129,7 @@ + " is expected", \ + TL, CHECK_MSG, _ ); \ + } catch( E const& ex ) { \ +- ::boost::unit_test::ut_detail::ignore_unused_variable_warning( ex ); \ ++ ::boost::ignore_unused( ex ); \ + BOOST_TEST_TOOL_IMPL( 2, P, prefix BOOST_STRINGIZE( E ) " is caught", \ + TL, CHECK_MSG, _ ); \ + } catch (...) { \ +@@ -168,7 +168,7 @@ + BOOST_CHECK_IMPL( false, "exception " BOOST_STRINGIZE( E ) \ + " is expected", TL, CHECK_MSG ); } \ + catch( E const& ex ) { \ +- boost::unit_test::ut_detail::ignore_unused_variable_warning( ex ); \ ++ boost::ignore_unused( ex ); \ + BOOST_CHECK_IMPL( P, prefix BOOST_STRINGIZE( E ) " is caught", \ + TL, CHECK_MSG ); \ + } \ +@@ -206,7 +206,7 @@ + + #ifdef BOOST_FIXTURE_TEST_CASE_NO_DECOR + # define NCBI_BOOST_DECORATOR_ARG \ +- , boost::unit_test::decorator::collector::instance() ++ , boost::unit_test::decorator::collector_t::instance() + #else + # define NCBI_BOOST_DECORATOR_ARG + #endif +@@ -785,7 +785,7 @@ + #ifdef BOOST_FIXTURE_TEST_CASE_WITH_DECOR + SNcbiTestRegistrar(boost::unit_test::test_case* tc, + unsigned int timeout, +- boost::unit_test::decorator::collector& decorator) ++ boost::unit_test::decorator::collector_t& decorator) + : TParent(tc, decorator) + { + tc->p_timeout.set(timeout); +diff -ur ncbi-blast-2.9.0+-src.orig/c++/src/corelib/teamcity_boost.cpp ncbi-blast-2.9.0+-src/c++/src/corelib/teamcity_boost.cpp +--- ncbi-blast-2.9.0+-src.orig/c++/src/corelib/teamcity_boost.cpp 2017-10-23 16:54:03.000000000 +0200 ++++ ncbi-blast-2.9.0+-src/c++/src/corelib/teamcity_boost.cpp 2019-05-24 16:50:56.825303031 +0200 +@@ -55,7 +55,7 @@ + + virtual void log_start(std::ostream&, boost::unit_test::counter_t test_cases_amount); + virtual void log_finish(std::ostream&); +- virtual void log_build_info(std::ostream&); ++ virtual void log_build_info(std::ostream&, bool log_build_info = true); + + virtual void test_unit_start(std::ostream&, boost::unit_test::test_unit const& tu); + virtual void test_unit_finish(std::ostream&, +@@ -135,7 +135,7 @@ + void TeamcityBoostLogFormatter::log_finish(std::ostream &/*out*/) + {} + +-void TeamcityBoostLogFormatter::log_build_info(std::ostream &/*out*/) ++void TeamcityBoostLogFormatter::log_build_info(std::ostream &/*out*/, bool log_build_info) + {} + + void TeamcityBoostLogFormatter::test_unit_start(std::ostream &out, boost::unit_test::test_unit const& tu) { +diff -ur ncbi-blast-2.9.0+-src.orig/c++/src/corelib/test_boost.cpp ncbi-blast-2.9.0+-src/c++/src/corelib/test_boost.cpp +--- ncbi-blast-2.9.0+-src.orig/c++/src/corelib/test_boost.cpp 2018-09-17 15:59:01.000000000 +0200 ++++ ncbi-blast-2.9.0+-src/c++/src/corelib/test_boost.cpp 2019-05-24 16:51:58.589513416 +0200 +@@ -248,7 +248,7 @@ + virtual + void log_finish (ostream& ostr); + virtual +- void log_build_info (ostream& ostr); ++ void log_build_info (ostream& ostr, bool log_build_info = true); + virtual + void test_unit_start (ostream& ostr, but::test_unit const& tu); + virtual +@@ -2086,9 +2086,9 @@ + } + + void +-CNcbiBoostLogger::log_build_info(ostream& ostr) ++CNcbiBoostLogger::log_build_info(ostream& ostr, bool log_build_info) + { +- m_Upper->log_build_info(ostr); ++ m_Upper->log_build_info(ostr, log_build_info); + } + + void diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.67.0-gompi-2019a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.67.0-gompi-2019a.eb deleted file mode 100644 index 2d27aa3c609..00000000000 --- a/easybuild/easyconfigs/b/Boost/Boost-1.67.0-gompi-2019a.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'Boost' -version = '1.67.0' - -homepage = 'http://www.boost.org/' -description = """Boost provides free peer-reviewed portable C++ source libraries.""" - -toolchain = {'name': 'gompi', 'version': '2019a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = [SOURCEFORGE_SOURCE] -sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['8aa4e330c870ef50a896634c931adf468b21f8a69b77007e45c444151229f665'] - -dependencies = [ - ('bzip2', '1.0.6'), - ('zlib', '1.2.11'), - ('XZ', '5.2.4'), -] - -configopts = '--without-libraries=python' - -# also build boost_mpi -boost_mpi = True - -moduleclass = 'devel' From 58963d4352031ad5ad0a3286335ecebdf6adee73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 May 2019 22:54:09 +0200 Subject: [PATCH 1728/5331] adding easyconfigs: CPLEX-12.9-GCCcore-8.2.0.eb --- .../c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..ed03453b0b0 --- /dev/null +++ b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb @@ -0,0 +1,24 @@ +name = 'CPLEX' +version = '12.9' + +homepage = 'https://www.ibm.com/analytics/cplex-optimizer' +description = """IBM ILOG CPLEX Optimizer's mathematical programming technology enables + analytical decision support for improving efficiency, + reducing costs, and increasing profitability.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +# the Academic Initiative version (as used in this file) can be downloaded as described on +# https://www.ibm.com/developerworks/community/blogs/jfp/entry/cplex_studio_in_ibm_academic_initiative?lang=en +# a restricted "Community edition" version can be found on +# https://www-01.ibm.com/software/websphere/products/optimization/cplex-studio-community-edition/ +sources = ['cplex_studio%s.linux-x86-64.bin' % ''.join(version.split('.'))] +checksums = ['89d4fde49f384155688fd0ac01fcef33f88ec615a67cdb43566f0d0df345044f'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [ + ('Java', '11', '', True), +] + +moduleclass = 'math' From 59239316aed65e03831eeaf1c6f0e2cbf2a96715 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 May 2019 19:36:04 +0200 Subject: [PATCH 1729/5331] adding easyconfigs: OpenFOAM-v1606+-foss-2018b.eb and patches: OpenFOAM-v1606+-cleanup.patch --- .../o/OpenFOAM/OpenFOAM-v1606+-cleanup.patch | 610 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-v1606+-foss-2018b.eb | 37 ++ 2 files changed, 647 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1606+-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1606+-foss-2018b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1606+-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1606+-cleanup.patch new file mode 100644 index 00000000000..8f3a828113b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v1606+-cleanup.patch @@ -0,0 +1,610 @@ +# - Replace the OpenFOAM third-party libraries with EASYBUILD variables. +# - Set install dir, compiler, etc using EASYBUILD +# +# authors: Ward Poelmans , Kenneth Hoste (HPC-UGent), Mark Olesen +diff -ru OpenFOAM-v1606+.orig/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-v1606+/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-v1606+.orig/applications/utilities/mesh/manipulation/setSet/Allwmake 2016-07-01 10:14:05.532480574 +0200 ++++ OpenFOAM-v1606+/applications/utilities/mesh/manipulation/setSet/Allwmake 2019-05-24 14:35:05.237631000 +0200 +@@ -9,11 +9,11 @@ + # + # use readline if available + # +-if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo "Found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" +- export LINK_FLAGS="-lreadline" ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake +diff -ru OpenFOAM-v1606+.orig/etc/bashrc OpenFOAM-v1606+/etc/bashrc +--- OpenFOAM-v1606+.orig/etc/bashrc 2016-07-01 10:14:05.620480272 +0200 ++++ OpenFOAM-v1606+/etc/bashrc 2019-05-24 14:29:16.285534000 +0200 +@@ -55,7 +55,8 @@ + # overridden from the prefs.sh file or from command-line specification + # + #- note the location for later use (eg, in job scripts) +-: ${FOAM_INST_DIR:=$foamInstall}; export FOAM_INST_DIR ++# Easybuild module sets FOAM_INST_DIR ++#: ${FOAM_INST_DIR:=$foamInstall}; export FOAM_INST_DIR + + #- Compiler location: + # WM_COMPILER_TYPE= system | ThirdParty (OpenFOAM) +@@ -87,7 +88,7 @@ + #- MPI implementation: + # WM_MPLIB = SYSTEMOPENMPI | OPENMPI | SYSTEMMPI | MPICH | MPICH-GM | HPMPI + # | MPI | QSMPI | SGIMPI +-export WM_MPLIB=SYSTEMOPENMPI ++export WM_MPLIB=EASYBUILDMPI + + #- Operating System: + # WM_OSTYPE = POSIX | ??? +@@ -121,7 +122,8 @@ + + # Location of third-party software + # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +-export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION ++# Easybuild handles all third-party ++export WM_THIRD_PARTY_DIR=$WM_PROJECT_DIR/ThirdParty + + # Location of site-specific templates etc + # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +diff -ru OpenFOAM-v1606+.orig/etc/config.sh/CGAL OpenFOAM-v1606+/etc/config.sh/CGAL +--- OpenFOAM-v1606+.orig/etc/config.sh/CGAL 2016-07-05 14:03:28.171127286 +0200 ++++ OpenFOAM-v1606+/etc/config.sh/CGAL 2019-05-24 14:34:13.376682000 +0200 +@@ -1,88 +1,3 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2014-2016 OpenFOAM Foundation +-# \\/ M anipulation | Copyright (C) 2016 OpenCFD Ltd. +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/CGAL +-# +-# Description +-# Setup file for CGAL (& boost) include/libraries. +-# Sourced from OpenFOAM-/etc/bashrc +-# +-# If using system-wide installations, use the following settings: +-# +-# boost_version=boost-system +-# cgal_version=cgal-system +-# +-# If the system boost/cgal is unusable (eg, too old) and you don't +-# have or want a ThirdParty installation: +-# +-# boost_version=boost-none +-# cgal_version=cgal-none +-# +-# If using a central installation, but not located under ThirdParty: +-# - specify boost-system / cgal-system +-# - provide full paths for BOOST_ARCH_PATH / CGAL_ARCH_PATH +-# +-# Note +-# When _foamAddLib is unset (eg, called from makeCGAL): +-# - boost_version / cgal_version variables are retained. +-# - the LD_LIBRARY_PATH is not adjusted. +-#------------------------------------------------------------------------------ +- +-boost_version=boost_1_61_0 +-cgal_version=CGAL-4.8 +- +-export BOOST_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$boost_version +-export CGAL_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cgal_version +- +-#------------------------------------------------------------------------------ +-if [ "$FOAM_VERBOSE" -a "$PS1" ] +-then +- echo "Using boost ($boost_version) -> $BOOST_ARCH_PATH" 1>&2 +- echo "Using CGAL ($cgal_version) -> $CGAL_ARCH_PATH" 1>&2 +-fi +- +-if type _foamAddLib > /dev/null 2>&1 # normal sourcing +-then +- +- # If BOOST_ARCH_PATH, CGAL_ARCH_PATH do not end with '-system' or '-none', +- # they are either located within ThirdParty, or a central installation +- # outside of ThirdParty and must be added to the lib-path. +- +- ending="${BOOST_ARCH_PATH##*-}" +- if [ "$ending" != none -a "$ending" != system ] +- then +- _foamAddLib $BOOST_ARCH_PATH/lib +- fi +- +- ending="${CGAL_ARCH_PATH##*-}" +- if [ "$ending" != none -a "$ending" != system ] +- then +- _foamAddLib $CGAL_ARCH_PATH/lib +- fi +- +- unset boost_version cgal_version ending +- +-fi +- +-#------------------------------------------------------------------------------ ++# EasyBuild settings ++export BOOST_ARCH_PATH=$EBROOTBOOST ++export CGAL_ARCH_PATH=$EBROOTCGAL +diff -ru OpenFOAM-v1606+.orig/etc/config.sh/ensight OpenFOAM-v1606+/etc/config.sh/ensight +--- OpenFOAM-v1606+.orig/etc/config.sh/ensight 2016-07-01 10:14:05.632480231 +0200 ++++ OpenFOAM-v1606+/etc/config.sh/ensight 2019-05-24 14:33:51.962865000 +0200 +@@ -1,60 +1,2 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation +-# \\/ M anipulation | +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/ensight +-# +-# Description +-# Setup file for Ensight +-# Sourced from OpenFOAM-*/etc/bashrc +-# +-#------------------------------------------------------------------------------ +- +-# fallback value +-if [ ! -d "$CEI_HOME" ] +-then +- export CEI_HOME=/usr/local/ensight/CEI +-fi +- +-if [ -r $CEI_HOME ] +-then +- +- # special treatment for 32bit OpenFOAM and 64bit Ensight +- if [ "$WM_ARCH" = linux -a `uname -m` = x86_64 ] +- then +- export CEI_ARCH=linux_2.6_32 +- fi +- +- # add to path if required +- if [ "$CEI_HOME/bin/ensight" != "`which ensight 2>/dev/null`" ] +- then +- export PATH=$CEI_HOME/bin:$PATH +- fi +- +- export ENSIGHT9_INPUT=dummy +- export ENSIGHT9_READER=$FOAM_LIBBIN +-else +- unset CEI_HOME +-fi +- +-#------------------------------------------------------------------------------ ++# Easybuild settings ++# ununsed +diff -ru OpenFOAM-v1606+.orig/etc/config.sh/FFTW OpenFOAM-v1606+/etc/config.sh/FFTW +--- OpenFOAM-v1606+.orig/etc/config.sh/FFTW 2016-07-05 14:01:31.459024527 +0200 ++++ OpenFOAM-v1606+/etc/config.sh/FFTW 2019-05-24 14:30:43.337695000 +0200 +@@ -1,77 +1,2 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2016 OpenCFD Ltd. +-# \\/ M anipulation | +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/FFTW +-# +-# Description +-# Setup file for FFTW include/libraries. +-# Sourced from OpenFOAM-/etc/bashrc +-# +-# If using system-wide installations, use the following settings: +-# +-# fftw_version=fftw-system +-# +-# If the system fftw is unusable (eg, too old) and you don't +-# have or want a ThirdParty installation: +-# +-# fftw_version=fftw-none +-# +-# If using a central installation, but not located under ThirdParty: +-# - specify fftw-system +-# - provide full paths for FFTW_ARCH_PATH +-# +-# Note +-# When _foamAddLib is unset (eg, called from makeFFTW): +-# - fftw_version variable is retained. +-# - the LD_LIBRARY_PATH is not adjusted. +-#------------------------------------------------------------------------------ +- +-fftw_version=fftw-3.3.4 +- +-export FFTW_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$fftw_version +- +-#------------------------------------------------------------------------------ +-if [ "$FOAM_VERBOSE" -a "$PS1" ] +-then +- echo "Using fftw ($fftw_version) -> $FFTW_ARCH_PATH" 1>&2 +-fi +- +-if type _foamAddLib > /dev/null 2>&1 # normal sourcing +-then +- +- # If FFTW_ARCH_PATH does not end with '-system' or '-none', +- # it is either located within ThirdParty, or a central installation +- # outside of ThirdParty and must be added to the lib-path. +- +- ending="${FFTW_ARCH_PATH_PATH##*-}" +- if [ "$ending" != none -a "$ending" != system ] +- then +- _foamAddLib $FFTW_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH +- fi +- +- unset fftw_version ending +- +-fi +- +-#------------------------------------------------------------------------------ ++# EasyBuild settings ++export FFTW_ARCH_PATH=$EBROOTFFTW +diff -ru OpenFOAM-v1606+.orig/etc/config.sh/gperftools OpenFOAM-v1606+/etc/config.sh/gperftools +--- OpenFOAM-v1606+.orig/etc/config.sh/gperftools 2016-07-01 10:14:05.632480231 +0200 ++++ OpenFOAM-v1606+/etc/config.sh/gperftools 2019-05-24 14:29:42.190267000 +0200 +@@ -1,41 +1,3 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2012-2016 OpenFOAM Foundation +-# \\/ M anipulation | +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/gperftools +-# +-# Description +-# Setup file for gperftools binaries libraries. +-# +-#------------------------------------------------------------------------------ +- +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH +- +-#------------------------------------------------------------------------------ ++# EasyBuild settings ++gperftools_version=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS +diff -ru OpenFOAM-v1606+.orig/etc/config.sh/metis OpenFOAM-v1606+/etc/config.sh/metis +--- OpenFOAM-v1606+.orig/etc/config.sh/metis 2016-07-01 10:14:05.632480231 +0200 ++++ OpenFOAM-v1606+/etc/config.sh/metis 2019-05-24 14:31:25.918501000 +0200 +@@ -1,39 +1,4 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2013-2016 OpenFOAM Foundation +-# \\/ M anipulation | +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/metis +-# +-# Description +-# Setup file for metis include/libraries. +-# Sourced during wmake process only. +-# +-# Note +-# A csh version is not needed, since the values here are only sourced +-# during the wmake process +-#------------------------------------------------------------------------------ +- +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$METIS_VERSION +- +-#------------------------------------------------------------------------------ ++# Easybuild settings ++METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS ++[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH=$METIS_ROOT +diff -ru OpenFOAM-v1606+.orig/etc/config.sh/mpi OpenFOAM-v1606+/etc/config.sh/mpi +--- OpenFOAM-v1606+.orig/etc/config.sh/mpi 2016-07-01 10:14:05.632480231 +0200 ++++ OpenFOAM-v1606+/etc/config.sh/mpi 2019-05-24 14:15:40.908339000 +0200 +@@ -62,6 +62,10 @@ + _foamAddMan $MPI_ARCH_PATH/share/man + ;; + ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; ++ + SYSTEMMPI) + export FOAM_MPI=mpi-system + +diff -ru OpenFOAM-v1606+.orig/etc/config.sh/paraview OpenFOAM-v1606+/etc/config.sh/paraview +--- OpenFOAM-v1606+.orig/etc/config.sh/paraview 2016-07-01 10:14:05.632480231 +0200 ++++ OpenFOAM-v1606+/etc/config.sh/paraview 2019-05-24 14:33:24.023397000 +0200 +@@ -33,32 +33,10 @@ + # are required for building plugins + #------------------------------------------------------------------------------ + +-# clean the PATH +-cleaned=$($WM_PROJECT_DIR/bin/foamCleanPath "$PATH" \ +- "$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/cmake- \ +- $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/paraview-" \ +- ) \ +- && PATH="$cleaned" +- +-# determine the cmake to be used +-unset CMAKE_HOME +-for cmake in cmake-3.2.1 cmake-2.8.12.1 cmake-2.8.8 cmake-2.8.4 cmake-2.8.3 \ +- cmake-2.8.1 +-do +- cmake=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$cmake +- if [ -r $cmake ] +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- export PATH=$CMAKE_HOME/bin:$PATH +- break +- fi +-done +- + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=4.4.0 +-export ParaView_VERSION=5.0.1 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + +@@ -99,7 +77,7 @@ + paraviewInstDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + paraviewArchName=ParaView-$ParaView_VERSION + +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$paraviewArchName ++export ParaView_DIR=$EBROOTPARAVIEW + + # set paths if binaries or source are present + if [ -r $ParaView_DIR -o -r $paraviewInstDir ] +@@ -125,17 +103,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi + else + unset PV_PLUGIN_PATH + fi +diff -ru OpenFOAM-v1606+.orig/etc/config.sh/scotch OpenFOAM-v1606+/etc/config.sh/scotch +--- OpenFOAM-v1606+.orig/etc/config.sh/scotch 2016-07-01 10:14:05.632480231 +0200 ++++ OpenFOAM-v1606+/etc/config.sh/scotch 2019-05-24 14:30:18.453333000 +0200 +@@ -1,39 +1,4 @@ +-#----------------------------------*-sh-*-------------------------------------- +-# ========= | +-# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox +-# \\ / O peration | +-# \\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation +-# \\/ M anipulation | +-#------------------------------------------------------------------------------ +-# License +-# This file is part of OpenFOAM. +-# +-# OpenFOAM is free software: you can redistribute it and/or modify it +-# under the terms of the GNU General Public License as published by +-# the Free Software Foundation, either version 3 of the License, or +-# (at your option) any later version. +-# +-# OpenFOAM is distributed in the hope that it will be useful, but WITHOUT +-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or +-# FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License +-# for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with OpenFOAM. If not, see . +-# +-# File +-# etc/config.sh/scotch +-# +-# Description +-# Setup file for scotch include/libraries. +-# Sourced during wmake process only. +-# +-# Note +-# A csh version is not needed, since the values here are only sourced +-# during the wmake process +-#------------------------------------------------------------------------------ +- +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_LABEL_OPTION/$SCOTCH_VERSION +- +-#------------------------------------------------------------------------------ ++# Easybuild settings ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH ++[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH=$SCOTCH_ROOT +diff -ru OpenFOAM-v1606+.orig/etc/config.sh/settings OpenFOAM-v1606+/etc/config.sh/settings +--- OpenFOAM-v1606+.orig/etc/config.sh/settings 2016-07-01 10:14:05.632480231 +0200 ++++ OpenFOAM-v1606+/etc/config.sh/settings 2019-05-24 14:15:40.912527926 +0200 +@@ -132,6 +132,15 @@ + esac + + ++##Easybuild## compiler settings ++CXXFLAGS="$CXXFLAGS -std=c++11" # C++11 is essential ++export WM_CC=$CC ++export WM_CXX=$CXX ++export WM_CFLAGS=$CFLAGS ++export WM_CXXFLAGS=$CXXFLAGS ++export WM_LDFLAGS=$LDFLAGS ++ ++ + #------------------------------------------------------------------------------ + + # Location of the jobControl directory +diff -ru OpenFOAM-v1606+.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-v1606+/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-v1606+.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2016-07-01 10:14:06.136478502 +0200 ++++ OpenFOAM-v1606+/src/parallel/decompose/ptscotchDecomp/Make/options 2019-05-24 14:35:41.485998000 +0200 +@@ -5,7 +5,6 @@ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +diff -ru OpenFOAM-v1606+.orig/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-v1606+/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-v1606+.orig/src/parallel/decompose/scotchDecomp/Make/options 2016-07-01 10:14:06.140478488 +0200 ++++ OpenFOAM-v1606+/src/parallel/decompose/scotchDecomp/Make/options 2019-05-24 14:15:40.918175000 +0200 +@@ -9,7 +9,6 @@ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ + + +fix for "wrmo error: could not find Make directory" +--- OpenFOAM-v1606+/src/Allwmake.orig 2016-07-05 14:47:12.740552888 +0200 ++++ OpenFOAM-v1606+/src/Allwmake 2019-05-24 17:21:51.071745000 +0200 +@@ -21,7 +21,7 @@ + set -x + + # Update OpenFOAM version strings if required +-wmakePrintBuild -check || wrmo OpenFOAM/global/global.o ++wmakePrintBuild -check || rm -f OpenFOAM/global/global.o + + wmakeLnInclude OpenFOAM + wmakeLnInclude OSspecific/${WM_OSTYPE:-POSIX} + +fix for: +metisDecomp.C:186:9: error: cannot convert ‘Foam::UList::iterator {aka float*}’ to ‘real_t* {aka double*}’ for argument ‘9’ +to ‘int METIS_PartGraphRecursive(idx_t*, idx_t*, idx_t*, idx_t*, idx_t*, idx_t*, idx_t*, idx_t*, real_t*, real_t*, idx_t*, idx_t*, idx_t*)’ +see https://bugs.openfoam.org/view.php?id=2085 +--- OpenFOAM-1606+/src/parallel/decompose/metisDecomp/metisDecomp.C.orig 2019-05-24 19:37:56.642864000 +0200 ++++ OpenFOAM-1606+/src/parallel/decompose/metisDecomp/metisDecomp.C 2019-05-24 19:38:45.650535519 +0200 +@@ -67,7 +67,7 @@ + + // processor weights initialised with no size, only used if specified in + // a file +- Field processorWeights; ++ Field processorWeights; + + // cell weights (so on the vertices of the dual) + List